• ChiP
• Epigenetics
• Folic acid
• Methylation
• Pregnancy
• Vitamin B12

• Pregnancy
• Female
• Animals
• Mice
• Placenta/metabolism
• Mice, Inbred C57BL
• Diet
• Folic Acid/metabolism
• Epigenesis, Genetic
• Vitamin B 12/metabolism

• Animals
• Female
• Male
• Mammals/metabolism
• Mice
• Ovary/metabolism
• Sertoli Cells/metabolism
• Sumoylation
• Testis/metabolism
• Transcription Factors/genetics
• Transcription Factors/metabolism
• Tripartite Motif-Containing Protein 28/genetics
• Tripartite Motif-Containing Protein 28/metabolism

• FC001107 Cancer Research UK
• U117512772 Medical Research Council
• FC001107 Arthritis Research UK
• FC001107 Wellcome Trust
• Wellcome Trust
• FC001107 Medical Research Council

• virology
• transcription

• Heterochromatin
• Histone demethylases
• Satellite DNA
• Transformation.

• A549 cells
• TXNIP
• butyrate
• histone modification
• mitochondrial superoxide

When skeletal muscle fibers are injured, they regenerate and grow until their sizes are adjusted to surrounding muscle fibers and other relevant organs. In this study, we examined whether Mest, one of paternally expressed imprinted genes that regulates body size during development, and miR-335 located in the second intron of the Mest gene play roles in muscle regeneration. We generated miR-335-deficient mice, and found that miR-335 is a paternally expressed imprinted microRNA. Although both Mest and miR-335 are highly expressed during muscle development and regeneration, only Mest^+/- (maternal/paternal) mice show retardation of body growth. In addition to reduced body weight in Mest^+/-; DMD-null mice, decreased muscle growth was observed in Mest^+/- mice during cardiotoxin-induced regeneration, suggesting roles of Mest in muscle regeneration. Moreover, expressions of H19 and Igf2r, maternally expressed imprinted genes were affected in tibialis anterior muscle of Mest^+/-; DMD-null mice compared to DMD-null mice. Thus, Mest likely mediates muscle regeneration through regulation of imprinted gene networks in skeletal muscle.

KAP1/TRIM28/TIF1β was identified nearly twenty years ago as a universal transcriptional co-repressor because it interacts with a large KRAB-containing zinc finger protein (KRAB-ZFP) transcription factor family. Many studies demonstrate that KAP1 affects gene expression by regulating the transcription of KRAB-ZFP-specific loci, trans-repressing as a transcriptional co-repressor or epigenetically modulating chromatin structure. Emerging evidence suggests that KAP1 also functions independent of gene regulation by serving as a SUMO/ubiquitin E3 ligase or signaling scaffold protein to mediate signal transduction. KAP1 is subjected to multiple post-translational modifications (PTMs), including serine/tyrosine phosphorylation, SUMOylation, and acetylation, which coordinately regulate KAP1 function and its protein abundance. KAP1 is involved in multiple aspects of cellular activities, including DNA damage response, virus replication, cytokine production and stem cell pluripotency. Moreover, knockout of KAP1 results in embryonic lethality, indicating that KAP1 is crucial for embryonic development and possibly impacts a wide-range of (patho)physiological manifestations. Indeed, studies from conditional knockout mouse models reveal that KAP1-deficiency significantly impairs vital physiological processes, such as immune maturation, stress vulnerability, hepatic metabolism, gamete development and erythropoiesis. In this review, we summarize and evaluate current literatures involving the biochemical and physiological functions of KAP1. In addition, increasing studies on the clinical relevance of KAP1 in cancer will also be discussed.

• KRAB domain-associated protein 1
• Transcriptional co-repressor
• Post-translational modification
• Chromatin remodeling
• KRAB-containing zinc finger protein

Active positive transcription elongation factor b (P-TEFb) is essential for cellular and human immunodeficiency virus type 1 (HIV-1) transcription elongation. CTIP2 represses P-TEFb activity in a complex containing 7SK RNA and HEXIM1. Recently, the inactive 7SK/P-TEFb small nuclear RNP (snRNP) has been detected at the HIV-1 core promoter as well as at the promoters of cellular genes, but a recruiting mechanism still remains unknown to date. Here we show global synergy between CTIP2 and the 7SK-binding chromatin master-regulator HMGA1 in terms of P-TEFb–dependent endogenous and HIV-1 gene expression regulation. While CTIP2 and HMGA1 concordingly repress the expression of cellular 7SK-dependent P-TEFb targets, the simultaneous knock-down of CTIP2 and HMGA1 also results in a boost in Tat-dependent and independent HIV-1 promoter activity. Chromatin immunoprecipitation experiments reveal a significant loss of CTIP2/7SK/P-TEFb snRNP recruitment to cellular gene promoters and the HIV-1 promoter on HMGA1 knock-down. Our findings not only provide insights into a recruiting mechanism for the inactive 7SK/P-TEFb snRNP, but may also contribute to a better understanding of viral latency.

