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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling [ChIP-seq]

ABSTRACT: Identfification of MEF2A target genes using ChIP-exo in skeletla muscle and primary cardiomyocytes. Identfification of MEF2A target genes using ChIP-exo and RNA-seq in skeletal muscle and primary cardiomyocytes. MEF2 plays a profound role in the regulation of transcription in cardiac and skeletal muscle lineages. To define the overlapping and unique MEF2A genomic targets, we utilized ChIP-exo analysis of cardiomyocytes and skeletal myoblasts. Of the 2783 and 1648 MEF2A binding peaks in skeletal myoblasts and cardiomyocytes, respectively, 294 common binding sites were identified. Genomic targets were compared to differentially expressed genes in RNA-seq analysis of MEF2A depleted myogenic cells. MEF2A target genes were identified in 48 hr DM C2C12 myoblasts cells and primary cardiomyocytes using ChIP-exo. Binding profiles on MEF2A in each cell type were compared. Cross sectional-analysis between ChIP-exo identified targets and RNA-seq analysis of MEF2A deplted myoblasts was also done.

ORGANISM(S): Rattus norvegicus

SUBMITTER: John McDermott

PROVIDER: E-GEOD-61204 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling [RNA-seq]

Project description:Identfification of MEF2A target genes using ChIP-exo and RNA-seq in skeletal muscle and primary cardiomyocytes. MEF2 plays a profound role in the regulation of transcription in cardiac and skeletal muscle lineages. To define the overlapping and unique MEF2A genomic targets, we utilized ChIP-exo analysis of cardiomyocytes and skeletal myoblasts. Of the 2783 and 1648 MEF2A binding peaks in skeletal myoblasts and cardiomyocytes, respectively, 294 common binding sites were identified. Genomic targets were compared to differentially expressed genes in RNA-seq analysis of MEF2A depleted myogenic cells. The effect of MEF2A gene silencing on gene expression in myoblasts was assessed at 48 hr DM. Up and downregulated genes were then compared to MEF2A target genes identified in ChIP-exo analysis of 48 hr DM C2C12 myoblasts cells and primary cardiomyocytes.

2014-09-09 | E-GEOD-61205 | biostudies-arrayexpress

Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling [ChIP-seq]

Project description:Identfification of MEF2A target genes using ChIP-exo in skeletla muscle and primary cardiomyocytes. Identfification of MEF2A target genes using ChIP-exo and RNA-seq in skeletal muscle and primary cardiomyocytes. MEF2 plays a profound role in the regulation of transcription in cardiac and skeletal muscle lineages. To define the overlapping and unique MEF2A genomic targets, we utilized ChIP-exo analysis of cardiomyocytes and skeletal myoblasts. Of the 2783 and 1648 MEF2A binding peaks in skeletal myoblasts and cardiomyocytes, respectively, 294 common binding sites were identified. Genomic targets were compared to differentially expressed genes in RNA-seq analysis of MEF2A depleted myogenic cells.

2014-09-09 | GSE61204 | GEO

Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling [RNA-seq]

2014-09-09 | GSE61205 | GEO

Expression data from transfected C2C12 cell lines

Project description:Skeletal muscle differentiation is a highly coordinated multistep process in which proliferating mononucleated myoblasts ﬁrst withdraw from the cell cycle, then differentiate into postmitotic mononucleated myocytes, and subsequently fuse into multinucleated myotubes which ﬁnally bundle to form mature muscle ﬁbers. All these processes are controlled by the sequential activation of myogenic regulatory factors, and especially MYOD1 is activated in the early phase to promote the transcription of muscle-specific genes coding for muscle proteins such as alpha-actin, myosin heavy chain and muscle creatine kinase. We used microarrays to detail the global gene expression changes associated with MYOD1 L122R mutation and identified MYOD1 L122R blocked myogenic differentiation and had a MYC-like transcriptional potential. C2C12 mouse myoblast cells were introduced wild type MYOD1, MYOD1 L122R, MYC, and GFP by retroviral infection. For retrovirus production, the pcx4 and pBabe vectors system were used. Retroviruses were obtained by using 293T cells as packaging cells, and were infected into C2C12 cell line and selected with 500 μg/ml Zeocin (Invitrogen, Carlsbad, CA, USA). After selection, RNAs were extracted and processed at MSKCC according to procedures recommended by Affymetrix (Santa Clara, CA, USA).

2014-05-01 | E-GEOD-56079 | biostudies-arrayexpress

VGLL3 Skeletal Muscle - VGLL3 operates via TEAD1, TEAD3 and TEAD4 to influence myogenesis in skeletal muscle

