• Animals
• RNA, Small Untranslated/genetics
• RNA, Small Untranslated/metabolism
• Humans
• RNA, Small Nucleolar/genetics
• RNA, Small Interfering/genetics
• MicroRNAs/genetics
• RNA, Transfer/genetics

• Angiogenesis
• Extracellular vesicles
• Globo H ceramide
• Glycosphingolipids
• Phospholipase Cβ1
• TRAX

• Calcium signaling
• Phospholipase Cβ
• RNA-induced silencing
• Stress granules

• C3PO
• DNA repair
• DNA-binding protein
• RNase activity
• TRAX
• Translin

• antiviral
• expression
• human host
• microRNA
• network
• target
• viruses
• web server

• CSIR - Institute of Microbial Technology
• Indian Council of Medical Research

• Argonautes
• MSCI
• Meiosis
• Meiotic sex chromosome inactivation
• Non-coding RNA
• RNA binding proteins
• Sex chromosomes
• Small RNA
• Spermatogenesis

• Animals
• Male
• Sex Chromosomes/genetics
• Chromatin/genetics
• Meiosis/genetics
• Histones/genetics
• RNA
• Mammals/genetics
• Mammals/metabolism

• P50 HD076210 NICHD NIH HHS
• P50 HD104454 NICHD NIH HHS

The conserved nucleic acid binding protein Translin contributes to numerous facets of mammalian biology and genetic diseases. It was first identified as a binder of cancer-associated chromosomal translocation breakpoint junctions leading to the suggestion that it was involved in genetic recombination. With a paralogous partner protein, Trax, Translin has subsequently been found to form a hetero-octomeric RNase complex that drives some of its functions, including passenger strand removal in RNA interference (RNAi). The Translin-Trax complex also degrades the precursors to tumour suppressing microRNAs in cancers deficient for the RNase III Dicer. This oncogenic activity has resulted in the Translin-Trax complex being explored as a therapeutic target. Additionally, Translin and Trax have been implicated in a wider range of biological functions ranging from sleep regulation to telomere transcript control. Here we reveal a Trax- and RNAi-independent function for Translin in dissociating RNA polymerase II from its genomic template, with loss of Translin function resulting in increased transcription-associated recombination and elevated genome instability. This provides genetic insight into the longstanding question of how Translin might influence chromosomal rearrangements in human genetic diseases and provides important functional understanding of an oncological therapeutic target.

Human genetic diseases, including cancers, are frequently driven by substantial changes to chromosomes, including translocations, where one arm of a chromosome is exchanged for another. The human nucleic acid binding protein Translin was first identified by its ability to bind to the chromosomal sites at which some of these translocations occur. This resulted in Translin being implicated in the mechanism that generated the translocation and thus the associated disease state. However, since its discovery there has been little evidence to directly indicate Translin does contribute to this process. It is, however, known to contribute to a number of biological functions including, amongst others, neurological regulation, sleep control, vascular stiffening, cancer immunomodulation and it has been recently identified as a potential therapeutic target in some cancers. Here we demonstrate that Translin has conserved function in genome stability maintenance when other primary pathways are defective, a function independent of a key binding partner protein, Trax. Specifically, we demonstrate that Translin contributes to minimizing the deleterious genome destabilizing effects of retaining gene expression machineries on chromosomes. This offers the first evidence for how Translin might contribute to genetic disease-causing chromosomal changes and offers insight to inform therapeutic design.

The Gαq/phospholipase Cβ1 (PLCβ1) signaling system mediates calcium responses from hormones and neurotransmitters. While PLCβ1 functions on the plasma membrane, there is an atypical cytosolic population that binds Argonaute 2 (Ago2) and other proteins associated with stress granules preventing their aggregation. Activation of Gαq relocalizes cytosolic PLCβ1 to the membrane, releasing bound proteins, promoting the formation of stress granules. Here, we have characterized Ago2 stress granules associated with Gαq activation in differentiated PC12 cells, which have a robust Gαq/PLCβ1 signaling system. Characterization of Ago2-associated stress granules shows shifts in protein composition when cells are stimulated with a Gαq agonist, or subjected to heat shock or osmotic stress, consistent with the idea that different stresses result in unique stress granules. Purified Ago2 stress granules from control cells do not contain RNA, while those from heat shock contain many different mRNAs and miRs. Surprisingly, Ago2 particles from cells where Gαq was stimulated show only two transcripts, chromogranin B, which is involved in secretory function, and ATP synthase 5f1b, which is required for ATP synthesis. RT-PCR, western blotting and other studies support the idea that Gαq-activation protects these transcripts. Taken together, these studies show a novel pathway where Gαq/PLCβ regulates the translation of specific proteins.

