TY - JOUR

T1 - System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

AU - Rigbolt, Kristoffer T.G.

AU - Prokhorova, Tatyana

AU - Akimov, Vyacheslav

AU - Henningsen, Jeanette

AU - Johansen, Pia Thermann

AU - Kratchmarova, Irina

AU - Kassem, Moustapha Saad El-Deen

AU - Mann, Matthias

AU - Olsen, Jesper V

AU - Blagoev, Blagoy

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

KW - Amino Acid Motifs

KW - Amino Acid Sequence

KW - Cell Differentiation

KW - Cell Line

KW - DNA (Cytosine-5-)-Methyltransferase

KW - Embryonic Stem Cells

KW - Epigenesis, Genetic

KW - Humans

KW - Models, Biological

KW - Nuclear Proteins

KW - Phosphorylation

KW - Phylogeny

KW - Pluripotent Stem Cells

KW - Protein Array Analysis

KW - Proteome

KW - Signal Transduction

KW - Transcription Factors

U2 - 10.1126/scisignal.2001570

DO - 10.1126/scisignal.2001570

M3 - Journal article

C2 - 21406692

VL - 4

SP - rs3

JO - Science Signaling

JF - Science Signaling

SN - 1945-0877

IS - 164

ER -