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

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Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B

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

Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.

PubMed ID
21406692 [ View in PubMed
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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.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialP56181Details
7-dehydrocholesterol reductaseQ9UBM7Details
RAF proto-oncogene serine/threonine-protein kinaseP04049Details
Pyruvate kinase PKMP14618Details
Androgen receptorP10275Details
Cationic amino acid transporter 3Q8WY07Details
Solute carrier family 12 member 6Q9UHW9Details
DNA ligase 3P49916Details
Bifunctional glutamate/proline--tRNA ligaseP07814Details
DNA ligase 1P18858Details
Large neutral amino acids transporter small subunit 1Q01650Details
Neutral amino acid transporter B(0)Q15758Details
5'-AMP-activated protein kinase subunit beta-1Q9Y478Details
GMP synthase [glutamine-hydrolyzing]P49915Details
Cystathionine beta-synthaseP35520Details
Vascular endothelial growth factor receptor 2P35968Details
Ferritin heavy chainP02794Details
Vitamin K-dependent gamma-carboxylaseP38435Details
Serine/threonine-protein kinase A-RafP10398Details
Tyrosine-protein kinase ABL2P42684Details
Isoleucine--tRNA ligase, cytoplasmicP41252Details
Choline-phosphate cytidylyltransferase BQ9Y5K3Details
Receptor tyrosine-protein kinase erbB-2P04626Details
Chromodomain-helicase-DNA-binding protein 1O14646Details
Glyceraldehyde-3-phosphate dehydrogenaseP04406Details
Methionine--tRNA ligase, cytoplasmicP56192Details
DNA polymerase alpha catalytic subunitP09884Details
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrialP08559Details
Solute carrier family 12 member 4Q9UP95Details
Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrialP29803Details
Choline-phosphate cytidylyltransferase AP49585Details
Tyrosine-protein phosphatase non-receptor type 1P18031Details
Acetyl-CoA carboxylase 1Q13085Details
Serine/threonine-protein kinase B-rafP15056Details
Cytosolic phospholipase A2P47712Details
Monocarboxylate transporter 1P53985Details
DNA polymerase alpha subunit BQ14181Details
Aspartate--tRNA ligase, cytoplasmicP14868Details
Pyrroline-5-carboxylate reductase 2Q96C36Details
DNA topoisomerase 2-alphaP11388Details
Sodium/hydrogen exchanger 1P19634Details
5'-AMP-activated protein kinase subunit beta-2O43741Details
Multidrug resistance-associated protein 1P33527Details
Tyrosine-protein kinase LckP06239Details
CTP synthase 1P17812Details
DNA (cytosine-5)-methyltransferase 1P26358Details
Mitogen-activated protein kinase 1P28482Details
Cyclic AMP-responsive element-binding protein 1P16220Details
DNA topoisomerase 1P11387Details
Catenin beta-1P35222Details
CalnexinP27824Details
Rho-associated protein kinase 1Q13464Details
Transcription factor JunP05412Details
Solute carrier family 2, facilitated glucose transporter member 1P11166Details
Mitogen-activated protein kinase 3P27361Details
Cyclin-dependent kinase 1P06493Details
Gap junction alpha-1 proteinP17302Details
Phosphatidylserine synthase 1P48651Details
Microtubule-associated protein 2P11137Details
CD44 antigenP16070Details
Heat shock protein HSP 90-alphaP07900Details
EndoplasminP14625Details
Microtubule-associated protein 1AP78559Details
14-3-3 protein zeta/deltaP63104Details
Phosphatidylethanolamine-binding protein 1P30086Details
Quinone oxidoreductaseQ08257Details
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrialP33316Details
3',5'-cyclic-AMP phosphodiesterase 4DQ08499Details
Protein kinase C theta typeQ04759Details
Tubulin alpha-1C chainQ9BQE3Details