Project description:Vestigial-like (Vgll) proteins are transcriptional co-factors that have been reported to bind Tead family transcription factors to regulate various functions ranging from wing development in the fly to muscle fibre composition and immune function in mice. Here, we characterise Vgll3 in the skeletal muscle lineage. Vgll3 is expressed at low levels in unchallenging muscle but its expression increases in mechanically stimulated and regenerating muscle. VGLL3 is also >3-fold more expressed in the muscles of Duchenne muscular dystrophy patients than in healthy controls and VGLL3 expression is highest in PAX3-FOXO1-associated alveolar rhabdomyosarcoma when compared to other rhabdomyosarcomas, related tumours and adult muscle. Immunoprecipitation of over expressed VGLL3-flag followed by proteomics reveals that VGLL3 binds Tead1,3,4 transcription factors in myoblasts and myotubes. However, unlike Yap, there is no evidence for interaction with a regulatory system such as a kinase cascade. VGLL3 overexpression affects reduces the expression of members of the Hippo negative feedback loop and affects the expression of genes with important functions in muscle or signalling such as Myf5, Pitx2/3 as well as genes that encode Wnt members and IGF-binding proteins. It mainly represses gene expression and regulates similar genes as YAP1 S127A and TAZ S89A but not in a clear agonistic or antagonistic fashion. A loss of Vgll3 almost completely blocks the proliferation of human myoblasts and VGLL3 overexpression promotes myoblasts differentiation. In vivo, the loss of Vgll3 does not prevent normal skeletal muscle development presumably due to feedback signalling and/or redundancy. Collectively, this work identifies Vgll3 as a disease-related transcriptional co-factor that competes with the Hippo effectors Yap and Taz to control myoblast proliferation and differentiation.

2019-06-17 | PXD012040 | Pride

A novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network

Project description:microRNAs (miRNAs) are non-coding RNAs that regulate gene expression post-transcriptionally, and mounting evidences support the prevalence and functional significance of their interplay with transcription factors (TFs). Here we describe the identification of a regulatory circuit between muscle miRNAs (miR-1, miR-133 and miR-206) and Yin Yang 1 (YY1), an epigenetic repressor of skeletal myogenesis. Genome-wide identification of potential YY1 down-stream targets by combining computational prediction with expression profiling data reveals a large number of putative miRNA targets of YY1 during skeletal myoblasts differentiation into myotubes with muscle miRs rank on top of the list. Murine skeletal muscle cells (C2C12 cells) were differentiated for 0, 1 or 3 days. Total RNAs were isolated from the cells and used for array profiling of miRNA expression.

2011-12-31 | E-GEOD-32238 | biostudies-arrayexpress

Genomic mapping of Six1 binding sites during skeletal myoblast differentiation

Project description:In this study, the C2C12 cell line, a model used to study myogenesis and regeneration, was allowed to differentiate from myoblast precursor cells to myotubes. Cells were harvested at 3 different timepoints to perform ChIP-on-Chip of Six1, which is a key muscle regulator. We identified global loci bound by Six1 during skeletal myoblast differentiation. C2C12 Myoblasts were allowed to differentiate into myotubes. Cells at three timepoints were harvested for ChIP-on-Chip, including myoblasts stage, 24h after differentiation and myotubes (96h after differentiation). Myotubes were detached from the undifferentiated myoblast reserve cells using diluted trypsin. 3 independent biological replicates were used for each time point experiment. A microarray set counts 3 arrays (Custom Arrays A, B and C) for a total of approximately 2.9 million probes.

2010-07-05 | E-GEOD-20150 | biostudies-arrayexpress

High-resolution genome-wide mapping of MEF2A binding sites by CUT&Tag-seq in chicken primary myoblasts

Project description:In this study, CUT&Tag-seq technology was employed to investigate MEF2A binding sites across the entire genome of chicken primary myoblasts. CUT&Tag was performed using CUT&Tag Assay Kit for Illumina Pro (TD904-1) from Vazyme. Antibody targeting MEF2A as well as IgG were used.The final DNA library on a HiSeq PE150 platform was subjected for the analyses. This study provides a wide landscape of MEF2A target genes from chicken primary myoblasts, which supports the active role of MEF2A in avian muscle development.

2023-12-05 | GSE249097 | GEO

MEF2A interactome in striated muscle by an affinity-purification followed by LC-MS-MS

Project description:Myocyte Enhancer Factor 2 (MEF2) proteins are involved in multiple developmental, physiological, and pathological processes in vertebrates. Protein:protein interactions underlie the plethora of biological processes impacted by MEF2A, necessitating a detailed characterization of the MEF2A interactome. A nanobody based affinity-purification/mass spectrometry strategy was employed to achieve this goal. Specifically, the MEF2A protein complexes were captured from myogenic lysates using a GFP-tagged MEF2A protein immobilized with a GBP-nanobody followed by LC-MS/MS proteomic analysis to identify MEF2A interactors.

2024-02-27 | PXD050042 | Pride

Dysregulated gene expression in Mef2a knockout mice subjected to cardiotoxin-induced muscle injury

Project description:We identified genes expressed in mouse skeletal muscle, during the process of muscle regeneration after injury, which are dysregulated in the absence of Mef2a expression. MEF2A is a member of the evolutionarily conserved MEF2 transcription factor family which has known roles in cardiac muscle development and function, but is not well studied in skeletal muscle. We performed a comparison of gene expression profiles in wild type and MEF2A knockout tibialis anterior muscle, seven days post-injury with cardiotoxin. The results indicated that a variety of genes expressed during muscle regeneration, predominantly microRNAs in the Gtl2-Dio3 locus, are dysregulated by the loss of MEF2A expression.

2013-02-12 | GSE41871 | GEO

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