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

Name	UniProt ID
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial	P56181	Details
7-dehydrocholesterol reductase	Q9UBM7	Details
RAF proto-oncogene serine/threonine-protein kinase	P04049	Details
Pyruvate kinase PKM	P14618	Details
Androgen receptor	P10275	Details
Cationic amino acid transporter 3	Q8WY07	Details
Solute carrier family 12 member 6	Q9UHW9	Details
DNA ligase 3	P49916	Details
Bifunctional glutamate/proline--tRNA ligase	P07814	Details
DNA ligase 1	P18858	Details
Large neutral amino acids transporter small subunit 1	Q01650	Details
Neutral amino acid transporter B(0)	Q15758	Details
5'-AMP-activated protein kinase subunit beta-1	Q9Y478	Details
GMP synthase [glutamine-hydrolyzing]	P49915	Details
Cystathionine beta-synthase	P35520	Details
Vascular endothelial growth factor receptor 2	P35968	Details
Ferritin heavy chain	P02794	Details
Vitamin K-dependent gamma-carboxylase	P38435	Details
Calmodulin	P0DP23	Details
Serine/threonine-protein kinase A-Raf	P10398	Details
Abelson tyrosine-protein kinase 2	P42684	Details
Isoleucine--tRNA ligase, cytoplasmic	P41252	Details
Choline-phosphate cytidylyltransferase B	Q9Y5K3	Details
Receptor tyrosine-protein kinase erbB-2	P04626	Details
Chromodomain-helicase-DNA-binding protein 1	O14646	Details
Glyceraldehyde-3-phosphate dehydrogenase	P04406	Details
米ethionine--tRNA ligase, cytoplasmic	P56192	Details
DNA polymerase alpha catalytic subunit	P09884	Details
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial	P08559	Details
Solute carrier family 12 member 4	Q9UP95	Details
Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial	P29803	Details
Choline-phosphate cytidylyltransferase A	P49585	Details
Tyrosine-protein phosphatase non-receptor type 1	P18031	Details
Acetyl-CoA carboxylase 1	Q13085	Details
Serine/threonine-protein kinase B-raf	P15056	Details
Cytosolic phospholipase A2	P47712	Details
米onocarboxylate transporter 1	P53985	Details
DNA polymerase alpha subunit B	Q14181	Details
Aspartate--tRNA ligase, cytoplasmic	P14868	Details
Pyrroline-5-carboxylate reductase 2	Q96C36	Details
DNA topoisomerase 2-alpha	P11388	Details
Sodium/hydrogen exchanger 1	P19634	Details
5'-AMP-activated protein kinase subunit beta-2	O43741	Details
米ultidrug resistance-associated protein 1	P33527	Details
Tyrosine-protein kinase Lck	P06239	Details
CTP synthase 1	P17812	Details
DNA (cytosine-5)-methyltransferase 1	P26358	Details
Mitogen-activated protein kinase 1	P28482	Details
Cyclic AMP-responsive element-binding protein 1	P16220	Details
DNA topoisomerase 1	P11387	Details
Catenin beta-1	P35222	Details
Calnexin	P27824	Details
Rho-associated protein kinase 1	Q13464	Details
Transcription factor AP-1	P05412	Details
Solute carrier family 2, facilitated glucose transporter member 1	P11166	Details
Mitogen-activated protein kinase 3	P27361	Details
Cyclin-dependent kinase 1	P06493	Details
Gap junction alpha-1 protein	P17302	Details
Phosphatidylserine synthase 1	P48651	Details
米icrotubule-associated protein 2	P11137	Details
CD44 antigen	P16070	Details
Heat shock protein HSP 90-alpha	P07900	Details
Endoplasmin	P14625	Details
米icrotubule-associated protein 1A	P78559	Details
14-3-3蛋白ζ/δ	P63104	Details
Phosphatidylethanolamine-binding protein 1	P30086	Details
醌氧化还原酶	Q08257	Details
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial	P33316	Details
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	Q08499	Details
Protein kinase C theta type	Q04759	Details
Tubulin alpha-1C chain	Q9BQE3	Details
Uridine-cytidine kinase 2	Q9BZX2	Details
DNA repair protein XRCC4	Q13426	Details
Fructose-bisphosphate aldolase A	P04075	Details
米-phase inducer phosphatase 2	P30305	Details
Poly [ADP-ribose] polymerase 1	P09874	Details
