A transcriptomic study of myogenic differentiation under the overexpression of PPARγ by RNA-Seq
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE99399 | GEO | 2018/02/23
REPOSITORIES: GEO
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Project description:Identifying tissue and condition-specific gene regulatory elements and the mechanisms by which they associate with their target genes in human cells remains a significant challenge, largely due to the vast amount of non-protein-coding sequence in the human genome. Despite increasing evidence of physical interactions between distant regulatory regions and gene promoters in a variety of mammalian cell types, many searches for regulatory regions still consider only genomic regions proximal to the gene promoter. We identify a set of putative cis-regulatory modules (CRMs) of human skeletal muscle differentiation by combining new ChIP-chip data measuring the binding of myogenic TFs MyoG, MyoD, and SRF over the timecourse of differentiation with previously generated histone modification data. A substantial proportion of these putative CRMs are located distant (> 20 kb) from muscle gene promoters, and these distantly located CRMs are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding. Examination of two distant CRMs, which were previously shown to activate transcription in differentiating muscle cells, revealed that they interact physically with their upstream or downstream gene promoters (PDLIM3 and ACTA1) specifically upon myogenic differentiation. Our results highlight the importance of considering CRMs located distant from their target genes in investigations of mammalian gene regulation and further support the hypothesis that enhancer-promoter looping contacts are a general mechanism of regulation by distant CRMs. ChIP-chip experiments were performed using a custom Agilent 1x244K oligonucleotide array format (AMADID # 015037) to achieve 25-bp resolution tiling of 100 kb surrounding each of 104 selected human genes as well as positive and negative control regions. Biological and technical replicates of ChIP-chip experiments were performed using antibodies for MyoG and SRF in primary human skeletal muscle myoblasts crosslinked at 0 and 48 h relative to the removal of serum to induce differentiation. Additional technical replicate ChIP-chip experiments were performed for MyoD at 0 and 48 hours post-differentiation and p300 at 48 h post-differentiation. Total Input DNA for each experiment was labeled with Cy3 and used to create log-ratios with the Cy5 labeled IP data. Negative control no antibody mock-IP ChIP experiments were performed at 0 and 48 h post-differentiation.
2012-02-01 | E-GEOD-29865 | biostudies-arrayexpress
Project description:We used a combination of genome-wide and promoter-specific DNA binding and expression analyses to assess the functional roles of Myod and Myog in regulating the program of skeletal muscle gene expression. Our findings indicate that Myod and Myog have distinct regulatory roles at a similar set of target genes. At genes expressed throughout the program of myogenic differentiation, Myod can bind and recruit histone acetyltransferases. At early targets, Myod is sufficient for near full expression; whereas, at late expressed genes Myod initiates regional histone modification but is not sufficient for gene expression. At these late genes, Myog does not bind efficiently without Myod, however, transcriptional activation requires the combined activity of Myod and Myog. Therefore, the role of Myog in mediating terminal differentiation is, in part, to enhance expression of a subset of genes previously initiated by Myod. Mouse embryonic fibroblasts isolated from Myod-/-Myf-/- mice were tranduced with either MDER or MDER+Myog. MDER was activated by the addition of beta-estradiol. Cells were induced to differentiate for various times, and triplate samples were collected from the indicated time points.
