Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/peptides_DNApd_ZBTB2_KO_ESC.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/proteinGroups_GFPpd_ESC_NPC.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/peptides_DNApd_ESC_NPC.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/proteinGroups_DNApd_ZBTB2_KO_ESC.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/proteinGroups_DNApd_ESC_NPC.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/peptides_GFPpd_ESC_NPC.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20161208_Fusion1_SA_IK_DNApd_region5_NPC_dimethyl_Reverse.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20161208_Fusion1_SA_IK_DNApd_region5_NPC_dimethyl_Forward.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160727_Fusion1_SA_IK_GFPpd_NPC_Zbtb2_nonGFP_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160311_Q1_QC_InKa_GFPpulldown_Zbtb2_BAC_IB10_nonGFP_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160311_Q1_QC_InKa_GFPpulldown_Zbtb2_BAC_IB10_GFP_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160727_Fusion1_SA_IK_GFPpd_NPC_Zbtb2_GFP_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20170203_Fusion1_SA_IK_DNApd_region5_Zbtb2_KO_ESC_dimethyl_Reverse.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160727_Fusion1_SA_IK_GFPpd_NPC_Zbtb2_nonGFP_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160311_Q1_QC_InKa_GFPpulldown_Zbtb2_BAC_IB10_GFP_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160727_Fusion1_SA_IK_GFPpd_NPC_Zbtb2_GFP_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20161208_Fusion1_SA_IK_DNApd_region5_ESC_dimethyl_Forward.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20161208_Fusion1_SA_IK_DNApd_region5_ESC_dimethyl_Reverse.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160727_Fusion1_SA_IK_GFPpd_NPC_Zbtb2_nonGFP_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20170203_Fusion1_SA_IK_DNApd_region5_Zbtb2_KO_ESC_dimethyl_Forward.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160311_Q1_QC_InKa_GFPpulldown_Zbtb2_BAC_IB10_nonGFP_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160311_Q1_QC_InKa_GFPpulldown_Zbtb2_BAC_IB10_GFP_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160727_Fusion1_SA_IK_GFPpd_NPC_Zbtb2_GFP_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD007099/20160311_Q1_QC_InKa_GFPpulldown_Zbtb2_BAC_IB10_nonGFP_1.rawprimaryOK200002570Michiel.Vermeulen@science.ru.nlIno KaremakerAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryNot availableNpcEscMouseZbtb2http://www.ebi.ac.uk/pride/archive/projects/PXD007099Cell CultureProteins were on-bead digested with trypsin, after which tryptic peptides were purified on C18-StageTips (Rappsilber et al. 2003). Samples from DNA pull-downs were labelled by on-StageTip dimethyl labelling, in which StageTips were loaded with 300 μl labelling buffer (2% of either CH2O (light) or CD2O (medium) in 10mM NaH2PO4, 35mM Na2HPO4, 0.6M NaBH3CN) and centrifuged. Tryptic peptides were eluted from Stage-Tips. For dimethyl labelled samples, the respective light and medium labelled samples were combined into a forward and a reverse reaction. Peptides were then separated on an Easy-nLC 1000 (Thermo) connected online to an LTQ-Orbitrap Fusion Tribrid mass spectrometer (Thermo) or an LTQ-Orbitrap Q-Exactive mass spectrometer (Thermo), using a gradient of acetonitrile (7%-32% or 5%-30%, respectively), followed by washes at 50% then 90% acetonitrile, for 140 min or 120 min of total data collection. For samples measured on the Fusion, scans were collected in data-dependent top-speed mode of a 3 second cycle with dynamic exclusion set at 60 