Death-associated protein kinase 1	P53355	Details
Kinesin-like protein KIF11	P52732	Details
Heat shock protein HSP 90-beta	P08238	Details
Cyclin-dependent kinase 7	P50613	Details
Keratin, type II cytoskeletal 8	P05787	Details
Laminin subunit gamma-1	P11047	Details
Syndecan-2	P34741	Details
Retinoblastoma-associated protein	P06400	Details
Pyridoxal-dependent decarboxylase domain-containing protein 1	Q6P996	Details
Peptidyl-glycine alpha-amidating monooxygenase	P19021	Details
Cyclin-dependent kinase 9	P50750	Details
米ultifunctional protein ADE2	P22234	Details
CAD protein	P27708	Details
Phosphoribosylformylglycinamidine合酶	O15067	Details
Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2	O94808	Details
Phosphatidylserine synthase 2	Q9BVG9	Details
Sphingomyelin phosphodiesterase 4	Q9NXE4	Details
Threonine--tRNA ligase, mitochondrial	Q9BW92	Details
Peptidyl-prolyl cis-trans isomerase G	Q13427	Details
Histone deacetylase 1	Q13547	Details
Histone deacetylase 2	Q92769	Details
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha	P49354	Details
DNA-dependent protein kinase catalytic subunit	P78527	Details
Serine/threonine-protein kinase mTOR	P42345	Details
Protein kinase C delta type	Q05655	Details
DNA topoisomerase 2-beta	Q02880	Details
Ribonucleoside-diphosphate reductase subunit M2	P31350	Details
E3 ubiquitin-protein ligase UBR4	Q5T4S7	Details
NAD-dependent protein deacetylase sirtuin-1	Q96EB6	Details
Voltage-dependent anion-selective channel protein 1	P21796	Details
Voltage-dependent anion-selective channel protein 2	P45880	Details
Prostaglandin E synthase 3	Q15185	Details
Gephyrin	Q9NQX3	Details
Kinesin-like protein KIF1A	Q12756	Details
Pleckstrin homology domain-containing family A member 1	Q9HB21	Details
Serine/threonine-protein kinase Chk1	O14757	Details
Tubulin beta-6 chain	Q9BUF5	Details
Far upstream element-binding protein 1	Q96AE4	Details
cAMP-dependent protein kinase type II-alpha regulatory subunit	P13861	Details
cAMP-dependent protein kinase type I-alpha regulatory subunit	P10644	Details
High mobility group protein B1	P09429	Details
Heat shock protein beta-1	P04792	Details
Ribosome-binding protein 1	Q9P2E9	Details
米icrotubule-associated protein 4	P27816	Details
Tumor necrosis factor receptor superfamily member 8	P28908	Details
Casein kinase I isoform epsilon	P49674	Details
Heat shock factor protein 1	Q00613	Details
Histone deacetylase 4	P56524	Details
Histone deacetylase 7	Q8WUI4	Details
Alkaline phosphatase, tissue-nonspecific isozyme	P05186	Details
DNA polymerase epsilon subunit 3	Q9NRF9	Details
Cation-independent mannose-6-phosphate receptor	P11717	Details
Carbonic anhydrase 14	Q9ULX7	Details
米onocarboxylate transporter 10	Q8TF71	Details
Disintegrin and metalloproteinase domain-containing protein 17	P78536	Details
S-phase kinase-associated protein 1	P63208	Details
Uracil-DNA glycosylase	P13051	Details
Poly [ADP-ribose] polymerase 2	Q9UGN5	Details
Inner centromere protein	Q9NQS7	Details
60S ribosomal protein L15	P61313	Details
60S ribosomal protein L23a	P62750	Details
60S ribosomal protein L37	P61927	Details
60S ribosomal protein L3	P39023	Details
ATP synthase subunit alpha, mitochondrial	P25705	Details
Triosephosphate isomerase	P60174	Details
Protein kinase C iota type	P41743	Details
米yosin-14	Q7Z406	Details
Proteasome subunit alpha type-3	P25788	Details
Proteasome subunit alpha type-5	P28066	Details
STE20-like serine/threonine-protein kinase	Q9H2G2	Details
Nuclear receptor coactivator 5	Q9HCD5	Details
Hydroxymethylglutaryl-CoA synthase, cytoplasmic	Q01581	Details
Cyclin-dependent kinase 16	Q00536	Details
Calcium/calmodulin-dependent protein kinase type II subunit delta	Q13557	Details
Serine/threonine-protein kinase 26	Q9P289	Details
米KL/myocardin-like protein 1	Q969V6	Details