Uridine-cytidine kinase 2Q9BZX2Details
DNA repair protein XRCC4Q13426Details
Fructose-bisphosphate aldolase AP04075Details
M-phase inducer phosphatase 2P30305Details
Poly [ADP-ribose] polymerase 1P09874Details
Death-associated protein kinase 1P53355Details
Kinesin-like protein KIF11P52732Details
Heat shock protein HSP 90-betaP08238Details
Cyclin-dependent kinase 7P50613Details
Keratin, type II cytoskeletal 8P05787Details
Laminin subunit gamma-1P11047Details
Syndecan-2P34741Details
Retinoblastoma-associated proteinP06400Details
Pyridoxal-dependent decarboxylase domain-containing protein 1Q6P996Details
Peptidyl-glycine alpha-amidating monooxygenaseP19021Details
Cyclin-dependent kinase 9P50750Details
Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetaseP22234Details
Multifunctional protein CADP27708Details
Phosphoribosylformylglycinamidine synthaseO15067Details
Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2O94808Details
Phosphatidylserine synthase 2Q9BVG9Details
Sphingomyelin phosphodiesterase 4Q9NXE4Details
Threonine--tRNA ligase, mitochondrialQ9BW92Details
Peptidyl-prolyl cis-trans isomerase GQ13427Details
Histone deacetylase 1Q13547Details
Histone deacetylase 2Q92769Details
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alphaP49354Details
DNA-dependent protein kinase catalytic subunitP78527Details
Serine/threonine-protein kinase mTORP42345Details
Protein kinase C delta typeQ05655Details
DNA topoisomerase 2-betaQ02880Details
Ribonucleoside-diphosphate reductase subunit M2P31350Details
E3 ubiquitin-protein ligase UBR4Q5T4S7Details
NAD-dependent protein deacetylase sirtuin-1Q96EB6Details
Non-selective voltage-gated ion channel VDAC1P21796Details
Voltage-dependent anion-selective channel protein 2P45880Details
Prostaglandin E synthase 3Q15185Details
GephyrinQ9NQX3Details
Kinesin-like protein KIF1AQ12756Details
Pleckstrin homology domain-containing family A member 1Q9HB21Details
Serine/threonine-protein kinase Chk1O14757Details
Tubulin beta-6 chainQ9BUF5Details
Far upstream element-binding protein 1Q96AE4Details
cAMP-dependent protein kinase type II-alpha regulatory subunitP13861Details
cAMP-dependent protein kinase type I-alpha regulatory subunitP10644Details
High mobility group protein B1P09429Details
Heat shock protein beta-1P04792Details
Ribosome-binding protein 1Q9P2E9Details
Microtubule-associated protein 4P27816Details
Tumor necrosis factor receptor superfamily member 8P28908Details
Casein kinase I isoform epsilonP49674Details
Heat shock factor protein 1Q00613Details
Histone deacetylase 4P56524Details
Histone deacetylase 7Q8WUI4Details
Alkaline phosphatase, tissue-nonspecific isozymeP05186Details
DNA polymerase epsilon subunit 3Q9NRF9Details
Cation-independent mannose-6-phosphate receptorP11717Details
Carbonic anhydrase 14Q9ULX7Details
Monocarboxylate transporter 10Q8TF71Details
Disintegrin and metalloproteinase domain-containing protein 17P78536Details
S-phase kinase-associated protein 1P63208Details
Uracil-DNA glycosylaseP13051Details
Poly [ADP-ribose] polymerase 2Q9UGN5Details
Inner centromere proteinQ9NQS7Details
Large ribosomal subunit protein eL15P61313Details
Large ribosomal subunit protein uL23P62750Details
Large ribosomal subunit protein eL37P61927Details
Large ribosomal subunit protein uL3P39023Details
ATP synthase subunit alpha, mitochondrialP25705Details
Triosephosphate isomeraseP60174Details
Protein kinase C iota typeP41743Details
Myosin-14Q7Z406Details
Proteasome subunit alpha type-3P25788Details
Proteasome subunit alpha type-5P28066Details
STE20-like serine/threonine-protein kinaseQ9H2G2Details
Nuclear receptor coactivator 5Q9HCD5Details
Hydroxymethylglutaryl-CoA synthase, cytoplasmicQ01581Details