Besides the canonical RNA-based RNase P, pre-tRNA 5’-end processing can also be catalyzed by protein-only RNase P (PRORP). To date, various PRORPs have been discovered, but the basis underlying substrate binding and cleavage by HARPs (homolog of Aquifex RNase P) remains elusive. Here, we report structural and biochemical studies of HARPs. Comparison of the apo- and pre-tRNA-complexed structures showed that HARP is able to undergo large conformational changes that facilitate pre-tRNA binding and catalytic site formation. Planctomycetes bacterium HARP exists as dimer in vitro, but gel filtration and electron microscopy analysis confirmed that HARPs from Thermococcus celer, Thermocrinis minervae and Thermocrinis ruber can assemble into larger oligomers. Structural analysis, mutagenesis and in vitro biochemical studies all supported one cooperative pre-tRNA processing mode, in which one HARP dimer binds pre-tRNA at the elbow region whereas 5’-end removal is catalyzed by the partner dimer. Our studies significantly advance our understanding on pre-tRNA processing by PRORPs.

HARP are member of protein-only RNase P, which catalyzes pre-tRNA 5’-end processing and maturation. Here, the authors present crystal structure and provide mechanistic insights into pre-tRNA binding and cleavage by HARP proteins.

• MicroRNAs/genetics
• MicroRNAs/metabolism
• RNA Viruses/genetics
• RNA, Viral/genetics
• RNA, Viral/metabolism
• Virus Replication
• Viruses/genetics

• National Natural Science Foundation of China

• 3-Hydroxybutyric Acid/metabolism
• 3-Hydroxybutyric Acid/pharmacology
• Acetylation/drug effects
• Animals
• Cells, Cultured
• Fibroblasts/drug effects
• Fibroblasts/metabolism
• Lysine/metabolism
• Mice
• Protein Binding/drug effects
• Protein Processing, Post-Translational/drug effects
• Proteome/drug effects
• Proteome/metabolism
• Proteomics/methods
• Signal Transduction/drug effects
• Up-Regulation/drug effects

Mounting data show that MIR139 is commonly silenced in solid cancer and hematological malignancies. MIR139 acts as a critical tumor suppressor by tuning the cellular response to different types of stress, including DNA damage, and by repressing oncogenic signaling pathways. Recently, novel insights into the mechanism of MIR139 silencing in tumor cells have been described. These include epigenetic silencing, inhibition of POL-II transcriptional activity on gene regulatory elements, enhanced expression of competing RNAs and post-transcriptional regulation by the microprocessor complex. Some of these MIR139-silencing mechanisms have been demonstrated in different types of cancer, suggesting that these are more general oncogenic events. Reactivation of MIR139 expression in tumor cells causes inhibition of tumor cell expansion and induction of cell death by the repression of oncogenic mRNA targets. In this review, we discuss the different aspects of MIR139 as a tumor suppressor gene and give an overview on different transcriptional mechanisms regulating MIR139 in oncogenic stress and across different types of cancer. The novel insights into the expression regulation and the tumor-suppressing activities of MIR139 may pave the way to new treatment options for cancer.