Destrin	P60981	Details
Cofilin-1	P23528	Details
Rho-associated protein kinase 2	O75116	Details
Actin-related protein 2/3 complex subunit 1B	O15143	Details
Ribosomal protein S6 kinase alpha-1	Q15418	Details
Elongation factor 2	P13639	Details
Tyrosine-protein kinase Lyn	P07948	Details
SRSF protein kinase 2	P78362	Details
Glycylpeptide N-tetradecanoyltransferase 1	P30419	Details
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial	Q15120	Details
米ediator of RNA polymerase II transcription subunit 1	Q15648	Details
Protein arginine N-methyltransferase 3	O60678	Details
Epsin-1	Q9Y6I3	Details
Phosphoglycerate kinase 1	P00558	Details
Phosphoglucomutase-1	P36871	Details
Vimentin	P08670	Details
Uridine 5'-monophosphate synthase	P11172	Details
Synapsin-1	P17600	Details
cAMP-dependent protein kinase type II-beta regulatory subunit	P31323	Details
T-complex protein 1 subunit gamma	P49368	Details
Carboxypeptidase D	O75976	Details
14-3-3 protein epsilon	P62258	Details
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial	O14874	Details
Transitional endoplasmic reticulum ATPase	P55072	Details
Ubiquitin-like modifier-activating enzyme 1	P22314	Details
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5	O60264	Details
Uridine-cytidine kinase-like 1	Q9NWZ5	Details
Spectrin beta chain, non-erythrocytic 1	Q01082	Details
Sodium bicarbonate cotransporter 3	Q9Y6M7	Details
米yc proto-oncogene protein	P01106	Details
Equilibrative nucleoside transporter 2	Q14542	Details
SH2B adapter protein 3	Q9UQQ2	Details
Breakpoint cluster region protein	P11274	Details
Dual specificity mitogen-activated protein kinase kinase 2	P36507	Details
Mitogen-activated protein kinase kinase kinase 2	Q9Y2U5	Details
RalA-binding protein 1	Q15311	Details
Ethanolamine-phosphate cytidylyltransferase	Q99447	Details
Ribosomal protein S6 kinase alpha-3	P51812	Details
米embrane-associated progesterone receptor component 1	O00264	Details
Cyclic AMP-dependent transcription factor ATF-2	P15336	Details
Cyclic AMP-dependent transcription factor ATF-7	P17544	Details
Intracellular hyaluronan-binding protein 4	Q5JVS0	Details
Histone H1.4	P10412	Details
Casein kinase II subunit beta	P67870	Details
Mitogen-activated protein kinase kinase kinase MLT	Q9NYL2	Details
Dihydropyrimidinase-related蛋白2	Q16555	Details
Protein PML	P29590	Details
Nucleolar and coiled-body phosphoprotein 1	Q14978	Details
Protein O-GlcNAcase	O60502	Details
Proprotein convertase subtilisin/kexin type 9	Q8NBP7	Details
Calmodulin-2	P0DP24	Details
Calmodulin-3	P0DP25	Details
Calcium-dependent secretion activator 2	Q86UW7	Details
60 kDa heat shock protein, mitochondrial	P10809	Details
Heterogeneous nuclear ribonucleoproteins A2/B1	P22626	Details
Heterogeneous nuclear ribonucleoprotein H	P31943	Details
Heterogeneous nuclear ribonucleoprotein H3	P31942	Details
Heterogeneous nuclear ribonucleoprotein L	P14866	Details
Splicing factor, proline- and glutamine-rich	P23246	Details
Receptor of activated protein C kinase 1	P63244	Details
Alpha-actinin-1	P12814	Details
Stress-induced-phosphoprotein 1	P31948	Details
Eukaryotic initiation factor 4A-I	P60842	Details
Hepatoma-derived growth factor	P51858	Details
Phosphoglycerate mutase 1	P18669	Details
Ran-specific GTPase-activating protein	P43487	Details
Huntingtin	P42858	Details
Pregnancy-specific beta-1-glycoprotein 5	Q15238	Details
Neural cell adhesion molecule L1	P32004	Details
Eukaryotic translation initiation factor 3 subunit F	O00303	Details
Heterogeneous nuclear ribonucleoprotein F	P52597	Details
Heterogeneous nuclear ribonucleoprotein K	P61978	Details
Heat shock 70 kDa protein 4	P34932	Details
Heat shock protein 105 kDa	Q92598	Details
Nuclear migration protein nudC	Q9Y266	Details
26S protease regulatory subunit 6A	P17980	Details
