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Iamborwornkun N, Kitkumthorn N, Stevenson A, Kirk A, Graham SV, Chuen-im T. Identifying regulatory elements and their RNA-binding proteins in the 3' untranslated regions of papillomavirus late mRNAs. Biomed Rep 2024; 21:125. [PMID: 39006509 PMCID: PMC11240274 DOI: 10.3892/br.2024.1813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/23/2024] [Indexed: 07/16/2024] Open
Abstract
Human papillomaviruses (HPVs) infect cutaneous and mucosal epithelia to cause benign (warts) and malignant lesions (e.g. cervical cancer). Bovine papillomaviruses (BPVs) infect fibroblasts to cause fibropapillomas but can also infect cutaneous epithelial cells. For HPV-1, -16, -31 and BPV-1, cis-acting RNA elements in the late 3' untranslated region (3'UTR) control expression of virus proteins by binding host cell proteins. The present study compared the effects on gene expression of the cis-acting elements of seven PV late 3'UTRs (HPV-6b, -11, -16, -31 and BPV-1, -3 and -4) representing a range of different genera and species and pathological properties. pSV-beta-galactosidase reporter plasmids containing the late 3'UTRs from seven PVs were transiently transfected into cervical adenocarcinoma HeLa cells, and reporter gene expression quantified by reverse transcription-quantitative PCR and a beta-galactosidase assay. All elements inhibited gene expression in keratinocytes. Cancer-related types HPV-16 and -31, had the greatest inhibitory activity whereas the lowest inhibition was found in the non-cancer related types, BPV-3 and HPV-11. Using RBPmap version 1.1, bioinformatics predictions of factors binding the elements identified proteins which function mainly in mRNA splicing. Markedly, in terms of protein binding motifs, BPV late 3'UTR elements were similar to those of HPV-1a but not to other HPVs. Using HPV-1a as a model and siRNA depletion, the bioinformatics predictions were tested and it was found that PABPC4 was responsible for some of the 3'UTR repressive activity. The data revealed candidate proteins that could control PV late gene expression.
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Affiliation(s)
- Nuttawan Iamborwornkun
- Department of Microbiology, Faculty of Science, Silpakorn University, Sanam Chandra Palace Campus, Nakhon Pathom 73000, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
| | - Andrew Stevenson
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical Veterinary and Life Sciences University of Glasgow, Glasgow, G61 1QH, UK
| | - Anna Kirk
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical Veterinary and Life Sciences University of Glasgow, Glasgow, G61 1QH, UK
| | - Sheila V. Graham
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical Veterinary and Life Sciences University of Glasgow, Glasgow, G61 1QH, UK
| | - Thanaporn Chuen-im
- Department of Microbiology, Faculty of Science, Silpakorn University, Sanam Chandra Palace Campus, Nakhon Pathom 73000, Thailand
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2
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Lorenzo-Orts L, Pauli A. The molecular mechanisms underpinning maternal mRNA dormancy. Biochem Soc Trans 2024; 52:861-871. [PMID: 38477334 PMCID: PMC11088918 DOI: 10.1042/bst20231122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
A large number of mRNAs of maternal origin are produced during oogenesis and deposited in the oocyte. Since transcription stops at the onset of meiosis during oogenesis and does not resume until later in embryogenesis, maternal mRNAs are the only templates for protein synthesis during this period. To ensure that a protein is made in the right place at the right time, the translation of maternal mRNAs must be activated at a specific stage of development. Here we summarize our current understanding of the sophisticated mechanisms that contribute to the temporal repression of maternal mRNAs, termed maternal mRNA dormancy. We discuss mechanisms at the level of the RNA itself, such as the regulation of polyadenine tail length and RNA modifications, as well as at the level of RNA-binding proteins, which often block the assembly of translation initiation complexes at the 5' end of an mRNA or recruit mRNAs to specific subcellular compartments. We also review microRNAs and other mechanisms that contribute to repressing translation, such as ribosome dormancy. Importantly, the mechanisms responsible for mRNA dormancy during the oocyte-to-embryo transition are also relevant to cellular quiescence in other biological contexts.
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Affiliation(s)
- Laura Lorenzo-Orts
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
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Xiang K, Ly J, Bartel DP. Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos. Dev Cell 2024; 59:1058-1074.e11. [PMID: 38460509 DOI: 10.1016/j.devcel.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/28/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
During oocyte maturation and early embryogenesis, changes in mRNA poly(A)-tail lengths strongly influence translation, but how these tail-length changes are orchestrated has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with millions of 3' UTR sequence variants) in frog oocytes and embryos and in fish embryos. Contrasting to previously proposed cytoplasmic polyadenylation elements (CPEs), we found that a shorter element, UUUUA, together with the polyadenylation signal (PAS), specify cytoplasmic polyadenylation, and we identified contextual features that modulate the activity of both elements. In maturing oocytes, this tail lengthening occurs against a backdrop of global deadenylation and the action of C-rich elements that specify tail-length-independent translational repression. In embryos, cytoplasmic polyadenylation becomes more permissive, and additional elements specify waves of stage-specific deadenylation. Together, these findings largely explain the complex tapestry of tail-length changes observed in early frog and fish development, with strong evidence of conservation in both mice and humans.
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Affiliation(s)
- Kehui Xiang
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jimmy Ly
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Mofayezi A, Jadaliha M, Zangeneh FZ, Khoddami V. Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1837. [PMID: 38485452 DOI: 10.1002/wrna.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Ahmadreza Mofayezi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- ReNAP Therapeutics, Tehran, Iran
| | - Mahdieh Jadaliha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Vahid Khoddami
- ReNAP Therapeutics, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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Liu X, Han W, Hu X. Post-transcriptional regulation of myeloid cell-mediated inflammatory responses. Adv Immunol 2023; 160:59-82. [PMID: 38042586 DOI: 10.1016/bs.ai.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2023]
Abstract
Myeloid cells, particularly macrophages, act as the frontline responders to infectious agents and initiate inflammation. While the molecular mechanisms driving inflammatory responses have primarily focused on pattern recognition by myeloid cells and subsequent transcriptional events, it is crucial to note that post-transcriptional regulation plays a pivotal role in this process. In addition to the transcriptional regulation of innate immune responses, additional layers of intricate network of post-transcriptional mechanisms critically determine the quantity and duration of key inflammatory products and thus the outcome of immune responses. A multitude of mechanisms governing post-transcriptional regulation in innate immunity have been uncovered, encompassing RNA alternative splicing, mRNA stability, and translational regulation. This review encapsulates the current insights into the post-transcriptional regulation of inflammatory genes within myeloid cells, with particular emphasis on translational regulation during inflammation. While acknowledging the advancements, we also shed light on the existing gaps in immunological research pertaining to post-transcriptional levels and propose perspectives that controlling post-transcriptional process may serve as potential targets for therapeutic interventions in inflammatory diseases.
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Affiliation(s)
- Xingxian Liu
- Institute for Immunology, Tsinghua University, Beijing, P.R. China; Department of Basic Medical Sciences, Tsinghua University, Beijing, P.R. China; Tsinghua-Peking Center for Life Sciences, Beijing, P.R. China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, P.R. China
| | - Weidong Han
- Department of Bio-therapeutic, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - Xiaoyu Hu
- Institute for Immunology, Tsinghua University, Beijing, P.R. China; Department of Basic Medical Sciences, Tsinghua University, Beijing, P.R. China; Tsinghua-Peking Center for Life Sciences, Beijing, P.R. China; The State Key Laboratory of Membrane Biology, Beijing, P.R. China.
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Huynh TN, Parker R. The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation. J Biol Chem 2023; 299:105139. [PMID: 37544646 PMCID: PMC10493513 DOI: 10.1016/j.jbc.2023.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023] Open
Abstract
The levels of non-coding RNAs (ncRNAs) are regulated by transcription, RNA processing, and RNA degradation pathways. One mechanism for the degradation of ncRNAs involves the addition of oligo(A) tails by non-canonical poly(A) polymerases, which then recruit processive sequence-independent 3' to 5' exonucleases for RNA degradation. This pathway of decay is also regulated by three 3' to 5' exoribonucleases, USB1, PARN, and TOE1, which remove oligo(A) tails and thereby can protect ncRNAs from decay in a manner analogous to the deubiquitination of proteins. Loss-of-function mutations in these genes lead to premature degradation of some ncRNAs and lead to specific human diseases such as Poikiloderma with Neutropenia (PN) for USB1, Dyskeratosis Congenita (DC) for PARN and Pontocerebellar Hypoplasia type 7 (PCH7) for TOE1. Herein, we review the biochemical properties of USB1, PARN, and TOE1, how they modulate ncRNA levels, and their roles in human diseases.
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Affiliation(s)
- Thao Ngoc Huynh
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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Zhang FW, Xie XW, Chen MH, Tong J, Chen QQ, Feng J, Chen FT, Liu WQ. Poly(A)-specific ribonuclease protein promotes the proliferation, invasion and migration of esophageal cancer cells. World J Gastroenterol 2023; 29:4783-4796. [PMID: 37664151 PMCID: PMC10473923 DOI: 10.3748/wjg.v29.i31.4783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/29/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Bioinformatics analysis showed that the expression of the poly(A)-specific ribonuclease (PARN) gene in gastric cancer, head and neck squamous cell carcinoma, melanoma, cervical cancer and lung squamous cell carcinoma tissues was significantly higher than that in normal tissues and was associated with high stage and poor prognosis. The expression of the PARN gene in esophageal cancer (EC) tissue is also significantly higher than that in normal tissues, but the effect of PARN on the proliferation, migration and invasion of EC cells remains unclear. AIM To investigate the relationship between PARN and the proliferation, migration and invasion of EC cells. METHODS The EC tissues of 91 patients after EC surgery and 63 paired precancerous healthy tissues were collected. PARN mRNA levels were measured using a tissue microarray, and the PARN expression level was evaluated using immunohistochemistry to analyze the relationship between PARN expression and clinicopathologic features as well as the survival and prognosis of patients. In addition, the effects of PARN gene knockout on tumor cell proliferation, invasion and migration were studied by using shRNA during the in vitro culture of EC cell lines Eca-109 and TE-1, and the effects of the PARN gene on tumor growth in vivo were verified by a xenotransplantation nude mice model. RESULTS The expression of PARN in EC tissues was higher than that in adjacent normal tissues, and the level of PARN expression was significantly positively correlated with lymphatic metastasis. Patients with high PARN levels had poor overall survival. BIM, IGFBP-5 and p21 levels were significantly increased in the PARN knockout group, while the expression levels of the antiapoptotic proteins Survivin and sTNF-R1 were significantly decreased in the apoptotic antibody array data. In addition, the expression levels of Akt, p-Akt, PIK3CA and CCND1 in the downstream signaling pathway regulating EC progression were significantly decreased. The culture of EC cell lines confirmed that the apoptosis rate of EC cells was significantly increased, the growth and proliferation of tumor cells were significantly inhibited, and the invasion and migration ability of tumor cells were significantly decreased after PARN gene knockout. In vivo experiments of BALB/c nude mice transfected with Eca-109 cells expressing control shRNA (sh-NC) and PARN shRNA (sh-PARN) showed that the tumor volume and weight of nude mice treated with sh-PARN were significantly decreased compared with those of nude mice treated with sh-NC, indicating that PARN knockdown significantly inhibited tumor growth in vivo. CONCLUSION PARN has antiapoptotic effects on EC cells and promotes their proliferation, invasion and migration, which is associated with the development of EC and poor patient prognosis. PARN may become a potential target for the diagnosis, prognosis prediction and treatment of EC.