Cyclin-dependent kinase 16Q00536Details
Calcium/calmodulin-dependent protein kinase type II subunit deltaQ13557Details
Serine/threonine-protein kinase 26Q9P289Details
Myocardin-related transcription factor AQ969V6Details
DestrinP60981Details
Cofilin-1P23528Details
Rho-associated protein kinase 2O75116Details
Actin-related protein 2/3 complex subunit 1BO15143Details
Ribosomal protein S6 kinase alpha-1Q15418Details
Elongation factor 2P13639Details
Tyrosine-protein kinase LynP07948Details
SRSF protein kinase 2P78362Details
Glycylpeptide N-tetradecanoyltransferase 1P30419Details
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrialQ15120Details
Mediator of RNA polymerase II transcription subunit 1Q15648Details
Protein arginine N-methyltransferase 3O60678Details
Epsin-1Q9Y6I3Details
Phosphoglycerate kinase 1P00558Details
Phosphoglucomutase-1P36871Details
VimentinP08670Details
Uridine 5'-monophosphate synthaseP11172Details
Synapsin-1P17600Details
cAMP-dependent protein kinase type II-beta regulatory subunitP31323Details
T-complex protein 1 subunit gammaP49368Details
Carboxypeptidase DO75976Details
14-3-3 protein epsilonP62258Details
Branched-chain alpha-ketoacid dehydrogenase kinaseO14874Details
Transitional endoplasmic reticulum ATPaseP55072Details
Ubiquitin-like modifier-activating enzyme 1P22314Details
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5O60264Details
Uridine-cytidine kinase-like 1Q9NWZ5Details
Spectrin beta chain, non-erythrocytic 1Q01082Details
Sodium bicarbonate cotransporter 3Q9Y6M7Details
Myc proto-oncogene proteinP01106Details
Equilibrative nucleoside transporter 2Q14542Details
SH2B adapter protein 3Q9UQQ2Details
Breakpoint cluster region proteinP11274Details
Dual specificity mitogen-activated protein kinase kinase 2P36507Details
Mitogen-activated protein kinase kinase kinase 2Q9Y2U5Details
RalA-binding protein 1Q15311Details
Ethanolamine-phosphate cytidylyltransferaseQ99447Details
Ribosomal protein S6 kinase alpha-3P51812Details
Membrane-associated progesterone receptor component 1O00264Details
Cyclic AMP-dependent transcription factor ATF-2P15336Details
Cyclic AMP-dependent transcription factor ATF-7P17544Details
Intracellular hyaluronan-binding protein 4Q5JVS0Details
Histone H1.4P10412Details
Casein kinase II subunit betaP67870Details
Mitogen-activated protein kinase kinase kinase 20Q9NYL2Details
Dihydropyrimidinase-related protein 2Q16555Details
Protein PMLP29590Details
Nucleolar and coiled-body phosphoprotein 1Q14978Details
Protein O-GlcNAcaseO60502Details
Proprotein convertase subtilisin/kexin type 9Q8NBP7Details
Calmodulin-2P0DP24Details
Calmodulin-3P0DP25Details
Calcium-dependent secretion activator 2Q86UW7Details
60 kDa heat shock protein, mitochondrialP10809Details
Heterogeneous nuclear ribonucleoproteins A2/B1P22626Details
Heterogeneous nuclear ribonucleoprotein HP31943Details
Heterogeneous nuclear ribonucleoprotein H3P31942Details
Heterogeneous nuclear ribonucleoprotein LP14866Details
Splicing factor, proline- and glutamine-richP23246Details
Small ribosomal subunit protein RACK1P63244Details
Alpha-actinin-1P12814Details
Stress-induced-phosphoprotein 1P31948Details
Eukaryotic initiation factor 4A-IP60842Details
Hepatoma-derived growth factorP51858Details
Phosphoglycerate mutase 1P18669Details
Ran-specific GTPase-activating proteinP43487Details
HuntingtinP42858Details
Pregnancy-specific beta-1-glycoprotein 5Q15238Details
Neural cell adhesion molecule L1P32004Details
Eukaryotic translation initiation factor 3 subunit FO00303Details
Heterogeneous nuclear ribonucleoprotein FP52597Details
Heterogeneous nuclear ribonucleoprotein KP61978Details
Heat shock 70 kDa protein 4P34932Details
Heat shock protein 105 kDaQ92598Details
