Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/07/PXD011782/proteinGroupsChromatin.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/07/PXD011782/pride_submission.rarprimaryOK200h.marks@ncmls.ru.nlGuido van MierloMass SpectrometryShotgun proteomicsNot availableLc-msChromatinMouseNaïve pluripotencyDifferentiationPrimed pluripotencyhttp://www.ebi.ac.uk/pride/archive/projects/PXD011782Cell CultureChromatin was enriched using a method described in Kustatscher et al, 2014. In brief, Serum ESCs, EpiSCs, and END cells were cross-linked and lysed to isolate nuclear pellets. Nuclear pellets were lysed using SDS and subsequently suspended in a buffer containing 8M Urea, in order to precipitate DNA and proteins that were cross-linked to it. Cross-links were then removed by boiling in SDS and β-mercaptoethanol. Decross-linked extracts were processed using filter-aided sample preparation (FASP). Digested and desalted using StageTips (as described in Rappsilber et al, 2007). Trypsin-digested peptide mixtures were measured using a 4 hour gradient on an LTQ-Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific).PrideNot availableNo PTMs are included in the datasetRaw files were analyzed with MaxQuant version 1.5.1.0 with default settings and the following alterations: match between runs enabled and LFQ values calculated. Potential contaminants and reverse hits were filtered using Perseus. Significant proteins were determined using Perseus multiple sample significance testing(ANOVA). Downstream analysis was performed using Python3 and Jupyter Notebook.ProteomicsHendrik MarksQ ExactivePARTIALMolecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the NetherlandsMus Musculus (mouse)31219242 van Mierlo G, Wester RA, Marks H. A mass spectrometry survey of chromatin-associated proteins in pluripotency and early lineage commitment. Proteomics. 2019:e1900047 10.1002/pmic.201900047guidovanmierlo@gmail.comRadboud UniversityNetherlandsPluripotency can be captured in vitro in the form of Embryonic Stem Cells (ESCs). These ESCs can be either maintained in the unrestricted "naïve" state of pluripotency, adapted to developmentally more constrained "primed" pluripotency or differentiated towards each of the three germ layers. Epigenetic protein complexes and transcription factors have been shown to specify and instruct transitions from ESCs to distinct cell states. In this study, proteomic profiling of the chromatin landscape by chromatin enrichment for proteomics (ChEP) is used in mouse naive pluripotent ESCs, primed pluripotent Epiblast stem cells (EpiSCs), and cells in early stages of differentiation. A comprehensive overview of epigenetic protein complexes associated with the chromatin is provided and proteins associated with the maintenance and loss of pluripotency are identified. The data reveal major compositional alterations of epigenetic complexes during priming and differentiation of naïve pluripotent ESCs. These results contribute to the understanding of ESC differentiation and provide a framework for future studies of lineage commitment of ESCs.A Mass Spectrometry Survey of Chromatin-Associated Proteins in Pluripotency and Early Lineage Commitment.van Mierlo Guido G, Wester Roelof Alexander RA, Marks Hendrik Hnuclear chromatin, F10B6_15, cytoplasmic chromatin, RP37, 2-ME, DNS, (Deoxyribonucleotide)n, Blood, DNAn+1, Proteins, AI836084, Gene, PNR, retinoschisis with early nyctalopia, SDH, Carbamide, RNR, Basodexan, Double-Stranded, Blood Serum, Serum, buffer, Cell, ur, Peptide, F10B6.15, Deoxyribonucleic acids, Buffer, enhanced S-cone syndrome, (Deoxyribonucleotide)n+m, Karbamid, polypeptide, peptide, SDS, Polypeptides, method, carbamide, Ethanol, ClvPrd, peptido, Deoxyribonucleic Acid, carbonyldiamide, method used in an experiment, Harnstoff, Protein, Gene Products, Urea, Carmol, ds-DNA, desoxyribose nucleic acid, END, Chromatins, ESCS, rd7, thymus nucleic acid, peptides, uree, E927b, urea, beta-Trypsin, Tripcellim, 2 Mercaptoethanol, 4733401P19Rik, SWDS, Double Stranded, Deoxyribonucleic acid, proteins, CGI-97, beta Trypsin, UREA, plan specification, Protein Gene Products, Gene Proteins, Trypure, H2NC(O)NH2, precipited material, h, SOLO DANCERS, Thermo Scientific., 2-Mercaptoethanol, chromosome scaffold, ds DNA, Desoxyribonukleinsaeure, 2-mercapto-, Peptid, peptidos, Double-Stranded DNA, (Deoxyribonucleotide)m, Polypeptide, DNA, deoxyribonucleic acids, DNAn, ORW1, 1728, Serums, HHT1Mass Spectrum Analysis, nuclear chromatin, lod, Mass Spectrum, cytoplasmic chromatin, advanced, DmelCG2684, Analyses, Proteins, Spectrometry, Gene, proteins, Spectrum Analyses, NTef2, Lds, Spectrum Analysis, early, Protein Gene Products, Spectroscopy, Gene Proteins, Horka, chromosome