Idiopathic pulmonary fibrosis (IPF) is a deadly disease characterized by chronic inflammation and excessive collagen accumulation in the lung. Myofibroblasts are the primary collagen-producing cells in pulmonary fibrosis. Histone deacetylase inhibitor (HDACi) can affect gene expression, and some, such as suberoylanilide hydroxamic acid (SAHA), are US FDA approved for cancer treatment. In this study, we investigated SAHA’s effects on the expression of collagen III alpha 1 (COL3A1) in primary human IPF fibroblasts and in a murine model of pulmonary fibrosis. We observed that increased COL3A1 expression in IPF fibroblasts can be substantially reduced by SAHA treatment at the level of transcription as detected by RT-PCR; collagen III protein level was also reduced, as detected by Western blots and immunofluorescence. The deacetylation inhibitor effect of SAHA was verified by observing higher acetylation levels of both histone H3 and H4 in treated IPF cells. Chromatin immunoprecipitation (ChIP) experiments demonstrated that the reduced expression of COL3A1 by SAHA is with increased association of the repressive chromatin marker, H3K27Me3, and decreased association of the active chromatin marker, H3K9Ac. In our murine model of bleomycin-induced pulmonary fibrosis, the SAHA treated group demonstrated significantly less collagen III, as detected by immunohistochemistry. Our data indicate that the HDACi SAHA alters the chromatin associated with COL3A1, resulting in its decreased expression.

• DNA methylation
• DNA repeats
• cancer
• genomic sequencing
• hypermethylation
• hypomethylation

• chromatin
• coregulator transcription
• cxcr4
• krüppel-like factor (klf)
• transcription regulation
• heterochromatin protein 1 (hp1)

• Animals
• Apoptosis Regulatory Proteins
• CHO Cells
• Cell Cycle Proteins/metabolism
• Cell Death/physiology
• Cell Division/physiology
• Cell Line, Tumor
• Cellular Senescence/physiology
• Chromatin/physiology
• Chromobox Protein Homolog 5
• Chromosomal Proteins, Non-Histone/metabolism
• Cricetinae
• Female
• Gene Expression Regulation, Neoplastic/physiology
• Genes, Tumor Suppressor/physiology
• Humans
• Metabolic Diseases/genetics
• Metabolic Diseases/metabolism
• Metabolic Diseases/pathology
• Mice
• Mice, Nude
• Neoplasm Transplantation
• Neoplasms/genetics
• Neoplasms/metabolism
• Neoplasms/pathology
• Promoter Regions, Genetic/physiology
• Receptors, CXCR4/genetics
• Repressor Proteins/metabolism
• Transcription, Genetic/physiology
• Transplantation, Heterologous

• DK76845 NIDDK NIH HHS
• R03 CA110022 NCI NIH HHS
• R01 DK052913 NIDDK NIH HHS
• P20 CA102701 NCI NIH HHS
• P30 DK084567 NIDDK NIH HHS
• DK52913 NIDDK NIH HHS
• T32 CA148073 NCI NIH HHS
• CA102701 NCI NIH HHS
• R56 DK052913 NIDDK NIH HHS
• CA110022-01 NCI NIH HHS
• P50 CA102701 NCI NIH HHS
• T32-CA148073 NCI NIH HHS
• K08 DK076845 NIDDK NIH HHS
• P30DK084567 NIDDK NIH HHS

