Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD047987/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD047987/20220812_E3_RSLC1_Hofbauer_Stark_IMP_ID864_onbead_dig_20per_sample_8_CG11247-TurboID_rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD047987/20220812_E3_RSLC1_Hofbauer_Stark_IMP_ID864_onbead_dig_20per_control_1_GFP-TurboID_rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD047987/20220812_E3_RSLC1_Hofbauer_Stark_IMP_ID864_onbead_dig_20per_control_2_GFP-TurboID_rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD047987/20220812_E3_RSLC1_Hofbauer_Stark_IMP_ID864_onbead_dig_20per_sample_9_CG11247-TurboID_rep3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD047987/20220812_E3_RSLC1_Hofbauer_Stark_IMP_ID864_onbead_dig_20per_sample_7_CG11247-TurboID_rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD047987/20220812_E3_RSLC1_Hofbauer_Stark_IMP_ID864_onbead_dig_20per_control_3_GFP-TurboID_rep3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD047987/20220812_E3_RSLC1_Hofbauer_Stark_IMP_ID864_onbead_dig_20per_4x3runs_Flybase_Step2_Limma.pdResultprimaryOK200alexander.stark@imp.ac.atRichard ImreMass SpectrometryBottom-up proteomicsData-independent acquisitionLc-msmsSchneider s2 cellsTurboidProximity labelingCg11247https://www.ebi.ac.uk/pride/archive/projects/PXD047987Schneider-2 CellNearly confluent Schneider S2 cells expressing CG11247-TurboID or control GFP-TurboID fusion proteins were cultured separately in three biological replicates with 500μM biotin (Merck) for 2h at 27°C. Nuclei from approximately 200 million cells were isolated by hypotonic swelling and cell lysis as described previously (Serebreni L. et al., EMBO J. 2023 15;42(10):e113519, TFIIA immunoprecipitation section). After pelleting, nuclei were disrupted in lysis buffer (50mM Tris pH 7.5, 150mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% Triton X-100, 1mM DTT, cOmplete Protease Inhibitor (Roche)) for 1h at 4°C. Nuclear lysate was cleared by centrifugation at 18000 g for 10 min. Biotinylated proteins in the nuclear lysate were precipitated overnight at 4°C with 100ul Pierce Streptavidin Magnetic Beads (ThermoFisher) per sample. Beads were subsequently washed once in lysis buffer, followed by 2% SDS (at room temperature), wash buffer 1 (50mM HEPES pH 7.5, 500mM NaCl, 1mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100) and wash buffer 2 (10mM Tris pH 7.5, 250mM LiCl, 1mM EDTA, 0.5% sodium deoxycholate, 1% NP-40) and finally five times in non-detergent washing buffer (20mM Tris pH 7.5, 137mM NaCl), each wash lasting 5-10 min. Protein sample preparation for nano LC-MS/MS analysis was performed as described in Klaus L. et al., EMBO J. 2023 Feb 1;42(3):e112100.PrideNot availableFor peptide identification, the RAW files were loaded into Proteome Discoverer (version 2.5.0.400, Thermo Scientific). All MS/MS spectra were searched using MSAmanda v2.0.0.19924 (Dorfer V. et al., J. Proteome Res. 2014 Aug 1;13(8):3679-84). The peptide and fragment mass tolerance was set to ±10 ppm, and the maximal number of missed cleavages was set to 2, using tryptic enzymatic specificity without proline restriction. Peptide and protein identification was performed in two steps. For an initial