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Affiliation(s)
- Fu-Wei Zhang
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, China
| | - Xiao-Wei Xie
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530000, Guangxi Zhuang Autonomous Region, China
| | - Meng-Hua Chen
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530000, Guangxi Zhuang Autonomous Region, China
| | - Jian Tong
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, China
| | - Qun-Qing Chen
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, China
| | - Jing Feng
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, China
| | - Feng-Ti Chen
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530000, Guangxi Zhuang Autonomous Region, China
| | - Wen-Qi Liu
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530000, Guangxi Zhuang Autonomous Region, China
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8
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. PLoS Genet 2023; 19:e1010845. [PMID: 37440598 PMCID: PMC10368294 DOI: 10.1371/journal.pgen.1010845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus. Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities similar to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far particular to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
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9
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540083. [PMID: 37214839 PMCID: PMC10197650 DOI: 10.1101/2023.05.09.540083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus . Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities analogous to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far unique to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261 U.S.A
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
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Xiao Y, Chen J, Yang S, Sun H, Xie L, Li J, Jing N, Zhu X. Maternal mRNA deadenylation and allocation via Rbm14 condensates facilitate vertebrate blastula development. EMBO J 2023; 42:e111364. [PMID: 36477743 PMCID: PMC9890236 DOI: 10.15252/embj.2022111364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Early embryonic development depends on proper utilization and clearance of maternal transcriptomes. How these processes are spatiotemporally regulated remains unclear. Here we show that nuclear RNA-binding protein Rbm14 and maternal mRNAs co-phase separate into cytoplasmic condensates to facilitate vertebrate blastula-to-gastrula development. In zebrafish, Rbm14 condensates were highly abundant in blastomeres and markedly reduced after prominent activation of zygotic transcription. They concentrated at spindle poles by associating with centrosomal γ-tubulin puncta and displayed mainly asymmetric divisions with a global symmetry across embryonic midline in 8- and 16-cell embryos. Their formation was dose-dependently stimulated by m6 A, but repressed by m5 C modification of the maternal mRNA. Furthermore, deadenylase Parn co-phase separated with these condensates, and this was required for deadenylation of the mRNAs in early blastomeres. Depletion of Rbm14 impaired embryonic cell differentiations and full activations of the zygotic genome in both zebrafish and mouse and resulted in developmental arrest at the blastula stage. Our results suggest that cytoplasmic Rbm14 condensate formation regulates early embryogenesis by facilitating deadenylation, protection, and mitotic allocation of m6 A-modified maternal mRNAs, and by releasing the poly(A)-less transcripts upon regulated disassembly to allow their re-polyadenylation and translation or clearance.
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Affiliation(s)
- Yue Xiao
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
| | - Jiehui Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Suming Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Honghua Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Lele Xie
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
| | - Xueliang Zhu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
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Blatnik MC, Gallagher TL, Amacher SL. Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1751. [PMID: 35851751 PMCID: PMC9840655 DOI: 10.1002/wrna.1751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 01/31/2023]
Abstract
Biological time keeping, or the duration and tempo at which biological processes occur, is a phenomenon that drives dynamic molecular and morphological changes that manifest throughout many facets of life. In some cases, the molecular mechanisms regulating the timing of biological transitions are driven by genetic oscillations, or periodic increases and decreases in expression of genes described collectively as a "molecular clock." In vertebrate animals, molecular clocks play a crucial role in fundamental patterning and cell differentiation processes throughout development. For example, during early vertebrate embryogenesis, the segmentation clock regulates the patterning of the embryonic mesoderm into segmented blocks of tissue called somites, which later give rise to axial skeletal muscle and vertebrae. Segmentation clock oscillations are characterized by rapid cycles of mRNA and protein expression. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short-lived. Faithful, rhythmic, genetic oscillations are sustained by precise regulation at many levels, including post-transcriptional regulation, and such mechanisms are essential for proper vertebrate development. This article is categorized under: RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Regulation.
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Affiliation(s)
- Monica C. Blatnik
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Thomas L. Gallagher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Sharon L. Amacher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
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12
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Kyritsis A, Papanastasi E, Kokkori I, Maragozidis P, Chatzileontiadou DSM, Pallaki P, Labrou M, Zarogiannis SG, Chrousos GP, Vlachakis D, Gourgoulianis KI, Balatsos NAA. Integrated Deadenylase Genetic Association Network and Transcriptome Analysis in Thoracic Carcinomas. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103102. [PMID: 35630580 PMCID: PMC9145511 DOI: 10.3390/molecules27103102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
The poly(A) tail at the 3′ end of mRNAs determines their stability, translational efficiency, and fate. The shortening of the poly(A) tail, and its efficient removal, triggers the degradation of mRNAs, thus, regulating gene expression. The process is catalyzed by a family of enzymes, known as deadenylases. As the dysregulation of gene expression is a hallmark of cancer, understanding the role of deadenylases has gained additional interest. Herein, the genetic association network shows that CNOT6 and CNOT7 are the most prevalent and most interconnected nodes in the equilibrated diagram. Subsequent silencing and transcriptomic analysis identifies transcripts possibly regulated by specific deadenylases. Furthermore, several gene ontologies are enriched by common deregulated genes. Given the potential concerted action and overlapping functions of deadenylases, we examined the effect of silencing a deadenylase on the remaining ones. Our results suggest that specific deadenylases target unique subsets of mRNAs, whilst at the same time, multiple deadenylases may affect the same mRNAs with overlapping functions.
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Affiliation(s)
- Athanasios Kyritsis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
| | - Eirini Papanastasi
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Ioanna Kokkori
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Department of Pneumonology-Oncology, Theagenio Cancer Hospital, 540 07 Thessaloniki, Greece
| | - Panagiotis Maragozidis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Demetra S. M. Chatzileontiadou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Paschalina Pallaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Maria Labrou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Sotirios G. Zarogiannis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Department of Physiology, Faculty of Medicine, University of Thessaly, Biopolis, 415 00 Larissa, Greece
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (G.P.C.); (D.V.)
- UNESCO Chair on Adolescent Health Care, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Center of Clinical, Experimental Surgery and Translational Research, Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Dimitrios Vlachakis
- University Research Institute of Maternal and Child Health and Precision Medicine, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (G.P.C.); (D.V.)
- UNESCO Chair on Adolescent Health Care, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Center of Clinical, Experimental Surgery and Translational Research, Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 118 55 Athens, Greece
| | - Konstantinos I. Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
| | - Nikolaos A. A. Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
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13
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Guillemin A, Kumar A, Wencker M, Ricci EP. Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. Front Immunol 2022; 12:796012. [PMID: 35087521 PMCID: PMC8787094 DOI: 10.3389/fimmu.2021.796012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Innate immunity is the frontline of defense against infections and tissue damage. It is a fast and semi-specific response involving a myriad of processes essential for protecting the organism. These reactions promote the clearance of danger by activating, among others, an inflammatory response, the complement cascade and by recruiting the adaptive immunity. Any disequilibrium in this functional balance can lead to either inflammation-mediated tissue damage or defense inefficiency. A dynamic and coordinated gene expression program lies at the heart of the innate immune response. This expression program varies depending on the cell-type and the specific danger signal encountered by the cell and involves multiple layers of regulation. While these are achieved mainly via transcriptional control of gene expression, numerous post-transcriptional regulatory pathways involving RNA-binding proteins (RBPs) and other effectors play a critical role in its fine-tuning. Alternative splicing, translational control and mRNA stability have been shown to be tightly regulated during the innate immune response and participate in modulating gene expression in a global or gene specific manner. More recently, microRNAs assisting RBPs and post-transcriptional modification of RNA bases are also emerging as essential players of the innate immune process. In this review, we highlight the numerous roles played by specific RNA-binding effectors in mediating post-transcriptional control of gene expression to shape innate immunity.
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Affiliation(s)
- Anissa Guillemin
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
| | - Anuj Kumar
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Mélanie Wencker
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, ENS de Lyon, CNRS, UMR 5308, INSERM, Lyon, France
| | - Emiliano P. Ricci
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
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14
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Nanjappa DP, Babu N, Khanna-Gupta A, O'Donohue MF, Sips P, Chakraborty A. Poly (A)-specific ribonuclease (PARN): More than just "mRNA stock clearing". Life Sci 2021; 285:119953. [PMID: 34520768 DOI: 10.1016/j.lfs.2021.119953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the balance between the synthesis and the degradation decides the steady-state levels of messenger RNAs (mRNA). The removal of adenosine residues from the poly(A) tail, called deadenylation, is the first and the most crucial step in the process of mRNA degradation. Poly (A)-specific ribonuclease (PARN) is one such enzyme that catalyses the process of deadenylation. Although PARN has been primarily known as the regulator of the mRNA stability, recent evidence clearly suggests several other functions of PARN, including a role in embryogenesis, oocyte maturation, cell-cycle progression, telomere biology, non-coding RNA maturation and ribosome biogenesis. Also, deregulated PARN activity is shown to be a hallmark of specific disease conditions. Pathogenic variants in the PARN gene have been observed in various cancers and inherited bone marrow failure syndromes. The focus in this review is to highlight the emerging functions of PARN, particularly in the context of human diseases.