• MIR139
• cancer
• microRNAs
• transcriptional regulation
• tumor suppressor

• Carcinogenesis/genetics
• Cell Proliferation/genetics
• Genes, Tumor Suppressor
• Humans
• MicroRNAs/genetics
• MicroRNAs/metabolism
• Neoplasms/genetics
• Neoplasms/pathology

MicroRNA (miRNA) is a small, single-stranded, non-coding RNA molecule that plays a variety of key roles in different biological processes through post-transcriptional regulation of gene expression. MiRNA has been proved to be a variety of cellular processes involved in development, differentiation, signal transduction, and is an important regulator of immune and autoimmune diseases. Therefore, it may act as potent modulators of the immune system and play an important role in the development of several autoimmune diseases. Immune thrombocytopenia (ITP) is an autoimmune systemic disease characterized by a low platelet count. Several studies suggest that like other autoimmune disorders, miRNAs are deeply involved in the pathogenesis of ITP, interacting with the function of innate and adaptive immune responses. In this review, we discuss emerging knowledge about the function of miRNAs in ITP and describe miRNAs in terms of their role in the immune system and autoimmune response. These findings suggest that miRNA may be a useful therapeutic target for ITP by regulating the immune system. In the future, we need to have a more comprehensive understanding of miRNAs and how they regulate the immune system of patients with ITP.

• autoimmune diseases
• autoimmunity
• gene regulation
• immune
• immune thrombocytopenia
• microRNA

• Spermatogenesis
• Testis-brain RNA-binding protein (TB-RBP)/Translin
• Tethering reporter assay
• Translin-associated factor X (TRAX)
• mRNA degradation

• Biacore
• Conformational changes
• Globo H Ceramide
• Glycan
• Glycosphingolipid
• Molecular docking
• Molecular dynamics
• Molecular modeling
• SPARC

• DNA synthesis
• Estrogen receptor α
• Mammary epithelial cells
• Puberty
• Translin/TRAX complex

• Animals
• DNA Repair/genetics
• DNA-Binding Proteins/genetics
• DNA-Binding Proteins/metabolism
• Drosophila Proteins/chemistry
• Drosophila Proteins/genetics
• Humans
• Mice
• Nucleic Acids/metabolism
• RNA Transport/genetics
• RNA, Messenger/genetics
• RNA-Binding Proteins/genetics
• RNA-Binding Proteins/metabolism

• MicroRNAs
• biogenesis
• non-canonical
• nuclear localization
• transcriptional regulation

• Animals
• Argonaute Proteins
• Cell Nucleus/genetics
• Cell Nucleus/metabolism
• Epigenesis, Genetic
• Gene Expression Regulation
• Gene Silencing
• Humans
• MicroRNAs/genetics
• MicroRNAs/metabolism
• Models, Biological
• Protein Binding
• RNA Interference
• RNA, Messenger/genetics
• RNA, Messenger/metabolism
• Transcription, Genetic

• G proteins
• Phosholipase C
• Protein domains
• Translational regulation

• Animals
• Calcium Signaling
• Cell Membrane/enzymology
• Cytosol/enzymology
• GTP-Binding Protein alpha Subunits, Gq-G11/metabolism
• Humans
• Phospholipase C beta/metabolism
• Protein Domains
• Structure-Activity Relationship

• R01 GM116178 NIGMS NIH HHS

In Drosophila and human, component 3 promoter of RISC (C3PO), a heteromeric complex, enhances RISC assembly and promotes RISC activity. Here, we report crystal structure of full-length Drosophila C3PO (E126Q), an inactive C3PO mutant displaying much weaker RNA binding ability, at 2.1 Å resolution. In addition, we also report the cryo-EM structures of full-length Drosophila C3PO (E126Q), C3PO (WT) and SUMO-C3PO (WT, sumo-TRAX + Translin) particles trapped at different conformations at 12, 19.7 and 12.8 Å resolutions, respectively. Crystal structure of C3PO (E126Q) displays a half-barrel architecture consisting of two Trax/Translin heterodimers, whereas cryo-EM structures of C3PO (E126Q), C3PO (WT) and SUMO-C3PO (WT) adopt a closed football-like shape with a hollow interior cavity. Remarkably, both cryo-EM structures of Drosophila C3PO (E126Q) and Drosophila SUMO-C3PO (WT) particles contain a wide side port (∼25 Å × ∼30 Å versus ∼15 Å × ∼20 Å) for RNA substrate entry and release, formed by a pair of anti-parallel packed long α1 helices of TRAX subunits. Notably, cryo-EM structure of SUMO-C3PO showed that four copies of extra densities belonging to N-terminal SUMO tag are located at the outside shell of SUMO-C3PO particle, which demonstrated that the stoichiometry of TRAX/Translin for the in vitro expressed and assembled full-length Drosophila-SUMO–C3PO particle is 4:4, suggesting Drosophila C3PO is composed by TRAX/translin at a ratio of 4:4. Remarkably, the comparison of the cryo-EM structures suggests that the C3PO side ports regulated by α1 helices of TRAX molecules are highly dynamic. Hence, we propose that C3PO particles could adopt a ‘Dynamic Side Port’ model to capture/digest nucleic acid duplex substrate and release the digested fragments through the dynamic side ports.