scaffold, Protein, Mass, Gene Products, precocious, CG2684, Fs(3)Horka, DmF2, Analysis, Fs(3)Sz11., associated, Fs(3)Hor, Mass Spectrum Analyses, Chromatins, Mass SpectroscopyProtein Gene Products, Svc, Gene Proteins, Bru, Col4a-1, Raw, determination, sample, Protein, Gene Products, Proteins, chemical analysis., Gene, Del(8)44H, assay, proteins, sample populationnuclear chromatin, screening, RP37, cytoplasmic chromatin, advanced, findings, Stem Cells, Proteins, ORE7, Gene, PNR, retinoschisis with early nyctalopia, RNR, Factor, Transcription Factor, ESCAROLA, Cell, results, Fs(3)Sz11, enhanced S-cone syndrome, ESCS., Readability, Stem Cell, AT-hook motif nuclear-localized protein 27, Protein, precocious, Gene Products, symptoms, L41867, DmF2, Fs(3)Hor, CG14941, Chromatins, ESCS, ORESARA 7, AHL27, Embryonic, lod, study, rd7, Transcription, DmelCG2684, Factors, DmelCG14941, distinct, Epigenetic, F9H16.12, Embryonic Stem Cell, sc, signs, ESC, Esc, proteins, F9H16_12, Understanding, NTef2, Lds, Maintenances, Epigenomic, early, dESC, Protein Gene Products, loss of, Gene Proteins, Horka, Cells, chromosome scaffold, CG2684, Fs(3)Horka, regulation, associated, Epigenetics, Embryonic StemForms, RP37, cytoplasmic chromatin, d230, advanced, Peptidomics, Colony-Forming Units, Stem Cells, Progenitor Cell, Gene, PNR, dTAFII250, protein, protein-containing complex, Transcription Factor, EfW1, enhanced S-cone syndrome, dmTAF[[II]]230, protein polypeptide chains, Readability, polypeptide chain, dmTAF1, Taf230, Mother Cells, Gene Products, L41867, DmF2, protein aggregate, Fs(3)Hor, Progenitor, Chromatins, TAF250, lod, study, rd7, Transcription, Taf200, DmelCG2684, Epiblasts, dTAF[[II]]250, DmelCG14941, TFIID TAF250, cel, cell, Embryonic Stem Cell, sc, primitive ectoderm, Mother, ESC, Esc, Taf1p, proteins, NTef2, Maintenances, Layers, Epigenomic, dESC, Hypoblast, dTAF250, Layer, chromosome scaffold, house mouse, associated, TAF, nuclear chromatin, data, dTAF[[II]]230, TAF[[II]]250, Colony Forming Unit, protein complex, Progenitor Cells, Proteins, ORE7, mouse, TAF200, l(3)84Ab, retinoschisis with early nyctalopia, Epiblast, RNR, Factor, BG:DS00004.13, ectoblast, Germ, TAFII-250, TAF250/230, ESCAROLA, Cell, results, Fs(3)Sz11, dTAF230, ESCS., TAFII250, native protein, Colony-Forming Unit, Stem Cell, Germ Layer, natural protein, Mus, p230, AT-hook motif nuclear-localized protein 27, Protein, precocious, TAF[[II]]250/230, TFIID, blastocyst, CG14941, ESCS, ORESARA 7, AHL27, Embryonic, Mother Cell, Taf[[II]]250, Factors, TAF[[II]]230, distinct, Epigenetic, F9H16.12, mice, Stem, epiblast, Colony Forming Units, TAF[II]250, Understanding, F9H16_12, Hypoblasts, CG17603, Lds, TAF[[II]], early, Protein Gene Products, loss of, Gene Proteins, DmelCG17603, Taf250, SR3-5, Horka, Cells, CG2684, Fs(3)Horka, Mouse, Epigenetics, epiblastus, Embryonic Stem, TAF230, TAF1Mass Spectrum Analysis, nuclear chromatin, lod, Mass Spectrum, cytoplasmic chromatin, advanced, DmelCG2684, Analyses, Proteins, Spectrometry, Gene, proteins, Spectrum Analyses, NTef2, Lds, Spectrum Analysis, early, Protein Gene Products, Spectroscopy, Gene Proteins, Horka, chromosome scaffold, Protein, Mass, Gene Products, precocious, CG2684, Fs(3)Horka, DmF2, Analysis, Fs(3)Sz11., associated, Fs(3)Hor, Mass Spectrum Analyses, Chromatins, Mass SpectroscopyfalseA mass spectrometry survey of chromatin-associated proteins in pluripotency and early lineage commitmentPluripotent Embryonic Stem Cells (ESCs) can be captured in vitro in different states, ranging from unrestricted ‘naïve’ to more developmentally constrained ‘primed’ pluripotency. Complexes involved in epigenetic regulation and key transcription factors have been shown to be involved in specifying these distinct states. In this study, we use proteomic profiling of the chromatin landscape in naive pluripotent ESCs, Epistem cells (EpiSCs) and early differentiated ESCs to survey the chromatin in naïve and primed pluripotency and during differentiation. We provide a comprehensive overview of epigenetic complexes situated on the chromatin and identify proteins associated with the maintenance and loss of pluripotency. The findings presented here indicate major compositional alterations of epigenetic complexes starting from ESC priming onwards. Our results contribute to the understanding of ESC differentiation and provide a framework for future studies of lineage commitment of