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Affiliation(s)
- Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India
| | - Arati Khanna-Gupta
- Consortium of Rare Genetic and Bone Marrow Disorders, India network@NitteDU, NITTE (Deemed to be University, Deralakatte, Mangaluru, India
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative CBI, Université de Toulouse- CNRS- UPS- Toulouse-, Dynamics and Disorders of Ribosome Synthesis, Toulouse, France
| | - Patrick Sips
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India.
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15
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Nasiri-Aghdam M, Garcia-Garduño TC, Jave-Suárez LF. CELF Family Proteins in Cancer: Highlights on the RNA-Binding Protein/Noncoding RNA Regulatory Axis. Int J Mol Sci 2021; 22:11056. [PMID: 34681716 PMCID: PMC8537729 DOI: 10.3390/ijms222011056] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional modifications to coding and non-coding RNAs are unquestionably a pivotal way in which human mRNA and protein diversity can influence the different phases of a transcript's life cycle. CELF (CUGBP Elav-like family) proteins are RBPs (RNA-binding proteins) with pleiotropic capabilities in RNA processing. Their responsibilities extend from alternative splicing and transcript editing in the nucleus to mRNA stability, and translation into the cytoplasm. In this way, CELF family members have been connected to global alterations in cancer proliferation and invasion, leading to their identification as potential tumor suppressors or even oncogenes. Notably, genetic variants, alternative splicing, phosphorylation, acetylation, subcellular distribution, competition with other RBPs, and ultimately lncRNAs, miRNAs, and circRNAs all impact CELF regulation. Discoveries have emerged about the control of CELF functions, particularly via noncoding RNAs, and CELF proteins have been identified as competing, antagonizing, and regulating agents of noncoding RNA biogenesis. On the other hand, CELFs are an intriguing example through which to broaden our understanding of the RBP/noncoding RNA regulatory axis. Balancing these complex pathways in cancer is undeniably pivotal and deserves further research. This review outlines some mechanisms of CELF protein regulation and their functional consequences in cancer physiology.
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Affiliation(s)
- Maryam Nasiri-Aghdam
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Texali C. Garcia-Garduño
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
- Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Ciencias Biomédicas, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Luis Felipe Jave-Suárez
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
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16
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Ma L, Zhang X, Yu K, Xu X, Chen T, Shi Y, Wang Y, Qiu S, Guo S, Cui J, Miao Y, Tian X, Du L, Yu Y, Xia J, Wang J. Targeting SLC3A2 subunit of system X C- is essential for m 6A reader YTHDC2 to be an endogenous ferroptosis inducer in lung adenocarcinoma. Free Radic Biol Med 2021; 168:25-43. [PMID: 33785413 DOI: 10.1016/j.freeradbiomed.2021.03.023] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/16/2022]
Abstract
The m6A reader YT521-B homology containing 2 (YTHDC2) has been identified to inhibit lung adenocarcinoma (LUAD) tumorigenesis by suppressing solute carrier 7A11 (SLC7A11)-dependent antioxidant function. SLC7A11 is a major functional subunit of system XC-. Inhibition of system XC- can induce ferroptosis. However, whether suppressing SLC7A11 is sufficient for YTHDC2 to be an endogenous ferroptosis inducer in LUAD is unknown. Here, we found that induction of YTHDC2 to a high level can induce ferroptosis in LUAD cells but not in lung and bronchus epithelial cells. In addition to SLC7A11, solute carrier 3A2 (SLC3A2), another subunit of system XC- was equally important for YTHDC2-induced ferroptosis. YTHDC2 m6A-dependently destabilized Homeo box A13 (HOXA13) mRNA because a potential m6A recognition site was identified within its 3' untranslated region (3'UTR). Interestingly, HOXA13 acted as a transcription factor to stimulate SLC3A2 expression. Thereby, YTHDC2 suppressed SLC3A2 via inhibiting HOXA13 in an m6A-indirect manner. Mouse experiments further confirmed the associations among YTHDC2, SLC3A2 and HOXA13, and demonstrated that SLC3A2 and SLC7A11 were both important for YTHDC2-impaired tumor growth and -induced lipid peroxidation in vivo. Moreover, higher expression of SLC7A11, SLC3A2 and HOXA13 indicate poorer clinical outcome in YTHDC2-suppressed LUAD patients. In conclusion, YTHDC2 is believed to be a powerful endogenous ferroptosis inducer and targeting SLC3A2 subunit of system XC- is essential for this process. Increasing YTHDC2 is an alternative ferroptosis-based therapy to treat LUAD.
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Affiliation(s)
- Lifang Ma
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Keke Yu
- Department of Bio-bank, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xin Xu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Tianxiang Chen
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorder, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yikun Wang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shiyu Qiu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Susu Guo
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Jiangtao Cui
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong province, China
| | - Yongchun Yu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Jinjing Xia
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Jiayi Wang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China; Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China.
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17
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Song XH, Liao XY, Zheng XY, Liu JQ, Zhang ZW, Zhang LN, Yan YB. Human Ccr4 and Caf1 Deadenylases Regulate Proliferation and Tumorigenicity of Human Gastric Cancer Cells via Modulating Cell Cycle Progression. Cancers (Basel) 2021; 13:cancers13040834. [PMID: 33671234 PMCID: PMC7922635 DOI: 10.3390/cancers13040834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/06/2021] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Cancer cells generally reprogram their gene expression profiles to satisfy continuous growth, proliferation, and metastasis. Most eukaryotic mRNAs are degraded in a deadenylation-dependent pathway, in which deadenylases are the key enzymes. We found that human Ccr4 (hCcr4a/b) and Caf1 (hCaf1a/b), the dominant cytosolic deadenylases, were dysregulated in several types of cancers including stomach adenocarcinoma. Stably knocking down hCaf1a/b or hCcr4a/b blocks cell cycle progression by enhancing the levels of cell cycle inhibitors and by inhibiting the formation of processing bodies, which are cytosolic foci involved in mRNA metabolism. More importantly, depletion of hCaf1a/b or hCcr4a/b dramatically inhibits cell proliferation and tumorigenicity. Our results suggest that perturbating global RNA metabolism may provide a potential novel strategy for cancer treatment. Abstract Cancer cells generally have reprogrammed gene expression profiles to meet the requirements of survival, continuous division, and metastasis. An interesting question is whether the cancer cells will be affected by interfering their global RNA metabolism. In this research, we found that human Ccr4a/b (hCcr4a/b) and Caf1a/b (hCaf1a/b) deadenylases, the catalytic components of the Ccr4-Not complex, were dysregulated in several types of cancers including stomach adenocarcinoma. The impacts of the four deadenylases on cancer cell growth were studied by the establishment of four stable MKN28 cell lines with the knockdown of hCcr4a/b or hCaf1a/b or transient knockdown in several cell lines. Depletion of hCcr4a/b or hCaf1a/b significantly inhibited cell proliferation and tumorigenicity. Mechanistic studies indicated that the cells were arrested at the G2/M phase by knocking down hCaf1a, while arrested at the G0/G1 phase by depleting hCaf1b or hCcr4a/b. The four enzymes did not affect the levels of CDKs and cyclins but modulated the levels of CDK–cyclin inhibitors. We identified that hCcr4a/b, but not hCaf1a/b, targeted the p21 mRNA in the MKN28 cells. Furthermore, depletion of any one of the four deadenylases dramatically impaired processing-body formation in the MKN28 and HEK-293T cells. Our results highlight that perturbating global RNA metabolism may severely affect cancer cell proliferation, which provides a potential novel strategy for cancer treatment.
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Affiliation(s)
- Xiao-Hui Song
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Xiao-Yan Liao
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Xu-Ying Zheng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Jia-Qian Liu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Zhe-Wei Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Li-Na Zhang
- College of Life Science and Chemistry, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
- Correspondence: (L.-N.Z.); (Y.-B.Y.); Tel.: +86-10-6739-6342 (L.-N.Z.); +86-10-6278-3477 (Y.-B.Y.)
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
- Correspondence: (L.-N.Z.); (Y.-B.Y.); Tel.: +86-10-6739-6342 (L.-N.Z.); +86-10-6278-3477 (Y.-B.Y.)
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18
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Kontur C, Jeong M, Cifuentes D, Giraldez AJ. Ythdf m 6A Readers Function Redundantly during Zebrafish Development. Cell Rep 2020; 33:108598. [PMID: 33378672 PMCID: PMC11407899 DOI: 10.1016/j.celrep.2020.108598] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/09/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022] Open
Abstract
During the maternal-to-zygotic transition (MZT), multiple mechanisms precisely control massive decay of maternal mRNAs. N6-methyladenosine (m6A) is known to regulate mRNA decay, yet how this modification promotes maternal transcript degradation remains unclear. Here, we find that m6A promotes maternal mRNA deadenylation. Yet, genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance, zygotic genome activation, or the onset of gastrulation, challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development, as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally, we show that the microRNA miR-430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.
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Affiliation(s)
- Cassandra Kontur
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Minsun Jeong
- Chey Institute for Advanced Studies, Seoul 06141, Republic of Korea
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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19
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Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements. Cell Rep 2020; 33:108531. [PMID: 33357440 DOI: 10.1101/401604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 05/24/2023] Open
Abstract
CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3' UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6 exerts an effect on sequences, it is largely to decrease RNA abundance, which is reversed by mutating UGU-rich motifs. This is also the case for CELF3-5, with a protein-dependent effect on magnitude. Finally, we demonstrate that targets are derepressed in CELF6-mutant mice, and at least two key CNS proteins, FOS and FGF13, show altered protein expression levels and localization. Our works find, in addition to previously identified roles in splicing, that CELF6 is associated with repression of its CNS targets via the 3' UTR in vivo.
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Affiliation(s)
- Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana M King
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Crosby
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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20
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Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements. Cell Rep 2020; 33:108531. [PMID: 33357440 PMCID: PMC7780154 DOI: 10.1016/j.celrep.2020.108531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 02/08/2023] Open
Abstract
CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3′ UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6 exerts an effect on sequences, it is largely to decrease RNA abundance, which is reversed by mutating UGU-rich motifs. This is also the case for CELF3–5, with a protein-dependent effect on magnitude. Finally, we demonstrate that targets are derepressed in CELF6-mutant mice, and at least two key CNS proteins, FOS and FGF13, show altered protein expression levels and localization. Our works find, in addition to previously identified roles in splicing, that CELF6 is associated with repression of its CNS targets via the 3′ UTR in vivo. Rieger et al. assay the function of the RNA-binding protein CELF6 by defining its targets in the brain. They show that CELF6 largely binds 3′ UTRs of synaptic mRNAs. Using a massively parallel reporter assay, they further show that CELF6 and other CELFs are associated with lower mRNA abundance and that targets are derepressed in Celf6-knockout mice in vivo.