sec. For samples measured on the Q-Exactive, the top ten most intense precursor ions were selected for fragmentation.PrideNot availableNo PTMs are included in the datasetPeptides were searched against the UniProt mouse proteome (release 2015_12) with MaxQuant v1.5.1.0 (Cox and Mann 2008), using default settings, the appropriate dimethyl labels, and re-quantify and/or match between runs enabled. Data were analysed with Perseus version 1.4.0.0 and in-house R scripts.ProteomicsMultiomicsMichiel VermeulenOrbitrap FusionQ ExactivePARTIALDepartment of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the NetherlandsMus Musculus (mouse)29437775 Karemaker ID, Vermeulen M. ZBTB2 reads unmethylated CpG island promoters and regulates embryonic stem cell differentiation. EMBO Rep. 2018 10.15252/embr.201744993ino.karemaker@uzh.chBiologicalUniversity of ZurichSwitzerlandProteins that bind to DNA depending on its methylation status play an important role in methylation-mediated regulation of gene expression. Using a variety of genomics and proteomics approaches, we identify zinc finger and BTB domain-containing protein 2 (ZBTB2) as a reader of unmethylated DNA in mouse embryonic stem cells. ZBTB2 preferentially binds to CpG island promoters, where it acts as a transcriptional activator. The binding of ZBTB2 to its targets is direct and independent of two other zinc finger proteins, ZBTB25 and ZNF639, which we show to interact with ZBTB2. Our data suggest an anticorrelation between ZBTB2 DNA binding and DNA methylation, indicating that ZBTB2-binding dynamics <i>in vivo</i> are sensitive to differential DNA methylation. ZBTB2 is intricately interwoven with DNA methylation, as we find not only that its binding to DNA is methylation sensitive, but also that ZBTB2 regulates the turnover of methylated DNA In ZBTB2 knockout cells, several pluripotency factors are upregulated, inducing a delay in differentiation. We propose that ZBTB2 is a novel DNA methylation-sensitive transcription factor that regulates cellular differentiation.ZBTB2 reads unmethylated CpG island promoters and regulates embryonic stem cell differentiation.Karemaker Ino D ID, Vermeulen Michiel M[H]C([H])=O, IPP2A2, MeCN, NCMe, ion, fond, Visible Light, CycEI, 5730420M11Rik, peptide, Polypeptides, peptido, Ccne, Method, Methanal, CH3-C#N, hnu, B1, SEC, Min, foton, DmelCG42273, SET, thymus nucleic acid, Divorced, peptides, Data Collection, TAF-I, phosphatase 2A inhibitor I2PP2A, sec, Formaldehyd, Oxomethane, min, mAPC, proteins, Divorces, InChI=1/CH2O/c1-2/h1H2, AI047805, DmelCG4299, reaction, set, IGAAD, DmelCG10574, D1, s, Double-Stranded DNA, stage, deoxyribonucleic acids, DNAn, gamma, phapii, Radiation, Dmel_CG7826, StF-IT-1, Light, Double-Stranded, Cyc E, br37, (Deoxyribonucleotide)n+m, LIGHT, BG:DS07108.3, Dm1, Ionen, desoxyribose nucleic acid, l(2)05206, Dmel_CG7835, Visible Radiations, Mnb, MNB, parent ion, Visible Radiation, HVEML, HLA-DR-associated protein II, Collection Methods, DI-2, I-2Dm, CG4299, inhibitor of granzyme A-activated DNase, AW124434, beta Trypsin, I-2PP1, light quantum, l35Dd, TAF-IBETA, precursor ion, ds DNA, TAF-Ibeta, Polypeptide, Dual Data Collection, DNA, methyl cyanide, Collection Method, i2pp2a, DNS, cycline, InChIKey=WSFSSNUMVMOOMR-UHFFFAOYAT, (Deoxyribonucleotide)n, DmcyclinE, developmental stage, Gene, cycE, precursor, l(2)br37, Deoxyribonucleic acids, CG7826, PHAPII, CYCLE, Buffer, Ly113, cdi7, cyclinE, Deoxyribonucleic Acid, template-activating factor I, Gene Products, CG7835, Cdi7, CDI7, CG42273, light, Data Collection Method, Separated, T6K12_14, iones., CYCE, Dual Data, Lichtquant, DmelCG3938, CyclE, Selb, ipp2a2, beta-Trypsin, 