• esi-2.1
• C3PO
• Trax
• miR-bantam
• translin

• RNA-binding protein SFARI gene
• autism spectrum disorder
• neurodevelopment
• translational control

• ATM
• Adenosine A(2A) receptors
• Synaptic tagging
• Translin
• microRNA system

• TRAX
• mesenchymal cell differentiation
• miRNA depletion
• translin

• RNAi
• antiviral
• defense systems
• insect
• insect pest control
• non-RNAi

• Animals
• Drosophila melanogaster/genetics
• Drosophila melanogaster/immunology
• Drosophila melanogaster/virology
• Immunity, Innate
• RNA Interference
• RNA, Double-Stranded
• Virus Diseases/immunology
• Virus Replication

• Argonaute
• Chaperone
• miRNA
• siRNA

• Ago2
• Complex immunoprecipitation
• Component
• Mass spectrometry
• RISC

Translin and Trax proteins are highly conserved nucleic acid binding proteins that have been implicated in RNA regulation in a range of biological processes including tRNA processing, RNA interference, microRNA degradation during oncogenesis, spermatogenesis and neuronal regulation. Here, we explore the function of this paralogue pair of proteins in the fission yeast. Using transcript analysis we demonstrate a reciprocal mechanism for control of telomere-associated transcripts. Mutation of tfx1⁺ (Trax) elevates transcript levels from silenced sub-telomeric regions of the genome, but not other silenced regions, such as the peri-centromeric heterochromatin. In the case of some sub-telomeric transcripts, but not all, this elevation is dependent on the Trax paralogue, Tsn1 (Translin). In a reciprocal fashion, Tsn1 (Translin) serves to repress levels of transcripts (TERRAs) from the telomeric repeats, whereas Tfx1 serves to maintain these elevated levels. This reveals a novel mechanism for the regulation of telomeric transcripts. We extend this to demonstrate that human Translin and Trax also control telomere-associated transcript levels in human cells in a telomere-specific fashion.

• C3PO
• Chromosome Section
• TERRA
• Translin
• Trax
• telomeres

• Dicer
• Lin-28
• MicroRNA degradation
• Translin
• Trax

Long-lasting forms of synaptic plasticity and memory require de novo protein synthesis. Yet, how learning triggers this process to form memory is unclear. Translin/trax is a candidate to drive this learning-induced memory mechanism by suppressing microRNA-mediated translational silencing at activated synapses. We find that mice lacking translin/trax display defects in synaptic tagging, which requires protein synthesis at activated synapses, and long-term memory. Hippocampal samples harvested from these mice following learning show increases in several disease-related microRNAs targeting the activin A receptor type 1C (ACVR1C), a component of the transforming growth factor-β receptor superfamily. Furthermore, the absence of translin/trax abolishes synaptic upregulation of ACVR1C protein after learning. Finally, synaptic tagging and long-term memory deficits in mice lacking translin/trax are mimicked by ACVR1C inhibition. Thus, we define a new memory mechanism by which learning reverses microRNA-mediated silencing of the novel plasticity protein ACVR1C via translin/trax.