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Affiliation(s)
- Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana M King
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Crosby
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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21
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Han X, Wang L, Han Q. Advances in the role of m 6A RNA modification in cancer metabolic reprogramming. Cell Biosci 2020; 10:117. [PMID: 33062255 PMCID: PMC7552565 DOI: 10.1186/s13578-020-00479-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/24/2020] [Indexed: 01/10/2023] Open
Abstract
N6-methyladenosine (m6A) modification is the most common internal modification of eukaryotic mRNA and is widely involved in many cellular processes, such as RNA transcription, splicing, nuclear transport, degradation, and translation. m6A has been shown to plays important roles in the initiation and progression of various cancers. The altered metabolic programming of cancer cells promotes their cell-autonomous proliferation and survival, leading to an indispensable hallmark of cancers. Accumulating evidence has demonstrated that this epigenetic modification exerts extensive effects on the cancer metabolic network by either directly regulating the expression of metabolic genes or modulating metabolism-associated signaling pathways. In this review, we summarized the regulatory mechanisms and biological functions of m6A and its role in cancer metabolic reprogramming.
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Affiliation(s)
- Xiu Han
- Center of Clinical Laboratory, Suzhou Dushu Lake Public Hospital, 9#, Chongwen Road, Suzhou, 215000 People’s Republic of China
| | - Lin Wang
- Center of Clinical Laboratory, Suzhou Dushu Lake Public Hospital, 9#, Chongwen Road, Suzhou, 215000 People’s Republic of China
| | - Qingzhen Han
- Center of Clinical Laboratory, Suzhou Dushu Lake Public Hospital, 9#, Chongwen Road, Suzhou, 215000 People’s Republic of China
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22
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Heat stress induced arginylation of HuR promotes alternative polyadenylation of Hsp70.3 by regulating HuR stability and RNA binding. Cell Death Differ 2020; 28:730-747. [PMID: 32929216 DOI: 10.1038/s41418-020-00619-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 11/08/2022] Open
Abstract
Arginylation was previously found to promote stabilization of heat shock protein 70.3 (Hsp70.3) mRNA and cell survival in mouse embryonic fibroblasts (MEFs) on exposure to heat stress (HS). In search of a factor responsible for these phenomena, the current study identified human antigen R (HuR) as a direct target of arginylation. HS induced arginylation of HuR affected its stability and RNA binding activity. Arginylated HuR failed to bind Hsp70.3 3' UTR, allowing the recruitment of cleavage stimulating factor 64 (CstF64) in the proximal poly-A-site (PAS), generating transcripts with short 3'UTR. However, HuR from Ate1 knock out (KO) MEFs bound to proximal PAS region with higher affinity, thus excluded CstF64 recruitment. This inhibited the alternative polyadenylation (APA) of Hsp70.3 mRNA and generated the unstable transcripts with long 3'UTR. The inhibition of RNA binding activity of HuR was traced to arginylation-coupled phosphorylation of HuR, by check point kinase 2 (Chk2). Arginylation of HuR occurred at the residue D15 and the arginylation was needed for the phosphorylation. Accumulation of HuR also decreased cell viability upon HS. In conclusion, arginylation dependent modifications of HuR maintained its cellular homeostasis, and promoted APA of Hsp70.3 pre-mRNA, during early HS response.
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23
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Yan YB. Diverse functions of deadenylases in DNA damage response and genomic integrity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1621. [PMID: 32790161 DOI: 10.1002/wrna.1621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022]
Abstract
DNA damage response (DDR) is a coordinated network of diverse cellular processes including the detection, signaling, and repair of DNA lesions, the adjustment of metabolic network and cell fate determination. To deal with the unavoidable DNA damage caused by either endogenous or exogenous stresses, the cells need to reshape the gene expression profile to allow efficient transcription and translation of DDR-responsive messenger RNAs (mRNAs) and to repress the nonessential mRNAs. A predominant method to adjust RNA fate is achieved by modulating the 3'-end oligo(A) or poly(A) length via the opposing actions of polyadenylation and deadenylation. Poly(A)-specific ribonuclease (PARN) and the carbon catabolite repressor 4 (CCR4)-Not complex, the major executors of deadenylation, are indispensable to DDR and genomic integrity in eukaryotic cells. PARN modulates cell cycle progression by regulating the stabilities of mRNAs and microRNA (miRNAs) involved in the p53 pathway and contributes to genomic stability by affecting the biogenesis of noncoding RNAs including miRNAs and telomeric RNA. The CCR4-Not complex is involved in diverse pathways of DDR including transcriptional regulation, signaling pathways, mRNA stabilities, translation regulation, and protein degradation. The RNA targets of deadenylases are tuned by the DDR signaling pathways, while in turn the deadenylases can regulate the levels of DNA damage-responsive proteins. The mutual feedback between deadenylases and the DDR signaling pathways allows the cells to precisely control DDR by dynamically adjusting the levels of sensors and effectors of the DDR signaling pathways. Here, the diverse functions of deadenylases in DDR are summarized and the underlying mechanisms are proposed according to recent findings. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
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24
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Cox DC, Guan X, Xia Z, Cooper TA. Increased nuclear but not cytoplasmic activities of CELF1 protein leads to muscle wasting. Hum Mol Genet 2020; 29:1729-1744. [PMID: 32412585 PMCID: PMC7322576 DOI: 10.1093/hmg/ddaa095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/16/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
mRNA processing is highly regulated during development through changes in RNA-binding protein (RBP) activities. CUG-BP, Elav-like family member 1 (CELF1, also called CUGBP1) is an RBP, the expression of which decreases in skeletal muscle soon after birth. CELF1 regulates multiple nuclear and cytoplasmic RNA processing events. In the nucleus, CELF1 regulates networks of postnatal alternative splicing (AS) transitions, while in the cytoplasm, CELF1 regulates mRNA stability and translation. Stabilization and misregulation of CELF1 has been implicated in human diseases including myotonic dystrophy type 1, Alzheimer's disease and multiple cancers. To understand the contribution of nuclear and cytoplasmic CELF1 activity to normal and pathogenic skeletal muscle biology, we generated transgenic mice for doxycycline-inducible and skeletal muscle-specific expression of active CELF1 mutants engineered to be localized predominantly to either the nucleus or the cytoplasm. Adult mice expressing nuclear, but not cytoplasmic, CELF1 are characterized by strong histopathological defects, muscle loss within 10 days and changes in AS. In contrast, mice expressing cytoplasmic CELF1 display changes in protein levels of targets known to be regulated at the level of translation by CELF1, with minimal changes in AS. These changes are in the absence of overt histopathological changes or muscle loss. RNA-sequencing revealed extensive gene expression and AS changes in mice overexpressing nuclear and naturally localized CELF1 protein, with affected genes involved in cytoskeleton dynamics, membrane dynamics, RNA processing and zinc ion binding. These results support a stronger role for nuclear CELF1 functions as compared to cytoplasmic CELF1 functions in skeletal muscle wasting.
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Affiliation(s)
- Diana C Cox
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Xiangnan Guan
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Thomas A Cooper
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston TX, 77030 USA
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25
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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26
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Timchenko L. Correction of RNA-Binding Protein CUGBP1 and GSK3β Signaling as Therapeutic Approach for Congenital and Adult Myotonic Dystrophy Type 1. Int J Mol Sci 2019; 21:ijms21010094. [PMID: 31877772 PMCID: PMC6982105 DOI: 10.3390/ijms21010094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 01/02/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a complex genetic disease affecting many tissues. DM1 is caused by an expansion of CTG repeats in the 3′-UTR of the DMPK gene. The mechanistic studies of DM1 suggested that DMPK mRNA, containing expanded CUG repeats, is a major therapeutic target in DM1. Therefore, the removal of the toxic RNA became a primary focus of the therapeutic development in DM1 during the last decade. However, a cure for this devastating disease has not been found. Whereas the degradation of toxic RNA remains a preferential approach for the reduction of DM1 pathology, other approaches targeting early toxic events downstream of the mutant RNA could be also considered. In this review, we discuss the beneficial role of the restoring of the RNA-binding protein, CUGBP1/CELF1, in the correction of DM1 pathology. It has been recently found that the normalization of CUGBP1 activity with the inhibitors of GSK3 has a positive effect on the reduction of skeletal muscle and CNS pathologies in DM1 mouse models. Surprisingly, the inhibitor of GSK3, tideglusib also reduced the toxic CUG-containing RNA. Thus, the development of the therapeutics, based on the correction of the GSK3β-CUGBP1 pathway, is a promising option for this complex disease.
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Affiliation(s)
- Lubov Timchenko
- Departments of Neurology and Pediatrics, Cincinnati Children's Hospital Medical Center and the University of Cincinnati, Cincinnati, OH 45229, USA
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27
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Uchida Y, Chiba T, Kurimoto R, Asahara H. Post-transcriptional regulation of inflammation by RNA-binding proteins via cis-elements of mRNAs. J Biochem 2019; 166:375-382. [PMID: 31511872 DOI: 10.1093/jb/mvz067] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/26/2019] [Indexed: 12/18/2022] Open
Abstract
In human genome, there are approximately 1,500 RNA-binding proteins (RBPs). They can regulate mRNA stability or translational efficiency via ribosomes and these processes are known as 'post-transcriptional regulation'. Accumulating evidences indicate that post-transcriptional regulation is the determinant of the accurate levels of cytokines mRNAs. While transcriptional regulation of cytokines mRNAs has been well studied and found to be important for the rapid induction of mRNA and regulation of the acute phase of inflammation, post-transcriptional regulation by RBPs is essential for resolving inflammation in the later phase, and their dysfunction may lead to severe autoimmune diseases such as rheumatoid arthritis or systemic lupus erythematosus. For post-transcriptional regulation, RBPs recognize and directly bind to cis-regulatory elements in 3' untranslated region of mRNAs such as AU-rich or constitutive decay elements and play various roles. In this review, we summarize the recent findings regarding the role of RBPs in the regulation of inflammation.