3938, Double Stranded, 2pp2a, Deoxyribonucleic acid, labeling, Visible, DmcycE, ions, CG10574, l(2)k05007, dm-cycE, 2PP2A, taf-ibeta, photon, dSET, dSet, peptidos, (Deoxyribonucleotide)m, TR2, PTHB1, DYRK1, data, Data Collection Methods, bead, 1-(14)C-labeled, 3H-labeled, DNAn+1, Proteins, igaad, acetonitrile, buffer, CD258, Peptide, CH2O, polypeptide, secret agent, l(2)k02514, DmCycE, I-2PP2A, C18, Protein, Dm I-2, I2PP2A, FORMALIN, Dyrk1, CyeE, ds-DNA, Collection, ACETONITRILE, cyanomethane, Methods, T6K12.14, Radiations, AU020952, Separation, l(2)k02602, HVEM-L, Separations, CC1, Photoradiation, l(2)35Dd, Tripcellim, ethanenitrile, Methylene oxide, LTg, ME-IV, Protein Gene Products, Gene Proteins, Trypure, D-CycE, dSET/TAF-Ibeta, 2610030F17Rik, Photoradiations, Oxomethylene, Ion, Data, velocity, data collection, Desoxyribonukleinsaeure, Peptid, AA407739, CG3938ZNF437., Gm1103Coproporphyrinogenase, cox4, peptides, Va, COXIV, Coprogen oxidase, mice, COX IV-1, mouse, tend, total expressed protein, COXA_DROME, Peptide, polypeptide, peptide, Polypeptides, CG10664, CG14724, peptido, Cox4, Mus, VA, data., COX, AL024441, IV, Peptid, peptidos, IV-1, Mouse, 1.3.3.3, Polypeptide, DmelCG14724, house mouse, COX IV, DmelCG10664, COX-VA, Proteomes, Cox4aDNS, (Deoxyribonucleotide)n, Peptidomics, DNAn+1, Proteins, Gene, Gm1103, DNA Methylations, Binding Site, Double-Stranded, Spectrum Analyses, genome methylation maintenance following DNA replication, Spectrum Analysis, Deoxyribonucleic acids, Binding, (Deoxyribonucleotide)n+m, Spectroscopy, DNA methylation maintenance following DNA replication, Zinc Finger Motifs, Deoxyribonucleic Acid, Zinc Finger DNA-Binding Domains, Protein, Sites, Mass, Gene Products, sequence, Analysis, ds-DNA, ZNF437, desoxyribose nucleic acid, Mass Spectrum Analyses, Mass Spectroscopy, Site, Mass Spectrum Analysis, study, Mass Spectrum, DNA methylation maintenance following cell division, thymus nucleic acid, DNA methylation maintenance, Analyses, Deoxyribonucleic acids., ligand, Zinc Finger Motif, Spectrometry, Combining, Double Stranded, Fingers, Deoxyribonucleic acid, proteins, DNA methylation, primary structure of sequence macromolecule, Zinc Finger, Protein Gene Products, Gene Proteins, Combining Site, Finger, ds DNA, Zinc, Desoxyribonukleinsaeure, Zinc Finger DNA Binding Domains, Motifs, Double-Stranded DNA, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, DNAn, Combining Sites, Methylations, Methylation, Motiftranscription factor, T-cell leukemia, Stem Cells, AGL4, protein, DNA Methylations, genome methylation maintenance following DNA replication, dmTAF[[II]]230, protein polypeptide chains, Mouse Embryonic, Kup, KUP, 6230400O18Rik, Roles, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, AA959943, Concepts, protein aggregate, ANC_2H01, thymus nucleic acid, DNA methylation maintenance, ZASC1, TFIID TAF250, cel, Comparative Genomics, F10N7_150, Fingers, proteins, DNA methylation, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, broad-complex, Acts, allergic reaction, Role Concepts, AGAMOUS-like 4, Double-Stranded DNA, zinc ion regulated proximal promoter sequence-specific DNA binding, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, deoxyribonucleic acids, DNAn, TRANSCRIPTION FACTOR, RNA polymerase II distal enhancer sequence-specific binding, Acta-2, close to, RNA polymerase II core promoter proximal region sequence-specific binding, dTAF[[II]]230, Genomics, ZNF46, Comparative, TAF200, Actsk-1, Double-Stranded, Functional Genomics, TAFII-250, TAF250/230, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, Mouse