• RNA-binding protein
• activin receptor
• miRNA
• mouse
• neuroscience
• synaptic tagging
• translin/trax

• SIT
• double‐stranded RNA
• environmental RNAi
• insect control
• non‐GM pest control

• BB/K000489/1 Biotechnology and Biological Sciences Research Council

• DNA repair
• Oryza sativa
• TB-RBP
• Translin
• Transmission electron microscopy

• Amino Acid Substitution
• DNA, Plant/genetics
• DNA, Plant/metabolism
• DNA-Binding Proteins/genetics
• DNA-Binding Proteins/metabolism
• Mutation, Missense
• Oryza/genetics
• Oryza/metabolism
• Plant Proteins/genetics
• Plant Proteins/metabolism
• Protein Binding
• Protein Multimerization/physiology
• RNA, Plant/genetics
• RNA, Plant/metabolism
• RNA-Binding Proteins/metabolism

• Argonaute
• RNA silencing
• RNA-induced silencing complex
• microRNA

• G protein signaling
• RNA interference
• calcium signaling
• component 3 of RNA-induced silencing
• phospholipase Cβ

RNA-induced silencing complex (RISC) is composed of miRNAs and AGO proteins. AGOs use miRNAs as guides to slice target mRNAs to produce truncated 5' and 3' RNA fragments. The 5' cleaved RNA fragments are marked with uridylation for degradation. Here, we identified novel cofactors of Arabidopsis AGOs, named RICE1 and RICE2. RICE proteins specifically degraded single-strand (ss) RNAs in vitro; but neither miRNAs nor miRNA*s in vivo. RICE1 exhibited a DnaQ-like exonuclease fold and formed a homohexamer with the active sites located at the interfaces between RICE1 subunits. Notably, ectopic expression of catalytically-inactive RICE1 not only significantly reduced miRNA levels; but also increased 5' cleavage RISC fragments with extended uridine tails. We conclude that RICEs act to degrade uridylated 5’ products of AGO cleavage to maintain functional RISC. Our study also suggests a possible link between decay of cleaved target mRNAs and miRNA stability in RISC.

DOI:http://dx.doi.org/10.7554/eLife.24466.001

DNA contains all the information needed to build a body, yet molecules of RNA carry these instructions to the sites in the cell where they can be used. Cells must control how much RNA they produce in order to ensure that they develop properly and can respond well to their environment. RNA silencing refers to a collection of mechanisms that use smaller RNA molecules called microRNAs to incapacitate certain RNA molecules and selectively switch off the genes that encode them to stop more from being made.

One key player in RNA silencing is the multi-protein complex called RISC, which contains microRNA and a group of proteins called AGOs. Once the microRNA has identified its RNA target, the AGOs cut the RNA into two pieces, known as the 5’ cleavage fragment and 3’ cleavage fragment. The two resulting fragments need to be cleared away swiftly, so that the RISC can move on to the next target. While it was known how the 3’ cleavage fragment was removed, it was less clear how the 5’ cleavage fragment was dealt with.

Previous studies had shown that the 5’ cleavage fragment was marked with a chemical called uridine, which somehow signals to the RISC that this fragment needs to be destroyed. Now, using biochemical techniques, Zhang et al. have identified two new proteins in the model plant Arabidopsis that attach to the AGO proteins and degrade the 5’ cleavage fragments that are marked with uridine. The two proteins are named RICE1 and RICE2.

Zhang et al. then analyzed the three-dimensional shape of RICE1 and identified the ‘active’ region that is responsible for degrading the RNA fragments. When these active regions were blocked, the microRNA levels were low, but the uridine-marked 5’ cleavage fragments were high. Also, the RISC complex could not work properly, which lead to problems during the development of the plant. These results suggest that RICE proteins degrade 5’ cleavage fragments modified with uridine to activate RISC.

RICE proteins are conserved between plants and animals, and it is likely that their counterparts in humans will have a similar role to the plant proteins. The next challenge will be to explore how RICE proteins work in more details, which may lead to new ways to manipulate the levels of microRNAs to change the architecture of the plant and to improve their tolerance to various stress conditions.