search, the RAW files were searched against the database dmel‐all‐translation‐r6.44.fasta (Flybase.org, 22,232 sequences; 20,321,723 residues), supplemented with common contaminants and sequences of tagged proteins of interest, using the following search parameters: beta‐methylthiolation of cysteine was set as a fixed modification, oxidation of methionine as variable modification. The result was filtered to 1 % FDR on protein using the Percolator algorithm (Käll L. et al., Nat Methods. 2007 Nov;4(11):923-5.) integrated into Proteome Discoverer. A subdatabase of proteins identified in this search was generated for further processing. For the second search, the RAW files were searched against the created subdatabase using the same settings as above plus considering additional variable modifications: Phosphorylation on serine, threonine, and tyrosine, deamidation on asparagine and glutamine, and glutamine to pyro‐glutamate conversion at peptide N‐terminal glutamine, and acetylation on protein N‐terminus were set as variable modifications. The localization of the post‐translational modification sites within the peptides was performed with the tool ptmRS, based on the tool phosphoRS (Taus T. et al., J. Proteome Res. 2011, 10, 5354-62). Identifications were filtered again to 1 % FDR on protein and PSM level; additionally, an Amanda score cutoff of at least 150 was applied. Peptides were subjected to label‐free quantification using IMP‐apQuant (Doblmann J. et al., J. Proteome Res. 2019, 18(1):535-541). Proteins were quantified by summing unique and razor peptides or only unique peptides and applying intensity‐based absolute quantification (iBAQ; Schwanhäusser B. et al., Nature. 2011 May 19;473(7347):337-42). Proteins were filtered to be identified by a minimum of three quantified peptides in at least one sample. Protein‐abundances‐normalization was done using sum normalization. Statistical significance of differential protein abundance was determined using limma (Smyth G.K. et al., Stat Appl Genet Mol Biol. 2004;3:Article3).ProteomicsAlexander StarkResearch Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, AustriaPARTIALDrosophila Melanogaster (fruit Fly)10.1016/J.MOLCEL.2024.10.041richard.imre@imba.oeaw.ac.atIMBA ViennaAustriaDinitrilotetraacetate, Ethylenedinitrilotetraacetic Acid, Product, chlorure de lithium, Laundry Pods, Potassium EDTA, Octoxinols, Triton X305, Syndet, SDH, TFIIA-42, Deoxycholic Acid, Strepavidin, prevention, Dicobalt, SCHNEIDER S2 Cell, SDS, Edetic, Biotin, Biological, Protease Inhibitor, 1, CG5930, 3, Biological Product, Disodium Salt, Octoxynol-9, Biologic Drugs, Glycine, DmelCG13176, N, cis-Hexahydro-2-oxo-1H-thieno(3, Salt, chemical analysis., ORF19, Edetate, AI047805, salt, Biological Medicine, Peptidohydrolase Inhibitor, sample, 3beta-Isomer, Medicine, 2-Ethanediylbis(N-(carboxymethyl)glycine), autolysin activity, Precipitations, Biologic Drug, Gallium EDTA, Magnesium (2:1) Salt, Octylphenoxy Polyethoxyethanol, RNA Polymerase II, LC-MS2, Detergent Pod, preventive therapy, Biologic Products, Rombellin, Dipotassium Salt, Triton X100, (3aS-(3aalpha, common salt, Tf2a, Dihydroxycholanoic Acid, Dm1, Hydrolase Inhibitor, Magnesium Salt, Laundry Detergent Pod, Cleansing