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DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2019-03-14
  • AnnouncementXML: Submission_2019-03-14_06:16:26.xml
  • DigitalObjectIdentifier: http://dx.doi.org/10.6019/PXD007589
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Supported dataset by repository
  • PrimarySubmitter: Zuo-Fei Yuan
  • Title: Human myogenesis is driven by proline-directed kinases and the trans-histone code, H3K9me3/H4K20me3
  • Description: System-level analysis of the (phospho)proteome during muscle formation and its interplay with epigenetic factors is critical to understand muscular diseases. Using stable isotope labeling (SILAC) and nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS), we analyzed the (phospho)proteome during myogenesis of LHCN-M2 human skeletal myoblast cell line. First, enriched phosphorylation motifs suggested that PKC, cyclin-dependent kinase and MAPK are regulatory kinases during myodifferentiation. Then, we uncovered that the drugs known to inhibit these kinases either promoted myogenesis (PD0325901 and GW8510) or stall differentiation (CHIR99021 and roscovitine). We identified differentiation-specific myogenic and chromatin-related proteins, including histone methyltransferases. We then analyzed histone post-translational modifications (PTMs), and observed regulation of two gene-silencing marks, H3K9me3 and H4K20me3, in a correlated manner with the observed phenotypes. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) confirmed that H3K9me3 is erased from the myogenic regulatory factors (MRFs) MyoD, MyoG and Myf5 in differentiating myotubes. Together, our work demonstrates that the integration of histone PTM, phosphoproteomics and full proteome analysis gives a comprehensive understanding of the close connection between signaling pathways and epigenetics during differentiation of myotube in vitro.
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: phosphorylated residue; formylated residue; acetylated residue; propanoylated residue; butanoylated residue
  • Instrument: LTQ Orbitrap

Dataset History

VersionDatetimeStatusChangeLog Entry
02017-08-29 06:02:44ID requested
12019-03-14 06:16:27announced

Publication List

  1. Dataset with its publication pending

Keyword List

  1. curator keyword: Biological
  2. submitter keyword: myotubes, kinase, chromatin, histones, mass spectrometry

Contact List

    Benjamin A. Garcia
    • contact affiliation: Penn Epigenetics Institute Department of Biochemistry and Biophysics Smilow Center for Translational Research University of Pennsylvania School of Medicine
    • contact email: bgarci@mail.med.upenn.edu
    • lab head:
    Zuo-Fei Yuan
    • contact affiliation: UPenn
    • contact email: zuoyuan@mail.med.upenn.edu
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
Repository Record List

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