Nuclear migration protein nudCQ9Y266Details
26S proteasome regulatory subunit 6AP17980Details
Splicing factor 3A subunit 3Q12874Details
Tumor protein D54O43399Details
Ubiquitin carboxyl-terminal hydrolase 14P54578Details
Chromobox protein homolog 5P45973Details
DesmoplakinP15924Details
Far upstream element-binding protein 2Q92945Details
Cysteine and glycine-rich protein 1P21291Details
Filamin-AP21333Details
Heterogeneous nuclear ribonucleoprotein D0Q14103Details
Heterochromatin protein 1-binding protein 3Q5SSJ5Details
NucleophosminP06748Details
Large ribosomal subunit protein eL14P50914Details
Large ribosomal subunit protein eL18Q07020Details
Small ribosomal subunit protein eS17P08708Details
Small ribosomal subunit protein eS6P62753Details
Splicing factor 1Q15637Details
Serine/arginine-rich splicing factor 4Q08170Details
Transgelin-2P37802Details
ZyxinQ15942Details
Serine/arginine-rich splicing factor 1Q07955Details
Survival motor neuron proteinB4DP61Details
TransgelinQ01995Details
Myosin-9P35579Details
Probable ATP-dependent RNA helicase DDX5P17844Details
Splicing factor 3B subunit 1O75533Details
Very long chain fatty acid elongase 5Q9NYP7Details
Ribosomal protein S6 kinase alpha-6Q9UK32Details
Serine/threonine-protein kinase 24Q9Y6E0Details
Serine/threonine-protein kinase 3Q13188Details
STE20/SPS1-related proline-alanine-rich protein kinaseQ9UEW8Details
Serine/threonine-protein kinase TAO1Q7L7X3Details
Serine/threonine-protein kinase TAO3Q9H2K8Details
Serine/threonine-protein kinase tousled-like 2Q86UE8Details
TRAF2 and NCK-interacting protein kinaseQ9UKE5Details
Non-receptor tyrosine-protein kinase TNK1Q13470Details
Serine/threonine-protein kinase ULK1O75385Details
AP2-associated protein kinase 1Q2M2I8Details
Citron Rho-interacting kinaseO14578Details
Serine/threonine-protein kinase DCLK1O15075Details
eIF-2-alpha kinase GCN2Q9P2K8Details
Ephrin type-A receptor 1P21709Details
Cyclin-G-associated kinaseO14976Details
Mitogen-activated protein kinase kinase kinase 4Q9Y6R4Details
Mitogen-activated protein kinase kinase kinase kinase 4O95819Details
Serine/threonine-protein kinase MARK1Q9P0L2Details
Serine/threonine-protein kinase MARK2Q7KZI7Details
MAP/microtubule affinity-regulating kinase 3P27448Details
CLIP-associating protein 1Q7Z460Details
Misshapen-like kinase 1Q8N4C8Details
Serine/threonine-protein kinase OSR1O95747Details
Serine/threonine-protein kinase PAK 1Q13153Details
Serine/threonine-protein kinase PAK 2Q13177Details
Serine/threonine-protein kinase PAK 4O96013Details
Cyclin-dependent kinase 17Q00537Details
Phosphatidylinositol 4-kinase betaQ9UBF8Details
Serine/threonine-protein kinase N1Q16512Details
Serine/threonine-protein kinase D1Q15139Details
Serine/threonine-protein kinase PRP4 homologQ13523Details
Serine/threonine-protein kinase RIO1Q9BRS2Details
Serine/threonine-protein kinase RIO2Q9BVS4Details
Serine/threonine-protein kinase 10O94804Details
Histone-lysine N-methyltransferase EZH2Q15910Details
POU domain, class 2, transcription factor 1P14859Details
ATP-citrate synthaseP53396Details
Sodium-coupled neutral amino acid symporter 1Q9H2H9Details
DNA (cytosine-5)-methyltransferase 3AQ9Y6K1Details
Zinc transporter ZIP10Q9ULF5Details
Proton-coupled zinc antiporter SLC30A1Q9Y6M5Details
Tyrosine-protein phosphatase non-receptor type 12Q05209Details
Plasma membrane calcium-transporting ATPase 1P20020Details
DNA (cytosine-5)-methyltransferase 3BQ9UBC3Details
Serine/threonine-protein kinase ATRQ13535Details
Eukaryotic translation initiation factor 4E-binding protein 1Q13541Details
Lysine-specific histone demethylase 1AO60341Details
Proliferation marker protein Ki-67P46013Details
Histone acetyltransferase p300Q09472Details
ELAV-like protein 1Q15717Details