Agents, 1110049F14Rik, Chromium EDTA, Detergent Pods, 5beta, 1H-Thieno(3, Acid, Antagonists, Biological Medicines, Biological Drug, TF2A1, TF2A2, Shwachman-Diamond type metaphyseal dysplasia, Biologics, Shwachman syndrome, N'-1, lithii chloridum, 12beta-Isomer Deoxycholic Acid, Sodium Salt, 5alpha-Isomer, liquid chromatography-tandem mass spectroscopy, bacteriolytic toxin activity, 3-tetramethylbutyl)phenyl)-omega-hydroxy-, Endopeptidase, Peptide Peptidohydrolase Inhibitor, Edetate Disodium Calcium, SL2, Disodium Versenate, D-(+)-biotin, Biokur, Polyethoxyethanol, Ethylenediaminetetraacetic Acid, Lithiumchlorid, 5alpha Isomer, F10B6_15, Gallium, Deacura, Biologic Pharmaceuticals, Endopeptidase Inhibitors, Medebiotin, Pierce, Ethylenediaminetetraacetic, Kern, protein-containing complex, 2-ethanediyl), F10B6.15, CG7826, Agent, Magnesium Disodium, 12-dihydroxy-, Triton X 305, LC-MSMS, Gene Products, Immune Precipitations, CG7835, CG42273, Peptide Hydrolase, 12alpha)-, nucleo atomico, Gelfert, Immune Precipitation, Biologicals, Synthetic, Biotin Hermes, 12beta Isomer, Schneider 2, FAM39E, Monosodium Salt, 3beta Isomer, 4733401P19Rik, alpha-(4-(1, Antagonist, Laundry Detergent, Tetracemate, 4-d]imidazole-4-valeric acid, Triton X45, Protease Antagonists, Stannous EDTA, congenital lipomatosis of pancreas, Kochsalz, Kybella, Peptide Peptidohydrolase Inhibitors, Choleic Acid, 4-(2-hydroxyethyl)-, Biologic, Potassium, Pharmaceuticals, Products, Biologic Medicines, 5alpha-Isomer Deoxycholic Acid, Proteins, Octoxinol, Stannous, Roche, Igepal CA-630, Coprin, buffer, Copper, Cell, Versene, Triton X 100, Wash2, Wash1, Temperatures, native protein, Natriumchlorid, Biopharmaceutical, 3beta-Isomer Deoxycholic Acid, Sodium, SL2 cell, NaCl, Edathamil, AU020952, Calcium, holin, Gabunat, prophylaxis, Ethylene Dinitrilotetraacetate, Magnetic, SWDS, Shwachman-Bodian-Diamond syndrome, Monopotassium Salt, Peptidohydrolase Inhibitors, 4)imidazole-4-valeric acid, CT18631, Magnesium Disodium EDTA, ME-IV, Gene Proteins, Peptidase, Antiprotease, control, Pancreatic insufficiency and bone marrow dysfunction, Disodium Ethylene Dinitrilotetraacetate, cloruro de litio, Nonidet P-40, TFIIAL, Schneider's Line S2 cell, liquid chromatography tandem mass spectrometry, Peptide Hydrolase Inhibitors, tfiia-l, Calcium Salt, liquid chromatography tandem mass spectroscopy, Co-Immunoprecipitations, Triton X-45, Endopeptidase Inhibitor, vitamin B7, determination, Synthetic Detergents, Triton X-305, Peptide Hydrolase Inhibitor, HEPES Monosodium Salt, Ethylenedinitrilotetraacetic, protein, NP-40, Calcium Disodium, Atomkern, Poly(oxy-1, Co Immunoprecipitation, 12beta-Isomer, Detergent, Pod, Synthetic Detergent, halite, Edetic Acid, congenital, Detergents, Octoxynol 9, 6aR)-Hexahydro-2-oxo-1H-thieno[3, Inhibitors, Min, protein aggregate, Hydrolase Inhibitors, prevention and control, DmelCG42273, Calcium Tetacine, HEPES Monosodium, nucleus atomi, Edetates, LCMSMS, reference sample, TFIIA-L, Natural, (3aS, Co-Immunoprecipitation, biotina, Precipitation, min, mAPC, biotine, Biological Drugs, lipomatosis of pancreas, Calcitetracemate, preventive measures, cloruro sodico, Calcium Disodium Versenate, Immune, Non-Idet P-40, Hermes, Disodium