Splicing factor 3A subunit 3	Q12874	Details
Tumor protein D54	O43399	Details
Ubiquitin carboxyl-terminal hydrolase 14	P54578	Details
Chromobox protein homolog 5	P45973	Details
Desmoplakin	P15924	Details
Far upstream element-binding protein 2	Q92945	Details
Cysteine and glycine-rich protein 1	P21291	Details
Filamin-A	P21333	Details
Heterogeneous nuclear ribonucleoprotein D0	Q14103	Details
Heterochromatin protein 1-binding protein 3	Q5SSJ5	Details
Nucleophosmin	P06748	Details
60S ribosomal protein L14	P50914	Details
60S ribosomal protein L18	Q07020	Details
40S ribosomal protein S17	P08708	Details
40S ribosomal protein S6	P62753	Details
Splicing factor 1	Q15637	Details
Serine/arginine-rich splicing factor 4	Q08170	Details
Transgelin-2	P37802	Details
Zyxin	Q15942	Details
Serine/arginine-rich splicing factor 1	Q07955	Details
Survival motor neuron protein	B4DP61	Details
Transgelin	Q01995	Details
米yosin-9	P35579	Details
Probable ATP-dependent RNA helicase DDX5	P17844	Details
Splicing factor 3B subunit 1	O75533	Details
Elongation of very long chain fatty acids protein 5	Q9NYP7	Details
Ribosomal protein S6 kinase alpha-6	Q9UK32	Details
Serine/threonine-protein kinase 24	Q9Y6E0	Details
Serine/threonine-protein kinase 3	Q13188	Details
STE20/SPS1-related proline-alanine-rich protein kinase	Q9UEW8	Details
Serine/threonine-protein kinase TAO1	Q7L7X3	Details
Serine/threonine-protein kinase TAO3	Q9H2K8	Details
Serine/threonine-protein kinase tousled-like 2	Q86UE8	Details
TRAF2 and NCK-interacting protein kinase	Q9UKE5	Details
Non-receptor tyrosine-protein kinase TNK1	Q13470	Details
Serine/threonine-protein kinase ULK1	O75385	Details
AP2-associated protein kinase 1	Q2M2I8	Details
Citron Rho-interacting kinase	O14578	Details
Serine/threonine-protein kinase DCLK1	O15075	Details
eIF-2-alpha kinase GCN2	Q9P2K8	Details
Ephrin type-A receptor 1	P21709	Details
Cyclin-G-associated kinase	O14976	Details
Mitogen-activated protein kinase kinase kinase 4	Q9Y6R4	Details
Mitogen-activated protein kinase kinase kinase kinase 4	O95819	Details
Serine/threonine-protein kinase MARK1	Q9P0L2	Details
Serine/threonine-protein kinase MARK2	Q7KZI7	Details
米AP/microtubule affinity-regulating kinase 3	P27448	Details
CLIP-associating protein 1	Q7Z460	Details
米isshapen-like kinase 1	Q8N4C8	Details
Serine/threonine-protein kinase OSR1	O95747	Details
Serine/threonine-protein kinase PAK 1	Q13153	Details
Serine/threonine-protein kinase PAK 2	Q13177	Details
Serine/threonine-protein kinase PAK 4	O96013	Details
Cyclin-dependent kinase 17	Q00537	Details
Phosphatidylinositol 4-kinase beta	Q9UBF8	Details
Serine/threonine-protein kinase N1	Q16512	Details
Serine/threonine-protein kinase D1	Q15139	Details
Serine/threonine-protein kinase PRP4 homolog	Q13523	Details
Serine/threonine-protein kinase RIO1	Q9BRS2	Details
Serine/threonine-protein kinase RIO2	Q9BVS4	Details
Serine/threonine-protein kinase 10	O94804	Details
Histone-lysine N-methyltransferase EZH2	Q15910	Details
POU domain, class 2, transcription factor 1	P14859	Details
atp柠檬酸合酶	P53396	Details
Sodium-coupled neutral amino acid transporter 1	Q9H2H9	Details
DNA (cytosine-5)-methyltransferase 3A	Q9Y6K1	Details
Zinc transporter ZIP10	Q9ULF5	Details
Zinc transporter 1	Q9Y6M5	Details
Tyrosine-protein phosphatase non-receptor type 12	Q05209	Details
Plasma membrane calcium-transporting ATPase 1	P20020	Details
DNA (cytosine-5)-methyltransferase 3B	Q9UBC3	Details
Serine/threonine-protein kinase ATR	Q13535	Details
Eukaryotic translation initiation factor 4E-binding protein 1	Q13541	Details
Lysine-specific histone demethylase 1A	O60341	Details
Proliferation marker protein Ki-67	P46013	Details
Histone acetyltransferase p300	Q09472	Details
ELAV-like protein 1	Q15717	Details