ESCs.2019-07-042018-11-21PXD0117822806551646099180498295358511145278728421880905811363336351524260119832758385NCBITaxon:128068888561896111430118726355557114526236493461327467073853883641135461582158236889547627211232944222911809923233654583334607925193659143205971293865581914932637371250232NCBITaxon:1272111957748186614885843451358672217554374081691804542668344530586126683514982250581496367458554528113208147956410039237514636942049433208964208963445974137979128384400667935293671521659940483216597216595455013152826930421659156271616968332183217292042779447623764543172030949801975255569781439843948840479NCBITaxon:2157525338551531051067439899037122857759515205968762311210884555588845587077918178081736309431794571698936160488409859NCBITaxon:371621047826794015059071483643204210613204913816936303555432046632633311994565453511025411103217459216129410026420369456941016763410210761277351131658239254727933428146135843017463345774449167547604893212873567568403019172651813019411192943936711041131023932025559863258278839659104759347495165299835525663175854310243260866310245980875741755518320196447145268045796190832331156114155421932555217634123598755529NCBITaxon:475185025476113615741465477180066556484337677299767982510216998238976413735115571108972444474153NCBITaxon:5055789969844100036465349334147147493548019467512991143597412764731370863265478765698353221599838192011103481985247946409860995861571871766859919157295137221171101107687834974198601488406334249235985988655974649987039202111072943311711397215987419085037117082841823502414511391902197822474636046147123743759392532566489050794526591972211915853101774208588596NCBITaxon:615750521028307989511051989972375059576131720002634196102641761792940772275689964975157244NCBITaxon:22023717NCBITaxon:1703612201999857050617476792745062724915961533355418400524643213686150596866629417347515363291018194301086731018557303963558633149286287132161865368595105135260710185687294296110091416333NCBITaxon:619184023210007348824187878645159812863577553470951451225786260704NCBITaxon:1335626260705260707658457405416233150561007133705654195NCBITaxon:3055504457913998781681928752829126806315327341478281055524NCBITaxon:9606469008150251930283672859300852NCBITaxon:56938268830640179469915101184991515482428381116041937047592723708281677285035158199011951953267386370249240536088385816224888175626158355837153337605726711935019980861193502167879371137127240719065037145712562745757270903113335503728142433747924910078711082NCBITaxon:961559463318586260799141262200298492670NCBITaxon:1263719281249212528303856838569591169266100658123756127504542666255151978837503600941293497905435247214012576499085151514389923745374744544641524323592887051580595536157932716029385114978633892894535936479437NCBITaxon:68544127542251171590109013416738715895521012966103061296715851584515849376593934327159100226376733889423451287689467041464792936576164280342164133159928038280353690910891768946218121410803481793922878892950271131174934681922732189038210760124719040072711431140206411981087135547743658142450722953379698204232124223129163218033470871453720916457331575469928777020206032811431933829355083329129221148725264999728303572710379085507176299707678926837041521405329412816078395639242273775962073220865955516936053307972551811354915974953502611595561432138406072587814144715094933491949634016143347936046316461046603815184547448500356709747751240174841833572042746076994688103762014887289093164358500713894649408941442423277422140921157781154756929793244704749906604162103591905158114452749907312989913112273170187103589915NCBITaxon:37296103609833418710491130798133679531640729946710340157863033373306383011306413992530642363650595478854698134317103372994044586207340115357111952965261174553111471613386541313166343055213231201798360253237993512993850573163176426197940115134584457726787286232193348621160791392227983516811961255228149539322116761757312108077213487999948861814084341033519963218496209913924882097209620953304393755699286266447NCBITaxon:2697049339862436941103121958832050920290610997586448643249952529724634389427863789426256737863912334355141998349317998686554055343529148654514712454661042986357124679151641358884019373345087718238039129039129529719748693102868899951337310548771251632138985076255470119380625631886571303443516558658862238NCBITaxon:44664946454636493NCBITaxon:11071142800628835649114151678458810874391459438543311167810778543144080439334NCBITaxon:1108295346939773821899318226900351283871459531168853399668695954186942003089544869724436620665639545300558623355180426430869220030228481242642815047514991051029910298414452386262903195418351208955749743117008930621864419306157558413101653823525577223994636010636010439947544404237610212790568813377518236355721162296298176771870931281105023824518557966946543186320518240974417394493235124501288531838891988531911137825591037164735166012615572283313NCBITaxon:101142845031631198573859523343237956026087121346395984275295952664373343232235443142752422430814336195931334565943274169963112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