Calcitetracemate, SOLO DANCERS, 1-Piperazineethanesulfonic acid, HsT18745, Shwachman-Bodian syndrome, Tetacine, Schneider, Medicines, necrosis, biotinum, Medobiotin, rock salt, DmelCG5930, Calcium Disodium Edetate, TX-144 surfactant, Peptidase Inhibitor, ORF 3617, LC-MS/MS, Dmel_CG7826, AI836084, Peptide Peptidohydrolase, 4S, 4-d)imidazole-4-pentanoic acid, Triton X-100, Versenate, Biopharmaceuticals, Distannous EDTA, Biologic Product, Biotin Ratiopharm, bacteriocin activity, WASH, 4-d)imidazoline-4-valeric acid, Copper EDTA, Dmel_CG7835, Triton X-114, D-Biotin, Mnb, MNB, LiCl, Biotine Roche, Distannous, Pods, Xylella fastidiosa str. Temecula1, AW124434, natrii chloridum, lysin activity, Peptidase Inhibitors, Agents, dTFIIA, Antiproteases, cis-(+)-Tetrahydro-2-oxothieno[3, HEPES, 2-ethanediylbis(N-(carboxymethyl))-, S-2 cell, Schneider cell, Inhibitor, Cholan-24-oic acid, 4-d]imidazol-4-yl)pentanoic acid, noyau atomique, SCHNEIDER-2 cell, Laundry Detergent Pods, Biotine, Lagodeoxycholic Acid, Gene, Protease, DmelCG11247, Vitamin H, LC-MS-MS, Buffer, Potassium Salt, potassium salt, Octoxynols, Octylphenoxy, Transcription Factor A, p63, 4beta, p65, Sodium Deoxycholate, Protease Antagonist, 6aalpha))-, Drugs, nuclei, Ethylene, Coenzyme R, S2 cell, nucleo, noyau, Natural Product, chlorure de sodium, Desoxycholic Acid, Xylella fastidiosa (strain Temecula1 / ATCC 700964), lysate, Chromium Salt, Octylphenoxypolyethoxyethanols, nucleus, (+)-cis-Hexahydro-2-oxo-1H-thieno[3, EDTA, Laundry Pod, N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, Dicobalt EDTA, Disodium EDTA, Controlled, Laundry, Monoammonium Salt, Controlling, DYRK1, protein complex, Biotin Gelfert, Deoxycholate, 5-(2-oxohexahydro-1H-thieno[3, 4]imidazole-4-valeric acid, Peptide, TfIIa, RCB1153, LC/MS/MS, cis-Tetrahydro-2-oxothieno(3, 4]imidazoline-4-valeric acid, biotin, Protein, TFIIA, table salt, Dyrk1, (3alpha, Disodium Ethylene, Biodermatin, CG13176, Cleansing, Biotin-Ratiopharm, Chelaton 3, Triton X 45, Dihydrate, CC1, hexahydro-2-oxo-, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, Disodium, CGI-97, sample population, Protein Gene Products, Drug, Cleansing Agent, Natural Products, assay, Chromiumnuclear chromatin, Delayed, cytoplasmic chromatin, False Memory, Memory, Repressed, Psychology Repression, False Memory Syndrome, Genomes, Delayed Memories, False, Repression, Delayed., Repressed Memory, chromosome scaffold, Syndrome, Delayed Memory, whole genome, Memory Syndrome, Chromatins, False Memory Syndromes, Memoriespara Tyrosine, Raw, AUTSX5, Irip, NOVH, NAALAdase, phosphorylation, 2-Amino-3-hydroxypropionic acid, 5730420M11Rik, Polypeptides, NAALADase I, FOLH, Method, L-Proline, B1, l(2)SH1330, 2, L-2-aminoglutaramic acid, C530001K22Rik, 2-amino-3-mercaptopropanoic acid, establishment and maintenance of substrate location, WMS, Threonin, DL-Asparagine, somitogenic mesoderm, SET, C, asparagina, Membrane glutamate carboxypeptidase, M, DmSTAT, N, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, L-Asparagine, P, Q, procedures, Y, Dstat 92E, (2S)-pyrrolidine-2-carboxylic acid, PROLINE, DmelCG4299, set, sample, s, Half Cystine, NOVh, SGS, Glutamin, NK/GPI, Gpi, D-stat, Zinc Cysteinate, unsegmented