Embryonic Stem Cell, (Deoxyribonucleotide)n+m, and bric-a-brac domain binding, TAFII250, Role Concept, Role, Znf46, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, desoxyribose nucleic acid, F14P3.4, DNA methylation maintenance following cell division, F14P3_4, CG17603, TAF[[II]], Transcription factor, regulation of protein expression, Finger, Taf250, 2810462M08Rik, SR3-5, ds DNA, Cells, hypersensitivity reaction disease, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, DNA, metal ion regulated sequence-specific DNA binding, Methylation, TAF230, metal ion regulated proximal promoter sequence-specific DNA binding, Zfp-50, d230, DNS, (Deoxyribonucleotide)n, Peptidomics, Gene, dTAFII250, Gm1103, SEPALLATA 2, protein-containing complex, Zfp50, EfW1, Deoxyribonucleic acids, regulation of gene product expression, Zinc Finger Motifs, Structural, zinc ion regulated core promoter proximal region sequence-specific DNA binding, Deoxyribonucleic Acid, polypeptide chain, dmTAF1, sensitive, Taf230, Gene Products, Functional, sequence-specific DNA binding, ZNF437, sensitivity, TAF250, Taf200, dTAF[[II]]250, cell, Zinc Finger Motif, ligand, copper ion regulated core promoter proximal region sequence-specific binding., plasmid binding, Double Stranded, Taf1p, Deoxyribonucleic acid, dTAF250, microtubule/chromatin interaction, RNA polymerase II proximal promoter sequence-specific DNA binding, copper ion regulated proximal promoter sequence-specific DNA binding, Zinc, Zinc Finger DNA Binding Domains, Motifs, Mouse Embryonic Stem, hypersensitivity reaction, (Deoxyribonucleotide)m, TAF, Methylations, tramtrack, data, TAF[[II]]250, structure-specific DNA binding, mESCs, protein complex, DNAn+1, Proteins, l(3)84Ab, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, BG:DS00004.13, BTB domain, Znf639, Cell, Concept, dTAF230, near to, DNA methylation maintenance following DNA replication, transcription factor activity, native protein, Zinc Finger DNA-Binding Domains, natural protein, p230, Protein, structure specific DNA binding, TAF[[II]]250/230, RNA polymerase II transcription factor activity, TFIID, gene regulation, methylation, ds-DNA, ANC-2H01, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, KNOTTED1-like homeobox gene 5, AI842128, Taf[[II]]250, hypersensitivity, hypersensitive, TAF[[II]]230, 2900064P18Rik, C14orf51, TAF[II]250, sequence-specific DNA binding RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding, Zinc Finger, F10N7.150, Protein Gene Products, Gene Proteins, DmelCG17603, approaches, vicinity of, Desoxyribonukleinsaeure, Structural Genomics, mESC, Motif, TAF1, sequence-specific transcription regulatory region DNA binding(Deoxyribonucleotide)n+m, thymus nucleic acid, DNS, Deoxyribonucleic Acid, (Deoxyribonucleotide)n, Deoxyribonucleic acids., DNAn+1, ds DNA, Desoxyribonukleinsaeure, Double-Stranded DNA, Double Stranded, (Deoxyribonucleotide)m, Gm1103, DNA, deoxyribonucleic acids, Deoxyribonucleic acid, DNAn, ds-DNA, Double-Stranded, ZNF437, desoxyribose nucleic acid257trueZBTB2 as a novel reader for unmethylated DNAIn this study, we investigated the dynamics during differentiation of the in vivo binding sites of ZBTB2, a putative reader for unmethylated DNA. We performed DNA pull-downs followed by mass spectrometry, using a genomic sequence containing either unmethylated or methylated CpGs, to study the influence of DNA methylation on ZBTB2 binding. Additionally, we performed interaction proteomics to identify ZBTB2 interaction partners. We found that ZBTB2 recruits a zinc finger module of three proteins to unmethylated 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