PXD007589

PXD007589 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:00:57.210.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD007589
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Zuo-Fei Yuan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; formylated residue; acetylated residue; propanoylated residue; butanoylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-29 06:02:44	ID requested
1	2019-03-14 06:16:27	announced
⏵ 2	2024-10-22 04:00:57	announced	2024-10-22: Updated project metadata.

10.6019/PXD007589;

curator keyword: Biological

submitter keyword: histones, mass spectrometry,myotubes, kinase, chromatin

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

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PRIDE project URI

• PRIDE
  1. PXD007589
     1. Label: PRIDE project
     2. Name: Human myogenesis is driven by proline-directed kinases and the trans-histone code, H3K9me3/H4K20me3