mesenchyme, DL-Proline, acetylation, pSTAT, D-STAT, para-Tyrosine, Procedure, 2-(acetylamino)-2-deoxy-, SH2-B PH domain-containing signaling mediator 1, Fsrg1, ACMICD, GIG27, RING3, l(2)br3, Algorithm, FSRG1, Methionin, NK|GPI, Hmet, (2R)-2-amino-3-sulfanylpropanoic acid, Stat92, l(2)SH2 1330., Plxn1, HLA-DR-associated protein II, DI-2, I-2Dm, FGCP, STAT92E, Methodological, (-)-proline, 2-amino-3-carbamoylpropanoic acid, (S)-2, mKIAA4053, L isomer, I-2PP1, Pro-rich, DmelCG4257, TAF-IBETA, (5Z, TAF-Ibeta, PLXN1, L-Tyrosine, D-Stat, Liquimeth, L-pyrrolidine-2-carboxylic acid, Fsrg-1, Bglap-rs1, establishment and maintenance of cellular component location, NAT, Nat, GLUTAMINE, 2-amino-4-(methylsulfanyl)butanoic acid, D17H6S113E, SD-stat, dstat, dSTAT, L-Zystein, Levoglutamide, Hasp, alpha-L-N-acetyltalosaminuronic acid, protein-containing complex, FSH, DmelCG4482, Glutaminsaeure-5-amid, pyrrolidine-2-carboxylic acid, Gene Products, Pgi, Half-Cystine, 2-Aminoglutaramic acid, dSTAT92E, Technique, Hpro, Gpi-1r, Gpi-1s, L Cysteine, (2S)-2, E-920, Phi, Gpi-1t, 2pp2a, Hcys, IGFBP9, CG10574, Study, Kiaa4053, 2PP2A, 2-amino-4-(methylthio)butanoic acid, CYSTEINE, L Proline, dSET, dSet, FREE CYSTEINE, peptidos, Tyrosin, (2R)-2-amino-3-mercaptopropanoic acid, metionina, l(3)j6C8, stat[92E], CG4482, prolina, DRODSRC, Proteins, Phosphorylations, KIAA1428, MF, L-Isomer, Amf, polypeptide, Serin, STAT 92E, native protein, I-2PP2A, tirosina, AW228947, Dm I-2, proline, Glutamic acid 5-amide, MFS1, segmental plate, Mopsm, Sh2bpsm1, NK, Met, dSTAT92E/marelle, Col4a-1, ensemble, Glutamic acid amide, Specificity, (R)-2-amino-3-mercaptopropanoic acid, 4-diamino-4-oxobutanoic acid, 2-Amino-3-mercaptopropionic acid, Stat1alpha-like, Folate hydrolase 1, Gene Proteins, br3, localisation, EG:95B7.8, E920, 2600013D04Rik, NIP, alpha-L-2-N-acetylamino-2-desoxytaluronic acid, SH2-Bb, Bru, IPP2A2, 11alpha, E 920, TalANAc, Dstat92E, 232, nip, L-Threonine, protein, Prolin, CCN3, QM, L-(+)-glutamine, peptide, L-Isomer Methionine, Techniques, Methionine, L-Glutaminsaeure-5-amid, DIP13A, peptido, Cystein, 3.4.17.21, protein aggregate, Gpi-1, fs(1)M104, Svc, SH2-B, appl, peptides, TAF-I, Nlk, cisteina, D-Glutamine, CG4257, Stat, 35Bb, NAALAD1, ASN, Asn, Folylpoly-gamma-glutamate carboxypeptidase, IBP-9, stat, IGAAD, 13E, Methodological Studies, 2-amino-3-hydroxypropanoic acid, DmelCG10574, Tyr, STAT, APPL, dip13alpha, GPHYSD2, Racemethionine, l(3)06346, phapii, establishment and maintenance of substance location, 2-Amino-4-(methylthio)butyric acid, 2-Amino-3-(p-hydroxyphenyl)propionic acid, StF-IT-1, Thermo Scientific, Cys, Tyrosine, stat92, single organism localization, l35Bb, mOC-X, 3-Hydroxyalanine, PSM, Psm, NOV, Prostate-specific membrane antigen, presumptive somite mesoderm, PlexA1, L Glutamine, Hgln, Org, ORG, Pteroylpoly-gamma-glutamate carboxypeptidase, prolinum, MS/MS, L-isomer, Gpi1-r, nov, Gpi1-s, L-Cysteine, MASS, CG4299, 15S)-, (S)-pyrrolidine-2-carboxylic acid, Gpi1-t, Methodological Study, fs(1)Y[b], L-Cystein, L-glutamic acid gamma-amide, Specificity and Sensitivity, C130088N23Rik, PSMA, L Serine, Polypeptide, BG:DS01219.1, DXS648E, L-Serine, i2pp2a, Proteomes, Gpi1s, SH2 domain-containing protein 1B, Cysteine