2007-12-07 | E-GEOD-3858 | biostudies-arrayexpress
Project description:We used a combination of genome-wide and promoter-specific DNA binding and expression analyses to assess the functional roles of Myod and Myog in regulating the program of skeletal muscle gene expression. Our findings indicate that Myod and Myog have distinct regulatory roles at a similar set of target genes. At genes expressed throughout the program of myogenic differentiation, Myod can bind and recruit histone acetyltransferases. At early targets, Myod is sufficient for near full expression; whereas, at late expressed genes Myod initiates regional histone modification but is not sufficient for gene expression. At these late genes, Myog does not bind efficiently without Myod, however, transcriptional activation requires the combined activity of Myod and Myog. Therefore, the role of Myog in mediating terminal differentiation is, in part, to enhance expression of a subset of genes previously initiated by Myod. Keywords: Myod, Myogenin, muscle differentiation, regulatory network, gene expression
2006-03-01 | GSE3858 | GEO
Project description:Skeletal muscle differentiation (myogenesis) is a complex and highly coordinated biological process regulated by a series of myogenic marker genes. Chromatin interactions between gene’s promoters and their enhancers have an important role in transcriptional control. However, the high-resolution chromatin interactions of myogenic genes and their functional enhancers during myogenesis remain largely unclear. Here, we used circularized chromosome conformation capture coupled with next-generation sequencing (4C-seq) to investigate eight myogenic marker genes in C2C12 myoblasts (C2C12-MBs) and C2C12 myotubes (C2C12-MTs). We revealed dynamic chromatin interactions of these marker genes during differentiation, and identified 163 and 314 significant interaction sites (SISs) in C2C12-MBs and C2C12-MTs, respectively. The interacting genes of SISs in C2C12-MTs were mainly involved in muscle development, and histone modifications of the SISs changed during differentiation. Through functional genomic screening, we also identified 25 and 41 putative active enhancers in C2C12-MBs and C2C12-MTs, respectively. Using luciferase reporter assays for putative enhancers of Myog and Myh3, we identified eight activating enhancers. Furthermore, dCas9-KRAB epigenome editing and RNA-seq revealed a role for Myog enhancers in the regulation of Myog expression and myogenic differentiation in the native genomic context. Taken together, this study lays the groundwork for understanding 3D chromatin interaction changes of myogenic genes during myogenesis and provides insights that contribute to our understanding of the role of enhancers in regulating myogenesis.
2022-06-10 | GSE201138 | GEO
Project description:While skeletal myogenesis is tightly coordinated by myogenic regulatory factors including MyoD and myogenin, chromatin modifications have emerged as vital mechanisms of myogenic regulation. We have previously established that bexarotene, a clinically approved agonist of retinoid X receptor, promotes the specification and differentiation of skeletal muscle lineage. Here, we examine a genome-wide impact of rexinoids on myogenic differentiation through integral RNA-seq and ChIP-seq analyses. We found that bexarotene promotes myoblast differentiation through the coordination of exit from the cell cycle and the activation of muscle-related genes. We uncovered a new mechanism of rexinoid action which is mediated by the nuclear receptor and largely reconciled through a direct regulation of MyoD gene expression. In addition, we determined a rexinoid-responsive residue-specific histone acetylation at a distinct chromatin state associated to MyoD and myogenin. Thus, we provide novel molecular insights into the interplay between retinoid X receptor signaling and chromatin states pertinent to myogenic programs in early myoblast differentiation.
2017-09-13 | GSE94560 | GEO
Project description:Skeletal muscle development requires the coordinated expression of numerous transcription factors to control the specification of the muscle fate in mesodermal cells and the differentiation of the committed myoblasts into functional contractile fibers. The bHLH transcription factor MyoD plays a key role in these processes, since its forced expression is sufficient to induce the myogenesis in a variety of non-muscle cells in culture. Consistent with this observation, the majority of skeletal muscle genes requires MyoD to activate their own transcription. In order to identify novel MyoD-target genes we generated C2C12 MyoD-silenced clones, and used a muscle-specific cDNA microarray to study the induced modifications of the transcriptional profile. Gene expression was analyzed at three different stages in differentiating MyoD(-)C2C12 myoblasts. These microarray data sets identified many additional uncharacterized downstream MyoD transcripts that may play important functions in muscle cell differentiation. Among these genes, we concentrated our study on the cell cycle regulators Cdkn1c and calcyclin and on the muscle-specific putative myogenic regulator Ankrd2. Bioinformatic and functional studies on the promoters of these genes clarified their dependence on MyoD activity. Clues of other regulatory mechanisms that might interact with the principal bHLH transcription factor have been revealed by the unexpected up regulation in MyoD(-) cells of these novel (and other) target transcripts, at the differentiation stage in which MyoD became normally down regulated. Keywords: MyoD, cell cycle regulation, cDNA microarray, myogenic differentiation, gene regulation
2005-07-28 | GSE3014 | GEO
Project description:While skeletal myogenesis is tightly coordinated by myogenic regulatory factors including MyoD and myogenin, chromatin modifications have emerged as vital mechanisms of myogenic regulation. We have previously established that bexarotene, a clinically approved agonist of retinoid X receptor, promotes the specification and differentiation of skeletal muscle lineage. Here, we examine a genome-wide impact of rexinoids on myogenic differentiation through integral RNA-seq and ChIP-seq analyses. We found that bexarotene promotes myoblast differentiation through the coordination of exit from the cell cycle and the activation of muscle-related genes. We uncovered a new mechanism of rexinoid action which is mediated by the nuclear receptor and largely reconciled through a direct regulation of MyoD gene expression. In addition, we determined a rexinoid-responsive residue-specific histone acetylation at a distinct chromatin state associated to MyoD and myogenin. Thus, we provide novel molecular insights into the interplay between retinoid X receptor signaling and chromatin states pertinent to myogenic programs in early myoblast differentiation.