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Affiliation(s)
- Yutaro Uchida
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryota Kurimoto
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, Japan
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28
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Baquero J, Varriano S, Ordonez M, Kuczaj P, Murphy MR, Aruggoda G, Lundine D, Morozova V, Makki AE, Alonso ADC, Kleiman FE. Nuclear Tau, p53 and Pin1 Regulate PARN-Mediated Deadenylation and Gene Expression. Front Mol Neurosci 2019; 12:242. [PMID: 31749682 PMCID: PMC6843027 DOI: 10.3389/fnmol.2019.00242] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
While nuclear tau plays a role in DNA damage response (DDR) and chromosome relaxation, the mechanisms behind these functions are not fully understood. Here, we show that tau forms complex(es) with factors involved in nuclear mRNA processing such as tumor suppressor p53 and poly(A)-specific ribonuclease (PARN) deadenylase. Tau induces PARN activity in different cellular models during DDR, and this activation is further increased by p53 and inhibited by tau phosphorylation at residues implicated in neurological disorders. Tau's binding factor Pin1, a mitotic regulator overexpressed in cancer and depleted in Alzheimer's disease (AD), also plays a role in the activation of nuclear deadenylation. Tau, Pin1 and PARN target the expression of mRNAs deregulated in AD and/or cancer. Our findings identify novel biological roles of tau and toxic effects of hyperphosphorylated-tau. We propose a model in which factors involved in cancer and AD regulate gene expression by interactions with the mRNA processing machinery, affecting the transcriptome and suggesting insights into alternative mechanisms for the initiation and/or developments of these diseases.
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Affiliation(s)
- Jorge Baquero
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Sophia Varriano
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Martha Ordonez
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Pawel Kuczaj
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Michael R. Murphy
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Gamage Aruggoda
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Devon Lundine
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Viktoriya Morozova
- Department of Biology and Center for Developmental Neuroscience, College of Staten Island, Graduate Center, The City University of New York, Staten Island, NY, United States
| | - Ali Elhadi Makki
- Department of Biology and Center for Developmental Neuroscience, College of Staten Island, Graduate Center, The City University of New York, Staten Island, NY, United States
| | - Alejandra del C. Alonso
- Department of Biology and Center for Developmental Neuroscience, College of Staten Island, Graduate Center, The City University of New York, Staten Island, NY, United States
| | - Frida E. Kleiman
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
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29
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Son A, Park JE, Kim VN. PARN and TOE1 Constitute a 3' End Maturation Module for Nuclear Non-coding RNAs. Cell Rep 2019; 23:888-898. [PMID: 29669292 DOI: 10.1016/j.celrep.2018.03.089] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 12/27/2017] [Accepted: 03/20/2018] [Indexed: 10/17/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A) tails. Rather, they promote the maturation of nuclear small non-coding RNAs (ncRNAs). PARN and TOE1 act redundantly on some ncRNAs, most prominently small Cajal body-specific RNAs (scaRNAs). scaRNAs are strongly downregulated when PARN and TOE1 are compromised together, leading to defects in small nuclear RNA (snRNA) pseudouridylation. They also function redundantly in the biogenesis of telomerase RNA component (TERC), which shares sequence motifs found in H/ACA box scaRNAs. Our findings extend the knowledge of nuclear ncRNA biogenesis, and they provide insights into the pathology of PARN/TOE1-associated genetic disorders whose therapeutic treatments are currently unavailable.
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Affiliation(s)
- Ahyeon Son
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Eun Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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30
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Duan TL, He GJ, Hu LD, Yan YB. The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage. Cells 2019; 8:836. [PMID: 31387300 PMCID: PMC6721724 DOI: 10.3390/cells8080836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN), a multifunctional multi-domain deadenylase, is crucial to the regulation of mRNA turnover and the maturation of various non-coding RNAs. Despite extensive studies of the well-folding domains responsible for PARN catalysis, the structure and function of the C-terminal domain (CTD) remains elusive. PARN is a cytoplasm-nucleus shuttle protein with concentrated nucleolar distribution. Here, we identify the nuclear and nucleolar localization signals in the CTD of PARN. Spectroscopic studies indicated that PARN-CTD is intrinsically disordered with loosely packed local structures/tertiary structure. Phosphorylation-mimic mutation S557D disrupted the local structure and facilitated the binding of the CTD with the well-folded domains, with no impact on PARN deadenylase activity. Under normal conditions, the nucleolus-residing PARN recruited CBP80 into the nucleoli to repress its deadenylase activity, while DNA damage-induced phosphorylation of PARN-S557 expelled CBP80 from the nucleoli to discharge activity inhibition and attracted nucleoplasm-located CstF-50 into the nucleoli to activate deadenylation. The structure switch-induced function switch of PARN reshaped the profile of small nuclear non-coding RNAs to respond to DNA damage. Our findings highlight that the structure switch of the CTD induced by posttranslational modifications redefines the subset of binding partners, and thereby the RNA targets in the nucleoli.
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Affiliation(s)
- Tian-Li Duan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guang-Jun He
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li-Dan Hu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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31
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Guo L, Sharma SD, Debes JD, Beisang D, Rattenbacher B, Louis IVS, Wiesner DL, Cameron CE, Bohjanen PR. The hepatitis C viral nonstructural protein 5A stabilizes growth-regulatory human transcripts. Nucleic Acids Res 2019; 46:2537-2547. [PMID: 29385522 PMCID: PMC5861452 DOI: 10.1093/nar/gky061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/22/2018] [Indexed: 12/11/2022] Open
Abstract
Numerous mammalian proto-oncogene and other growth-regulatory transcripts are upregulated in malignancy due to abnormal mRNA stabilization. In hepatoma cells expressing a hepatitis C virus (HCV) subgenomic replicon, we found that the viral nonstructural protein 5A (NS5A), a protein known to bind to viral RNA, also bound specifically to human cellular transcripts that encode regulators of cell growth and apoptosis, and this binding correlated with transcript stabilization. An important subset of human NS5A-target transcripts contained GU-rich elements, sequences known to destabilize mRNA. We found that NS5A bound to GU-rich elements in vitro and in cells. Mutation of the NS5A zinc finger abrogated its GU-rich element-binding and mRNA stabilizing activities. Overall, we identified a molecular mechanism whereby HCV manipulates host gene expression by stabilizing host transcripts in a manner that would promote growth and prevent death of virus-infected cells, allowing the virus to establish chronic infection and lead to the development of hepatocellular carcinoma.
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Affiliation(s)
- Liang Guo
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA
- Graduate Program in Comparative and Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Suresh D Sharma
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University 201 Althouse Laboratory, University Park, PA 16802, USA
| | - Jose D Debes
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel Beisang
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bernd Rattenbacher
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Irina Vlasova-St Louis
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
| | - Darin L Wiesner
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Craig E Cameron
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University 201 Althouse Laboratory, University Park, PA 16802, USA
- Correspondence may also be addressed to Craig E. Cameron.
| | - Paul R Bohjanen
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA
- Graduate Program in Comparative and Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- To whom correspondence should be addressed.
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32
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Vastenhouw NL, Cao WX, Lipshitz HD. The maternal-to-zygotic transition revisited. Development 2019; 146:146/11/dev161471. [PMID: 31189646 DOI: 10.1242/dev.161471] [Citation(s) in RCA: 266] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The development of animal embryos is initially directed by maternal gene products. Then, during the maternal-to-zygotic transition (MZT), developmental control is handed to the zygotic genome. Extensive research in both vertebrate and invertebrate model organisms has revealed that the MZT can be subdivided into two phases, during which very different modes of gene regulation are implemented: initially, regulation is exclusively post-transcriptional and post-translational, following which gradual activation of the zygotic genome leads to predominance of transcriptional regulation. These changes in the gene expression program of embryos are precisely controlled and highly interconnected. Here, we review current understanding of the mechanisms that underlie handover of developmental control during the MZT.
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Affiliation(s)
- Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
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33
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Herpin A, Schmidt C, Kneitz S, Gobé C, Regensburger M, Le Cam A, Montfort J, Adolfi MC, Lillesaar C, Wilhelm D, Kraeussling M, Mourot B, Porcon B, Pannetier M, Pailhoux E, Ettwiller L, Dolle D, Guiguen Y, Schartl M. A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specific genes prior to the sex-determination stage in medaka. PLoS Biol 2019; 17:e3000185. [PMID: 30947255 PMCID: PMC6448818 DOI: 10.1371/journal.pbio.3000185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/04/2019] [Indexed: 12/20/2022] Open
Abstract
Dmrt1 is a highly conserved transcription factor, which is critically involved in regulation of gonad development of vertebrates. In medaka, a duplicate of dmrt1-acting as master sex-determining gene-has a tightly timely and spatially controlled gonadal expression pattern. In addition to transcriptional regulation, a sequence motif in the 3' UTR (D3U-box) mediates transcript stability of dmrt1 mRNAs from medaka and other vertebrates. We show here that in medaka, two RNA-binding proteins with antagonizing properties target this D3U-box, promoting either RNA stabilization in germ cells or degradation in the soma. The D3U-box is also conserved in other germ-cell transcripts, making them responsive to the same RNA binding proteins. The evolutionary conservation of the D3U-box motif within dmrt1 genes of metazoans-together with preserved expression patterns of the targeting RNA binding proteins in subsets of germ cells-suggest that this new mechanism for controlling RNA stability is not restricted to fishes but might also apply to other vertebrates.
