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

Kristoffer T.G. Rigbolt; Tatyana Prokhorova; Vyacheslav Akimov; Jeanette Henningsen; Pia Thermann Johansen; Irina Kratchmarova; Moustapha Saad El-Deen Kassem; Matthias Mann; Jesper V Olsen; Blagoy Blagoev

doi:10.1126/scisignal.2001570

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

Kristoffer T.G. Rigbolt, Tatyana Prokhorova, Vyacheslav Akimov, Jeanette Henningsen, Pia Thermann Johansen, Irina Kratchmarova, Moustapha Saad El-Deen Kassem, Matthias Mann, Jesper V Olsen, Blagoy Blagoev

327 Citations (Scopus)

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.

Original language	English
Journal	Science Signaling
Volume	4
Issue number	164
Pages (from-to)	rs3
ISSN	1945-0877
DOIs	https://doi.org/10.1126/scisignal.2001570
Publication status	Published - 15 Mar 2011

Keywords

Amino Acid Motifs
Amino Acid Sequence
Cell Differentiation
Cell Line
DNA (Cytosine-5-)-Methyltransferase
Embryonic Stem Cells
Epigenesis, Genetic
Humans
Models, Biological
Nuclear Proteins
Phosphorylation
Phylogeny
Pluripotent Stem Cells
Protein Array Analysis
Proteome
Signal Transduction
Transcription Factors

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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.",

keywords = "Amino Acid Motifs, Amino Acid Sequence, Cell Differentiation, Cell Line, DNA (Cytosine-5-)-Methyltransferase, Embryonic Stem Cells, Epigenesis, Genetic, Humans, Models, Biological, Nuclear Proteins, Phosphorylation, Phylogeny, Pluripotent Stem Cells, Protein Array Analysis, Proteome, Signal Transduction, Transcription Factors",

author = "Rigbolt, {Kristoffer T.G.} and Tatyana Prokhorova and Vyacheslav Akimov and Jeanette Henningsen and Johansen, {Pia Thermann} and Irina Kratchmarova and Kassem, {Moustapha Saad El-Deen} and Matthias Mann and Olsen, {Jesper V} and Blagoy Blagoev",

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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 - 2011/3/15

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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

SN - 1945-0877

VL - 4

SP - rs3

JO - Science Signaling

JF - Science Signaling

IS - 164

ER -

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

Abstract

Keywords

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