DOI:http://dx.doi.org/10.7554/eLife.24466.002

• A. thaliana
• RICE
• RISC
• argonaute
• biochemistry
• exoribonuclease
• miRNAs
• plant biology
• uridylation

• Cancer
• Hematopoiesis
• Leukemia
• MiRNA
• MiRNA therapeutics
• MicroRNA

• Animals
• Argonaute Proteins/genetics
• Argonaute Proteins/metabolism
• Female
• Gene Knockdown Techniques
• Hepatitis B Surface Antigens/blood
• Hepatitis B Surface Antigens/genetics
• Hepatitis B virus/genetics
• Hepatitis B virus/metabolism
• Hepatitis B, Chronic/metabolism
• Hepatitis B, Chronic/therapy
• Hepatitis B, Chronic/virology
• Humans
• Kinetics
• Liver/metabolism
• Liver/virology
• Mice
• Mice, Inbred ICR
• Mice, Inbred NOD
• Mice, SCID
• Mice, Transgenic
• Peptide Nucleic Acids/genetics
• Peptide Nucleic Acids/metabolism
• Phosphorylation
• RNA Interference
• RNA, Small Interfering/genetics
• RNA, Small Interfering/metabolism
• RNA, Viral/genetics
• RNA, Viral/metabolism
• RNA-Induced Silencing Complex/genetics
• RNA-Induced Silencing Complex/metabolism
• Tissue Distribution

• Ago2
• RNAi
• duplex thermodynamics
• functional asymmetry
• siRNA
• terminal nucleotide

• Argonaute Proteins/genetics
• Argonaute Proteins/metabolism
• Half-Life
• HeLa Cells
• Humans
• Kinetics
• Nucleic Acid Hybridization
• RNA Interference
• RNA Stability
• RNA, Messenger/antagonists & inhibitors
• RNA, Messenger/genetics
• RNA, Messenger/metabolism
• RNA, Small Interfering/genetics
• RNA, Small Interfering/metabolism
• RNA-Induced Silencing Complex/genetics
• RNA-Induced Silencing Complex/metabolism
• Structure-Activity Relationship
• Thermodynamics

• R01 GM089866 NIGMS NIH HHS
• R01 GM079688 NIGMS NIH HHS
• R21 CA176854 NCI NIH HHS

• Dicer
• High-throughput screen
• Small molecule
• Translin
• Trax
• miRNA therapeutics

• G protein
• Phospholipase C
• calcium intracellular release
• cell differentiation
• fluorescence resonance energy transfer (FRET)

• Argonaute
• HCV
• RNA silencing
• hepatitis C virus
• miR-122
• microRNA

• Gene therapy
• RNA structure
• RNAi
• miRNA
• shRNA
• siRNA

• Animals
• Base Sequence
• Gene Knockdown Techniques
• Genetic Therapy
• Humans
• Inverted Repeat Sequences
• MicroRNAs/genetics
• Promoter Regions, Genetic
• RNA Interference
• RNA, Small Interfering/genetics

• ZIA BC011566-01 Intramural NIH HHS

• Lin-28
• MicroRNA
• Plasticity
• Pre-microRNA degradation
• Silencing
• Translin
• Trax

• Argonaute
• Cryptosporidium
• Cryptosporidium parvum
• cryptosporidiosis
• siRNA
• silencing

• Argonaute Proteins/genetics
• Argonaute Proteins/metabolism
• Cryptosporidiosis/parasitology
• Cryptosporidium/genetics
• Cryptosporidium/metabolism
• Gene Silencing
• Host-Parasite Interactions/genetics
• Humans
• RNA, Protozoan/genetics
• RNA, Protozoan/metabolism
• RNA, Small Interfering/genetics
• RNA, Small Interfering/metabolism
• Transfection

• UL1 TR000071 NCATS NIH HHS
• UL1TR000071 NCATS NIH HHS
• National Institutes of Health

• Animals
• Apoptosis/genetics
• Ataxia Telangiectasia Mutated Proteins/physiology
• Cells, Cultured
• DNA Damage/genetics
• DNA Repair/genetics
• DNA-Binding Proteins/genetics
• DNA-Binding Proteins/physiology
• Embryo, Mammalian
• HEK293 Cells
• Humans
• Mice
• Mice, Knockout
• PC12 Cells
• Rats
• Signal Transduction/genetics