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Affiliation(s)
- Amaury Herpin
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
- University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany
- * E-mail:
| | - Cornelia Schmidt
- University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany
| | - Susanne Kneitz
- University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany
| | - Clara Gobé
- UMR BDR, INRA, ENVA, Université Paris Saclay, Jouy en Josas, France
| | | | - Aurélie Le Cam
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | | | - Mateus C. Adolfi
- University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany
| | - Christina Lillesaar
- University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany
| | - Dagmar Wilhelm
- University of Melbourne, Department of Anatomy & Neuroscience, Parkville, Victoria, Australia
| | - Michael Kraeussling
- University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany
| | | | | | - Maëlle Pannetier
- UMR BDR, INRA, ENVA, Université Paris Saclay, Jouy en Josas, France
| | - Eric Pailhoux
- UMR BDR, INRA, ENVA, Université Paris Saclay, Jouy en Josas, France
| | - Laurence Ettwiller
- University of Heidelberg, Centre for Organismal Studies (COS), Department of Developmental Biology, Heidelberg, Germany
| | - Dirk Dolle
- University of Heidelberg, Centre for Organismal Studies (COS), Department of Developmental Biology, Heidelberg, Germany
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | - Manfred Schartl
- University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Hospital, Wuerzburg, Germany
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas, United States of America
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Gomez-Cambronero J. Lack of effective translational regulation of PLD expression and exosome biogenesis in triple-negative breast cancer cells. Cancer Metastasis Rev 2019; 37:491-507. [PMID: 30091053 DOI: 10.1007/s10555-018-9753-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is difficult to treat since cells lack the three receptors (ES, PR, or HER) that the most effective treatments target. We have used a well-established TNBC cell line (MDA-MB-231) from which we found evidence in support for a phospholipase D (PLD)-mediated tumor growth and metastasis: high levels of expression of PLD, as well as the absence of inhibitory miRs (such as miR-203) and 3'-mRNA PARN deadenylase activity in these cells. Such findings are not present in a luminal B cell line, MCF-7, and we propose a new miR•PARN•PLD node that is not uniform across breast cancer molecular subtypes and as such TNBC could be pharmacologically targeted differentially. We review the participation of PLD and phosphatidic acid (PA), its enzymatic product, as new "players" in breast cancer biology, with the aspects of regulation of the tumor microenvironment, macrophage polarization, regulation of PLD transcripts by specific miRs and deadenylases, and PLD-regulated exosome biogenesis. A new signaling miR•PARN•PLD node could serve as new biomarkers for TNBC abnormal signaling and metastatic disease staging, potentially before metastases are able to be visualized using conventional imaging.
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Affiliation(s)
- Julian Gomez-Cambronero
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, 3640 Colonel Glenn Highway, Dayton, OH, 45435, USA.
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35
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Yap K, Mukhina S, Zhang G, Tan JSC, Ong HS, Makeyev EV. A Short Tandem Repeat-Enriched RNA Assembles a Nuclear Compartment to Control Alternative Splicing and Promote Cell Survival. Mol Cell 2018; 72:525-540.e13. [PMID: 30318443 PMCID: PMC6224606 DOI: 10.1016/j.molcel.2018.08.041] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/31/2018] [Accepted: 08/27/2018] [Indexed: 11/25/2022]
Abstract
Functions of many long noncoding RNAs (lncRNAs) depend on their ability to interact with multiple copies of specific RNA-binding proteins (RBPs). Here, we devised a workflow combining bioinformatics and experimental validation steps to systematically identify RNAs capable of multivalent RBP recruitment. This uncovered a number of previously unknown transcripts encoding high-density RBP recognition arrays within genetically normal short tandem repeats. We show that a top-scoring hit in this screen, lncRNA PNCTR, contains hundreds of pyrimidine tract-binding protein (PTBP1)-specific motifs allowing it to sequester a substantial fraction of PTBP1 in a nuclear body called perinucleolar compartment. Importantly, PNCTR is markedly overexpressed in a variety of cancer cells and its downregulation is sufficient to induce programmed cell death at least in part by stimulating PTBP1 splicing regulation activity. This work expands our understanding of the repeat-containing fraction of the human genome and illuminates a novel mechanism driving malignant transformation of cancer cells.
Human genome encodes many transcripts enriched in short tandem repeats (strRNAs) strRNA PNCTR recruits RNA-binding protein PTBP1 to a nuclear body called PNC PNCTR antagonizes splicing regulation function of PTBP1 and promotes cell survival PNCTR is dramatically upregulated in a wide range of cancer cells
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Affiliation(s)
- Karen Yap
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Svetlana Mukhina
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Gen Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Jason S C Tan
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Hong Sheng Ong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
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36
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Liu C, Ma Y, Shang Y, Huo R, Li W. Post-translational regulation of the maternal-to-zygotic transition. Cell Mol Life Sci 2018; 75:1707-1722. [PMID: 29427077 PMCID: PMC11105290 DOI: 10.1007/s00018-018-2750-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/24/2017] [Accepted: 01/08/2018] [Indexed: 02/07/2023]
Abstract
The maternal-to-zygotic transition (MZT) is essential for the developmental control handed from maternal products to newly synthesized zygotic genome in the earliest stages of embryogenesis, including maternal component (mRNAs and proteins) degradation and zygotic genome activation (ZGA). Various protein post-translational modifications have been identified during the MZT, such as phosphorylation, methylation and ubiquitination. Precise post-translational regulation mechanisms are essential for the timely transition of early embryonic development. In this review, we summarize recent progress regarding the molecular mechanisms underlying post-translational regulation of maternal component degradation and ZGA during the MZT and discuss some important issues in the field.
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Affiliation(s)
- Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanjie Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- Department of Animal Science and Technology, Northeast Agricultural University, Haerbin, 150030, People's Republic of China
| | - Yongliang Shang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029, People's Republic of China.
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, People's Republic of China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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Abstract
Viruses alter host-cell gene expression at many biochemical levels, such as transcription, translation, mRNA splicing and mRNA decay in order to create a cellular environment suitable for viral replication. In this review, we discuss mechanisms by which viruses manipulate host-gene expression at the level of mRNA decay in order to enable the virus to evade host antiviral responses to allow viral survival and replication. We discuss different cellular RNA decay pathways, including the deadenylation-dependent mRNA decay pathway, and various strategies that viruses exploit to manipulate these pathways in order to create a virus-friendly cellular environment.
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Affiliation(s)
- Liang Guo
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA.,Graduate Program in Comparative & Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Irina Vlasova-St Louis
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul R Bohjanen
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA.,Graduate Program in Comparative & Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
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38
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Zhang X, Xiao S, Rameau RD, Devany E, Nadeem Z, Caglar E, Ng K, Kleiman FE, Saxena A. Nucleolin phosphorylation regulates PARN deadenylase activity during cellular stress response. RNA Biol 2018; 15:251-260. [PMID: 29168431 PMCID: PMC5798948 DOI: 10.1080/15476286.2017.1408764] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/11/2017] [Accepted: 11/16/2017] [Indexed: 01/28/2023] Open
Abstract
Nucleolin (NCL) is an abundant stress-responsive, RNA-binding phosphoprotein that controls gene expression by regulating either mRNA stability and/or translation. NCL binds to the AU-rich element (ARE) in the 3'UTR of target mRNAs, mediates miRNA functions in the nearby target sequences, and regulates mRNA deadenylation. However, the mechanism by which NCL phosphorylation affects these functions and the identity of the deadenylase involved, remain largely unexplored. Earlier we demonstrated that NCL phosphorylation is vital for cell cycle progression and proliferation, whereas phosphorylation-deficient NCL at six consensus CK2 sites confers dominant-negative effect on proliferation by increasing p53 expression, possibly mimicking cellular DNA damage conditions. In this study, we show that NCL phosphorylation at those CK2 consensus sites in the N-terminus is necessary to induce deadenylation upon oncogenic stimuli and UV stress. NCL-WT, but not hypophosphorylated NCL-6/S*A, activates poly (A)-specific ribonuclease (PARN) deadenylase activity. We further demonstrate that NCL interacts directly with PARN, and under non-stress conditions also forms (a) complex (es) with factors that regulate deadenylation, such as p53 and the ARE-binding protein HuR. Upon UV stress, the interaction of hypophosphorylated NCL-6/S*A with these proteins is favored. As an RNA-binding protein, NCL interacts with PARN deadenylase substrates such as TP53 and BCL2 mRNAs, playing a role in their downregulation under non-stress conditions. For the first time, we show that NCL phosphorylation offers specificity to its protein-protein, protein-RNA interactions, resulting in the PARN deadenylase regulation, and hence gene expression, during cellular stress responses.
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Affiliation(s)
- Xiaokan Zhang
- Chemistry Department, Hunter College, New York, NY, USA
| | - Shu Xiao
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| | | | - Emral Devany
- Chemistry Department, Hunter College, New York, NY, USA
| | - Zaineb Nadeem
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| | - Elif Caglar
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| | - Kenneth Ng
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| | | | - Anjana Saxena
- Biology Department, Brooklyn College, Brooklyn, NY, USA
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39
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Deregulation of RNA Metabolism in Microsatellite Expansion Diseases. ADVANCES IN NEUROBIOLOGY 2018; 20:213-238. [PMID: 29916021 DOI: 10.1007/978-3-319-89689-2_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RNA metabolism impacts different steps of mRNA life cycle including splicing, polyadenylation, nucleo-cytoplasmic export, translation, and decay. Growing evidence indicates that defects in any of these steps lead to devastating diseases in humans. This chapter reviews the various RNA metabolic mechanisms that are disrupted in Myotonic Dystrophy-a trinucleotide repeat expansion disease-due to dysregulation of RNA-Binding Proteins. We also compare Myotonic Dystrophy to other microsatellite expansion disorders and describe how some of these mechanisms commonly exert direct versus indirect effects toward disease pathologies.
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40
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Guo L, Louis IVS, Bohjanen PR. Post-transcriptional regulation of cytokine expression and signaling. CURRENT TRENDS IN IMMUNOLOGY 2018; 19:33-40. [PMID: 30568341 PMCID: PMC6296478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cytokines and cytokine signaling pathways are crucial for regulating cellular functions, including cell growth, proliferation, differentiation, and cell death. Cytokines regulate physiological processes such as immune responses and maintain immune homeostasis, and they also mediate pathological conditions such as autoimmune diseases and cancer. Hence, the precise control of the expression of cytokines and the transduction of cytokine signals is tightly regulated at transcriptional and post-transcriptional levels. In particular, post-transcriptional regulation at the level of mRNA stability is critical for coordinating cytokine expression and cytokine signaling. Numerous cytokine transcripts contain AU-rich elements (AREs), whereas transcripts encoding numerous components of cytokine signaling pathways contain GU-rich elements (GREs). AREs and GREs are mRNA decay elements that mediate rapid mRNA degradation. Through ARE- and GRE-mediated decay mechanisms, immune cells selectively and specifically regulate cytokine networks during immune responses. Aberrant expression and stability of ARE- or GRE-containing transcripts that encode cytokines or components of cytokine signaling pathways are observed in disease states, including cancer. In this review, we focus on the role of AREs and GREs in regulating cytokine expression and signal transduction at the level of mRNA stability.
