title: System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.
abstract: To elucidate cellular events underlying the pluripotency of human embryonic stem cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic analyses of hESCs during differentiation initiated by a diacylglycerol analog or transfer to media that had not been conditioned by feeder cells. We profiled 6521 proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic changes in phosphorylation status during 24 hours of differentiation. These data are a resource for studies of the events associated with the maintenance of hESC pluripotency and those accompanying their differentiation. From these data, we identified a core hESC phosphoproteome of sites with similar robust changes in response to the two distinct treatments. These sites exhibited distinct dynamic phosphorylation patterns, which were linked to known or predicted kinases on the basis of the matching sequence motif. In addition to identifying previously unknown phosphorylation sites on factors associated with differentiation, such as kinases and transcription factors, we observed dynamic phosphorylation of DNA methyltransferases (DNMTs). We found a specific interaction of DNMTs during early differentiation with the PAF1 (polymerase-associated factor 1) transcriptional elongation complex, which binds to promoters of the pluripotency and known DNMT target genes encoding OCT4 and NANOG, thereby providing a possible molecular link for the silencing of these genes during differentiation.
authors.affiliation: Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Kristoffer T G
authors.initials: KT
authors.lastname: Rigbolt
authors.forename: Tatyana A
authors.initials: TA
authors.lastname: Prokhorova
authors.forename: Vyacheslav
authors.initials: V
authors.lastname: Akimov
authors.forename: Jeanette
authors.initials: J
authors.lastname: Henningsen
authors.forename: Pia T
authors.initials: PT
authors.lastname: Johansen
authors.forename: Irina
authors.initials: I
authors.lastname: Kratchmarova
authors.forename: Moustapha
authors.initials: M
authors.lastname: Kassem
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.forename: Jesper V
authors.initials: JV
authors.lastname: Olsen
authors.forename: Blagoy
authors.initials: B
authors.lastname: Blagoev
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D002454:Cell Differentiation / Q000235:genetics / Q000502:physiology; D002460:Cell Line; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism*; D044127:Epigenesis, Genetic; D006801:Humans; D008954:Models, Biological; D009687:Nuclear Proteins / Q000378:metabolism; D010766:Phosphorylation; D010802:Phylogeny; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D040081:Protein Array Analysis; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D009687:Nuclear Proteins; C501972:PAF1 protein, human; D020543:Proteome; D014157:Transcription Factors; D004248:DNA (Cytosine-5-)-Methyltransferases