2017-09-13 | GSE94558 | GEO
Project description:Identifying tissue and condition-specific gene regulatory elements and the mechanisms by which they associate with their target genes in human cells remains a significant challenge, largely due to the vast amount of non-protein-coding sequence in the human genome. Despite increasing evidence of physical interactions between distant regulatory regions and gene promoters in a variety of mammalian cell types, many searches for regulatory regions still consider only genomic regions proximal to the gene promoter. We identify a set of putative cis-regulatory modules (CRMs) of human skeletal muscle differentiation by combining new ChIP-chip data measuring the binding of myogenic TFs MyoG, MyoD, and SRF over the timecourse of differentiation with previously generated histone modification data. A substantial proportion of these putative CRMs are located distant (> 20 kb) from muscle gene promoters, and these distantly located CRMs are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding. Examination of two distant CRMs, which were previously shown to activate transcription in differentiating muscle cells, revealed that they interact physically with their upstream or downstream gene promoters (PDLIM3 and ACTA1) specifically upon myogenic differentiation. Our results highlight the importance of considering CRMs located distant from their target genes in investigations of mammalian gene regulation and further support the hypothesis that enhancer-promoter looping contacts are a general mechanism of regulation by distant CRMs.
2012-02-01 | GSE29865 | GEO
Project description:Rhabdomyosarcoma is a pediatric tumor of skeletal muscle that expresses the myogenic basic helix-loop-helix protein MyoD but fails to undergo terminal differentiation. Prior work has determined that DNA binding by MyoD occurs in the tumor cells, but myogenic targets fail to activate. Using MyoD chromatin immunoprecipitation coupled to high-throughput sequencing and gene expression analysis in both primary human muscle cells and RD rhabdomyosarcoma cells, we demonstrate that MyoD binds in a similar genome-wide pattern in both tumor and normal cells but binds poorly at a subset of myogenic genes that fail to activate in the tumor cells. Binding differences are found both across genomic regions and locally at specific sites that are associated with binding motifs for RUNX1, MEF2C, JDP2, and NFIC. These factors are expressed at lower levels in RD cells than muscle cells and rescue myogenesis when expressed in RD cells. MEF2C is located in a genomic region that exhibits poor MyoD binding in RD cells, whereas JDP2 exhibits local DNA hypermethylation in its promoter in both RD cells and primary tumor samples. These results demonstrate that regional and local silencing of differentiation factors contributes to the differentiation defect in rhabdomyosarcomas. ChIP-Seq profiling of MyoD in human myotube, myoblast and rhabdomyosarcoma cells
2013-08-29 | E-GEOD-50413 | biostudies-arrayexpress
Project description:We identified four major temporal patterns of Calcineurin (Cn)-dependent gene expression in differentiating myoblasts and determined that Cn is broadly required for the activation of the myogenic gene expression program. Cn promotes gene expression through direct binding to myogenic promoter sequences and facilitating the binding of BRG1 and other SWI/SNF subunit proteins as well as the binding of MyoD, a critical lineage determinant for skeletal muscle differentiation. We conclude that the Cn phosphatase directly impacts the expression of myogenic genes by promoting ATP-dependent chromatin remodeling and formation of transcription-competent promoters.
2019-08-06 | GSE125914 | GEO