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Affiliation(s)
- Liang Guo
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA
- Graduate Program in Comparative and Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Irina Vlasova-St. Louis
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul R. Bohjanen
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA
- Graduate Program in Comparative and Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
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41
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Nutter CA, Kuyumcu-Martinez MN. Emerging roles of RNA-binding proteins in diabetes and their therapeutic potential in diabetic complications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 29280295 DOI: 10.1002/wrna.1459] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/19/2017] [Accepted: 11/05/2017] [Indexed: 12/11/2022]
Abstract
Diabetes is a debilitating health care problem affecting 422 million people around the world. Diabetic patients suffer from multisystemic complications that can cause mortality and morbidity. Recent advancements in high-throughput next-generation RNA-sequencing and computational algorithms led to the discovery of aberrant posttranscriptional gene regulatory programs in diabetes. However, very little is known about how these regulatory programs are mis-regulated in diabetes. RNA-binding proteins (RBPs) are important regulators of posttranscriptional RNA networks, which are also dysregulated in diabetes. Human genetic studies provide new evidence that polymorphisms and mutations in RBPs are linked to diabetes. Therefore, we will discuss the emerging roles of RBPs in abnormal posttranscriptional gene expression in diabetes. Questions that will be addressed are: Which posttranscriptional mechanisms are disrupted in diabetes? Which RBPs are responsible for such changes under diabetic conditions? How are RBPs altered in diabetes? How does dysregulation of RBPs contribute to diabetes? Can we target RBPs using RNA-based methods to restore gene expression profiles in diabetic patients? Studying the evolving roles of RBPs in diabetes is critical not only for a comprehensive understanding of diabetes pathogenesis but also to design RNA-based therapeutic approaches for diabetic complications. WIREs RNA 2018, 9:e1459. doi: 10.1002/wrna.1459 This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing Translation > Translation Regulation.
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Affiliation(s)
- Curtis A Nutter
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas.,Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas.,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas
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42
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Ray M, Autieri MV. Regulation of pro- and anti-atherogenic cytokines. Cytokine 2017; 122:154175. [PMID: 29221669 DOI: 10.1016/j.cyto.2017.09.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/29/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022]
Abstract
Despite advances in prevention and treatment, vascular diseases continue to account for significant morbidity and mortality in the developed world. Incidence is expected to worsen as the number of patients with common co-morbidities linked with atherosclerotic vascular disease, such as obesity and diabetes, continues to increase, reaching epidemic proportions. Atherosclerosis is a lipid-driven vascular inflammatory disease involving multiple cell types in various stages of inflammation, activation, apoptosis, and necrosis. One commonality among these cell types is that they are activated and communicate with each other in a paracrine fashion via a complex network of cytokines. Cytokines mediate atherogenesis by stimulating expression of numerous proteins necessary for induction of a host of cellular responses, including inflammation, extravasation, proliferation, apoptosis, and matrix production. Cytokine expression is regulated by a number of transcriptional and post-transcriptional mechanisms. In this context, proteins that control and fine-tune cytokine expression can be considered key players in development of atherosclerosis and also represent targets for rational drug therapy to combat this disease. This review will describe the cellular and molecular mechanisms that drive atherosclerotic plaque progression and present key cytokines that participate in this process. We will also describe RNA binding proteins that mediate cytokine mRNA stability and regulate cytokine abundance. Identification and characterization of the cytokines and proteins that regulate their abundance are essential to our ability to identify therapeutic approaches to ameliorate atherosclerotic vascular disease.
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Affiliation(s)
- Mitali Ray
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Michael V Autieri
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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43
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Shin J, Paek KY, Ivshina M, Stackpole EE, Richter JD. Essential role for non-canonical poly(A) polymerase GLD4 in cytoplasmic polyadenylation and carbohydrate metabolism. Nucleic Acids Res 2017; 45:6793-6804. [PMID: 28383716 PMCID: PMC5499868 DOI: 10.1093/nar/gkx239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/30/2017] [Indexed: 11/16/2022] Open
Abstract
Regulation of gene expression at the level of cytoplasmic polyadenylation is important for many biological phenomena including cell cycle progression, mitochondrial respiration, and learning and memory. GLD4 is one of the non-canonical poly(A) polymerases that regulates cytoplasmic polyadenylation-induced translation, but its target mRNAs and role in cellular physiology is not well known. To assess the full panoply of mRNAs whose polyadenylation is controlled by GLD4, we performed an unbiased whole genome-wide screen using poy(U) chromatography and thermal elution. We identified hundreds of mRNAs regulated by GLD4, several of which are involved in carbohydrate metabolism including GLUT1, a major glucose transporter. Depletion of GLD4 not only reduced GLUT1 poly(A) tail length, but also GLUT1 protein. GLD4-mediated translational control of GLUT1 mRNA is dependent of an RNA binding protein, CPEB1, and its binding elements in the 3΄ UTR. Through regulating GLUT1 level, GLD4 affects glucose uptake into cells and lactate levels. Moreover, GLD4 depletion impairs glucose deprivation-induced GLUT1 up-regulation. In addition, we found that GLD4 affects glucose-dependent cellular phenotypes such as migration and invasion in glioblastoma cells. Our observations delineate a novel post-transcriptional regulatory network involving carbohydrate metabolism and glucose homeostasis mediated by GLD4.
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Affiliation(s)
- Jihae Shin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ki Young Paek
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Maria Ivshina
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Emily E Stackpole
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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44
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Chang KT, Cheng CF, King PC, Liu SY, Wang GS. CELF1 Mediates Connexin 43 mRNA Degradation in Dilated Cardiomyopathy. Circ Res 2017; 121:1140-1152. [DOI: 10.1161/circresaha.117.311281] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/10/2017] [Accepted: 09/01/2017] [Indexed: 12/26/2022]
Abstract
Rationale:
Downregulation of Cx43 (connexin 43), the major cardiac gap junction protein, is often associated with arrhythmia, dilated cardiomyopathy (DCM), and heart failure. However, the cause of the reduced expression remains elusive. Reinduction of a nuclear RNA-binding protein CELF1 (CUGBP Elav-like family member 1) in the adult heart has been implicated in the cardiac pathogenesis of myotonic dystrophy type 1. However, how elevated CELF1 level leads to cardiac dysfunction, such as conduction defect, DCM, and heart failure, remains unclear.
Objective:
We investigated the mechanism of CELF1-mediated Cx43 mRNA degradation and determined whether elevated CELF1 expression is also a shared feature of the DCM heart.
Methods and Results:
RNA immunoprecipitation revealed the involvement of CELF1-regulated genes, including Cx43, in controlling contractility and conduction. CELF1 mediated Cx43 mRNA degradation by binding the UG-rich element in the 3′ untranslated region of Cx43. Mutation of the nuclear localization signal in CELF1 abolished the ability to downregulate Cx43 mRNA, so nuclear localization was required for its function. We further identified a 3′ to 5′ exoribonuclease, RRP6 (ribosomal RNA processing protein 6), as a CELF1-interacting protein. The interaction of CELF1 and RRP6 was RNA-independent and nucleus specific. With knockdown of endogenous RRP6, CELF1 failed to downregulate Cx43 mRNA, which suggests that RRP6 was required for CELF1-mediated Cx43 mRNA degradation. In addition, increased CELF1 level accompanied upregulated RRP6, and reduced Cx43 level was detected in mouse models with DCM, including myotonic dystrophy type 1 and CELF1 overexpression models and a myocardial infarction model. Importantly, depletion of CELF1 in the infarcted heart preserved Cx43 mRNA level and ameliorated the cardiac phenotypes of the infarcted heart.
Conclusions:
Our results suggest a mechanism for increased CELF1 expression downregulating Cx43 mRNA level and a pathogenic role for elevated CELF1 level in the DCM heart.
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Affiliation(s)
- Kuei-Ting Chang
- From the Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan (K.-T.C., G.-S.W.); Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (K.-T.C., C.-F.C., P.-C.K., S.-Y.L., G.-S.W.); Department of Medical Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan (C.-F.C.); and Department of Pediatrics, Tzu Chi University, Hualien, Taiwan (C.-F.C.)
| | - Ching-Feng Cheng
- From the Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan (K.-T.C., G.-S.W.); Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (K.-T.C., C.-F.C., P.-C.K., S.-Y.L., G.-S.W.); Department of Medical Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan (C.-F.C.); and Department of Pediatrics, Tzu Chi University, Hualien, Taiwan (C.-F.C.)
| | - Pei-Chih King
- From the Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan (K.-T.C., G.-S.W.); Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (K.-T.C., C.-F.C., P.-C.K., S.-Y.L., G.-S.W.); Department of Medical Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan (C.-F.C.); and Department of Pediatrics, Tzu Chi University, Hualien, Taiwan (C.-F.C.)
| | - Shin-Yi Liu
- From the Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan (K.-T.C., G.-S.W.); Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (K.-T.C., C.-F.C., P.-C.K., S.-Y.L., G.-S.W.); Department of Medical Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan (C.-F.C.); and Department of Pediatrics, Tzu Chi University, Hualien, Taiwan (C.-F.C.)
| | - Guey-Shin Wang
- From the Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan (K.-T.C., G.-S.W.); Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (K.-T.C., C.-F.C., P.-C.K., S.-Y.L., G.-S.W.); Department of Medical Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan (C.-F.C.); and Department of Pediatrics, Tzu Chi University, Hualien, Taiwan (C.-F.C.)
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Gomez-Cambronero J, Fite K, Miller TE. How miRs and mRNA deadenylases could post-transcriptionally regulate expression of tumor-promoting protein PLD. Adv Biol Regul 2017; 68:107-119. [PMID: 28964725 DOI: 10.1016/j.jbior.2017.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 12/11/2022]
Abstract
Phospholipase D (PLD) plays a key role in both cell membrane lipid reorganization and architecture, as well as a cell signaling protein via the product of its enzymatic reaction, phosphatidic acid (PA). PLD is involved in promoting breast cancer cell growth, proliferation, and metastasis and both gene and protein expression are upregulated in breast carcinoma human samples. In spite of all this, the ultimate reason as to why PLD expression is high in cancer cells vs. their normal counterparts remains largely unknown. Until we understand this and the associated signaling pathways, it will be difficult to establish PLD as a bona fide target to explore new potential cancer therapeutic approaches. Recently, our lab has identified several molecular mechanisms by which PLD expression is high in breast cancer cells and they all involve post-transcriptional control of its mRNA. First, PA, a mitogen, functions as a protein and mRNA stabilizer that counteracts natural decay and degradation. Second, there is a repertoire of microRNAs (miRs) that keep PLD mRNA translation at low levels in normal cells, but their effects change with starvation and during endothelial-to-mesenchymal transition (EMT) in cancer cells. Third, there is a novel way of post-transcriptional regulation of PLD involving 3'-exonucleases, specifically the deadenylase, Poly(A)-specific Ribonuclease (PARN), which tags mRNA for mRNA for degradation. This would enable PLD accumulation and ultimately breast cancer cell growth. We review in depth the emerging field of post-transcriptional regulation of PLD, which is only recently beginning to be understood. Since, surprisingly, so little is known about post-transcriptional regulation of PLD and related phospholipases (PLC or PLA), this new knowledge could help our understanding of how post-transcriptional deregulation of a lipid enzyme expression impacts tumor growth.