Retinoic acid receptors (RARs) α, β and γ are key regulators of embryonic development. Hematopoietic differentiation is regulated by RARα, and several types of leukemia show aberrant RARα activity. Through microarray expression analysis, we identified transcripts differentially expressed between F9 wild-type (Wt) and RARα knockout cells cultured in the absence or presence of the RAR-specific ligand all trans retinoic acid (RA). We validated the decreased Mest, Tex13, Gab1, Bcl11a, Tcfap2a and HMGcs1 transcript levels, and increased Slc38a4, Stmn2, RpL39l, Ref2L, Mobp and Rlf1 transcript levels in the RARa knockout cells. The decreased Mest and Tex13 transcript levels were associated with increased promoter CpG-island methylation and increased repressive histone modifications (H3K9me3) in RARα knockout cells. Increased Slc38a4 and Stmn2 transcript levels were associated with decreased promoter CpG-island methylation and increased permissive histone modifications (H3K9/K14ac, H3K4me3) in RARα knockout cells. We demonstrated specific association of RARα and RXRα with the Mest promoter. Importantly, stable expression of a dominant negative, oncogenic PML–RARα fusion protein in F9 Wt cells recapitulated the decreased Mest transcript levels observed in RARα knockout cells. We propose that RARα plays an important role in cellular memory and imprinting by regulating the CpG methylation status of specific promoter regions.

• Embryonic Development
• Endogenous Retroviruses/genetics
• Fetal Development
• Fetus/virology
• Gene Expression Regulation, Viral
• Humans

Krüppel-associated box domain-zinc finger proteins (KRAB–ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB–mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB–containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB–mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 β (HP1β) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1–dependent transcriptional repression at an endogenous KRAB–ZFP gene cluster, where KAP1 binds to the 3′ end of genes and mediates propagation of H3K9me3 and HP1β towards their 5′ end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB–ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB–ZFPs and KAP1.

The regulation of gene activity by transcription factors is crucial to the function of all cells. Here, we studied the mechanisms of action of the largest family of gene regulators encoded by the human genome, the so-called KRAB–containing zinc finger proteins (KRAB–ZFPs), which in concert with their universal cofactor KAP1 act as transcriptional repressors. For this, we used two parallel approaches. First, by targeting an ectopic KRAB domain to hundreds of different genes, we found that KRAB/KAP1 can repress promoters located several tens of kilobases from the repressor DNA docking site. We further could show that KRAB induces such long-range effects by mediating the spread of repressive chromatin marks along the body of the gene, resulting in a block of transcriptional initiation at the promoter. In a second set of experiments, we analyzed an endogenous KRAB–ZFP gene cluster, where we could also document KAP1–dependent heterochromatin spreading and transcriptional repression. Together, these results support a model whereby KRAB–ZFPs and KAP1 can mediate long-range transcriptional repression through the spread of silencing chromatin marks. This study thus provides insight into KRAB/KAP1–induced gene regulation at KRAB–ZFP gene clusters, and will further help interpret genome-wide studies of KRAB–ZFPs and KAP1 DNA binding patterns.

• Acetylation
• Base Pairing
• Binding Sites
• Cell Line
• Chromobox Protein Homolog 5
• Chromosomal Proteins, Non-Histone/metabolism
• Gene Silencing
• Heterochromatin/metabolism
• Histones/metabolism
• Humans
• Methylation
• Promoter Regions, Genetic/genetics
• RNA Polymerase II/metabolism
• Repressor Proteins/metabolism
• Transcription, Genetic
• Tripartite Motif-Containing Protein 28
• Zinc Fingers

• Animals
• Chromatin/genetics
• Chromatin/metabolism
• DNA Methylation
• Embryo, Mammalian
• Gene Expression Regulation, Developmental
• Genomic Imprinting
• Histones/genetics
• Histones/metabolism
• Humans

• maize
• epigenetics
• histone modification
• dna methylation
• small rna
• transcriptome
• next-generation sequencing

• R01 GM047850 NIGMS NIH HHS
• R37 GM047850 NIGMS NIH HHS

• DNA Methylation
• Epigenesis, Genetic
• Gene Expression Profiling
• Gene Expression Regulation, Plant
• Genome, Plant
• Histones/metabolism
• MicroRNAs/chemistry
• MicroRNAs/metabolism
• Nucleic Acid Conformation
• RNA, Messenger/chemistry
• RNA, Messenger/metabolism
• RNA, Plant/chemistry
• RNA, Plant/metabolism
• RNA, Small Interfering/chemistry
• RNA, Small Interfering/metabolism
• Sequence Analysis, RNA
• Zea mays/genetics
• Zea mays/metabolism

• R01 GM047850 NIGMS NIH HHS
• R01 HG004069-03 NHGRI NIH HHS
• GM047850 NIGMS NIH HHS
• R37 GM047850 NIGMS NIH HHS
• R01 HG004069 NHGRI NIH HHS