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Affiliation(s)
- Julian Gomez-Cambronero
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA.
| | - Kristen Fite
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| | - Taylor E Miller
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
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Shukla S, Elson G, Blackshear PJ, Lutz CS, Leibovich SJ. 3'UTR AU-Rich Elements (AREs) and the RNA-Binding Protein Tristetraprolin (TTP) Are Not Required for the LPS-Mediated Destabilization of Phospholipase-Cβ-2 mRNA in Murine Macrophages. Inflammation 2017; 40:645-656. [PMID: 28124257 DOI: 10.1007/s10753-017-0511-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have shown previously that bacterial lipopolysaccharide (LPS)-mediated suppression of phospholipase-Cβ-2 (PLCβ-2) expression is involved in M1 (inflammatory) to M2-like (wound healing) phenotypic switching of macrophages triggered by adenosine. This suppression is mediated post-transcriptionally by destabilization of PLCβ-2 mRNA (messenger ribonucleic acid). To investigate the mechanism of this LPS-mediated destabilization, we examined the roles of RNA-binding agents including microRNAs and RNA-binding proteins that are involved in regulating stability of mRNAs encoding growth factors, inflammatory mediators, and proto-oncogenes. Adenylate and uridylate (AU)-rich elements (AREs) in 3'UTRs are specific recognition sites for RNA-binding proteins including tristetraprolin (TTP), HuR, and AUF1 and for microRNAs that are involved in regulating mRNA stability. In this study, we investigated the role of TTP and AREs in regulating PLCβ-2 mRNA stability. The 3'UTR of the PLCβ-2 gene was inserted into the pLightswitch luciferase reporter plasmid and transfected into RAW264.7 cells. LPS suppressed luciferase expression from this reporter. Luciferase expression from mutant 3'UTR constructs lacking AREs was similarly downregulated, suggesting that these regions are not required for LPS-mediated suppression of PLCβ-2. TTP was rapidly upregulated in both primary murine macrophages and RAW264.7 cells in response to LPS. Suppression of PLCβ-2 by LPS was examined using macrophages from mice lacking TTP (TTP-/-). LPS suppressed PLCβ-2 expression to the same extent in wild type (WT) and TTP-/- macrophages. Also, the rate of decay of PLCβ-2 mRNA in LPS-treated macrophages following transcriptional blockade was similar in WT and TTP-/- macrophages, clearly indicating that TTP is not involved in LPS-mediated destabilization of PLCβ-2 mRNA in macrophages.
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Affiliation(s)
- Smita Shukla
- Department of Cell Biology & Molecular Medicine, New Jersey Medical School, Rutgers University School of Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07103, USA.,The Graduate School of Biomedical Sciences, New Jersey Medical School, Rutgers University School of Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07103, USA
| | - Genie Elson
- Department of Cell Biology & Molecular Medicine, New Jersey Medical School, Rutgers University School of Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07103, USA
| | - Perry J Blackshear
- The Post-Transcriptional Gene Expression Group, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Carol S Lutz
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University School of Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07103, USA
| | - S Joseph Leibovich
- Department of Cell Biology & Molecular Medicine, New Jersey Medical School, Rutgers University School of Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07103, USA.
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Miller TE, Gomez-Cambronero J. A feedback mechanism between PLD and deadenylase PARN for the shortening of eukaryotic poly(A) mRNA tails that is deregulated in cancer cells. Biol Open 2017; 6:176-186. [PMID: 28011629 PMCID: PMC5312095 DOI: 10.1242/bio.021261] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The removal of mRNA transcript poly(A) tails by 3′→5′ exonucleases is the rate-limiting step in mRNA decay in eukaryotes. Known cellular deadenylases are the CCR4-NOT and PAN complexes, and poly(A)-specific ribonuclease (PARN). The physiological roles and regulation for PARN is beginning to be elucidated. Since phospholipase D (PLD2 isoform) gene expression is upregulated in breast cancer cells and PARN is downregulated, we examined whether a signaling connection existed between these two enzymes. Silencing PARN with siRNA led to an increase in PLD2 protein, whereas overexpression of PARN had the opposite effect. Overexpression of PLD2, however, led to an increase in PARN expression. Thus, PARN downregulates PLD2 whereas PLD2 upregulates PARN. Co-expression of both PARN and PLD2 mimicked this pattern in non-cancerous cells (COS-7 fibroblasts) but, surprisingly, not in breast cancer MCF-7 cells, where PARN switches from inhibition to activation of PLD2 gene and protein expression. Between 30 and 300 nM phosphatidic acid (PA), the product of PLD enzymatic reaction, added exogenously to culture cells had a stabilizing role of both PARN and PLD2 mRNA decay. Lastly, by immunofluorescence microscopy, we observed an intracellular co-localization of PA-loaded vesicles (0.1-1 nm) and PARN. In summary, we report for the first time the involvement of a phospholipase (PLD2) and PA in mediating PARN-induced eukaryotic mRNA decay and the crosstalk between the two enzymes that is deregulated in breast cancer cells. Summary: Cell signaling enzyme phospholipase D2 (PLD2) and its reaction product, phospholipid phosphatidic acid (PA), are involved in mediating PARN-induced eukaryotic mRNA decay.
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Affiliation(s)
- Taylor E Miller
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, OH 45435, USA
| | - Julian Gomez-Cambronero
- Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA .,Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, OH 45435, USA
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Russo J, Lee JE, López CM, Anderson J, Nguyen TMP, Heck AM, Wilusz J, Wilusz CJ. The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts. PLoS One 2017; 12:e0170680. [PMID: 28129347 PMCID: PMC5271678 DOI: 10.1371/journal.pone.0170680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023] Open
Abstract
We previously identified several mRNAs encoding components of the secretory pathway, including signal recognition particle (SRP) subunit mRNAs, among transcripts associated with the RNA-binding protein CELF1. Through immunoprecipitation of RNAs crosslinked to CELF1 in myoblasts and in vitro binding assays using recombinant CELF1, we now provide evidence that CELF1 directly binds the mRNAs encoding each of the subunits of the SRP. Furthermore, we determined the half-lives of the Srp transcripts in control and CELF1 knockdown myoblasts. Our results indicate CELF1 is a destabilizer of at least five of the six Srp transcripts and that the relative abundance of the SRP proteins is out of balance when CELF1 is depleted. CELF1 knockdown myoblasts exhibit altered secretion of a luciferase reporter protein and are impaired in their ability to migrate and close a wound, consistent with a defect in the secreted extracellular matrix. Importantly, similar defects in wound healing are observed when SRP subunit imbalance is induced by over-expression of SRP68. Our studies support the existence of an RNA regulon containing Srp mRNAs that is controlled by CELF1. One implication is that altered function of CELF1 in myotonic dystrophy may contribute to changes in the extracellular matrix of affected muscle through defects in secretion.
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Affiliation(s)
- Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jerome E. Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carolina M. López
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - John Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Thuy-mi P. Nguyen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Adam M. Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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Bryant CD, Yazdani N. RNA-binding proteins, neural development and the addictions. GENES BRAIN AND BEHAVIOR 2016; 15:169-86. [PMID: 26643147 DOI: 10.1111/gbb.12273] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022]
Abstract
Transcriptional and post-transcriptional regulation of gene expression defines the neurobiological mechanisms that bridge genetic and environmental risk factors with neurobehavioral dysfunction underlying the addictions. More than 1000 genes in the eukaryotic genome code for multifunctional RNA-binding proteins (RBPs) that can regulate all levels of RNA biogenesis. More than 50% of these RBPs are expressed in the brain where they regulate alternative splicing, transport, localization, stability and translation of RNAs during development and adulthood. Dysfunction of RBPs can exert global effects on their targetomes that underlie neurodegenerative disorders such as Alzheimer's and Parkinson's diseases as well as neurodevelopmental disorders, including autism and schizophrenia. Here, we consider the evidence that RBPs influence key molecular targets, neurodevelopment, synaptic plasticity and neurobehavioral dysfunction underlying the addictions. Increasingly well-powered genome-wide association studies in humans and mammalian model organisms combined with ever more precise transcriptomic and proteomic approaches will continue to uncover novel and possibly selective roles for RBPs in the addictions. Key challenges include identifying the biological functions of the dynamic RBP targetomes from specific cell types throughout subcellular space (e.g. the nuclear spliceome vs. the synaptic translatome) and time and manipulating RBP programs through post-transcriptional modifications to prevent or reverse aberrant neurodevelopment and plasticity underlying the addictions.
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Affiliation(s)
- C D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - N Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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Łabno A, Tomecki R, Dziembowski A. Cytoplasmic RNA decay pathways - Enzymes and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:3125-3147. [PMID: 27713097 DOI: 10.1016/j.bbamcr.2016.09.023] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022]
Abstract
RNA decay plays a crucial role in post-transcriptional regulation of gene expression. Work conducted over the last decades has defined the major mRNA decay pathways, as well as enzymes and their cofactors responsible for these processes. In contrast, our knowledge of the mechanisms of degradation of non-protein coding RNA species is more fragmentary. This review is focused on the cytoplasmic pathways of mRNA and ncRNA degradation in eukaryotes. The major 3' to 5' and 5' to 3' mRNA decay pathways are described with emphasis on the mechanisms of their activation by the deprotection of RNA ends. More recently discovered 3'-end modifications such as uridylation, and their relevance to cytoplasmic mRNA decay in various model organisms, are also discussed. Finally, we provide up-to-date findings concerning various pathways of non-coding RNA decay in the cytoplasm.
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Affiliation(s)
- Anna Łabno
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
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