Hydrochloride, alpha-L-Talopyranuronic acid, Procedures, YB, (-)-(S)-proline, AI461847, mol, 5-diamino-5-oxopentanoic acid, L-alpha-pyrrolidinecarboxylic acid, unsegmented paraxial mesoderm, L Isomer, FBN, Gene, (2S)-2-amino-4-carbamoylbutanoic acid, somitomeric mesoderm, GCPII, PHAPII, DSRC, Yb, ECTOL1, Studies, establishment and maintenance of position, L-Methionine, N-acetylated-alpha-linked acidic dipeptidase I, mKIAA1299, Del(8)44H, CG2706, Pedameth, l(2)br23, SH2B, mrL, MS2, ipp2a2, 2-Pyrrolidinecarboxylic acid, Acetylations, mGCP, Ring3, L Threonine, d-STAT, OCTD, Asparagin, (S)-2-pyrrolidinecarboxylic acid, mrl, L Tyrosine, taf-ibeta, L10, Dstat, Sensitivity, L-Glutamine, stat92e, (S)-2-carboxypyrrolidine, DSTAT, DL-Methionine, protein complex, DmelCG2706, igaad, l(2)35Bb, total expressed protein, DXS648, stat92E, L-2-Aminoglutaramic acid, Peptide, group, GCP2, Glutamate carboxypeptidase II, Cell growth-inhibiting gene 27 protein, IGFBP-9, Protein, I2PP2A, establishment and maintenance of localization, DIP13alpha, mKIAA4005, techniques, L-Glutamin, mrl stat92E, tandem MS, Zystein, WMS2, Data Base, D6S113E, PH and SH2 domain-containing signaling mediator, (-)-2-pyrrolidinecarboxylic acid, L-Prolin, 2-amino-3-sulfanylpropanoic acid, RNF3, Rnf3, Frg-1, L-2-Amino-3-mercaptopropionic acid, single-organism localization, CG15268, sample population, D-stat/stat92E, Protein Gene Products, dSET/TAF-Ibeta, 2-amino-4-carbamoylbutanoic acid, 2610030F17Rik, D Glutamine, glutamic acid gamma-amide, SSKS, AI425885, alpha-amino-gamma-methylmercaptobutyric acid, Peptid, L-(-)-proline, AA407739, methodologyfruit fly, Materials, postnatal development, metazoans, growth and development, Nuclear Receptor, 2610511A05Rik, melanogaster, element, BB234005, ter, dmTAF[[II]]230, Readability, DSmurf, Tier, D17Ertd710e, animal, Chromatins, Animalia, thymus nucleic acid, TFIID TAF250, Genomes, cel, FATE, Receptor Co-Repressors, methylase, Futurology, inhibition of homeostatic process, Nuclear Hormone Receptor Co-Repressor, Co Repressor Proteins, Smurf, Bsg75C, chromosome scaffold, Co Repressors, Protein G18, Double-Stranded DNA, deoxyribonucleic acids, DNAn, transcription from bacterial-type RNA polymerase promoter, CG4943, Receptor Corepressor, Nuclear Receptor Co Repressor, D-smurf, Predictions and Projections, nuclear chromatin, dTAF[[II]]230, animalia, TAF200, Double-Stranded, Lack, TAFII-250, TAF250/230, GAT8, Receptor Co-Repressor, (Deoxyribonucleotide)n+m, KMT1C, organism, TAFII250, Nuclear Receptor Corepressor, Term, Cis, CIS, G18, CT43, Genetic Materials, atomo, C6orf30, desoxyribose nucleic acid, atome, Genetic Material, CIS-1, Corepressors, Element, Factors, whole organism, DmelCG4943, Nuclear Hormone Receptor Co Repressor, atoms, 9030605P22Rik, INSDC_feature:gene, whole genome, CG17603, TAF[[II]], Nuclear Receptor Co Repressors, Co-Repressor Protein, Drosophila, Taf250, Material, SR3-5, bacterial transcription, ds DNA, Koerper, Cistron, DNA, Bat8, TAF230, BAT8, LOT1, cytoplasmic chromatin, d230, multi-cellular organism, DNS, (Deoxyribonucleotide)n, dSmurf1, Gene, dTAFII250, Sophophora melanogaster, DmelCG11247, animals, Transcription Factor, EfW1, Deoxyribonucleic acids, Deoxyribonucleic Acid, dmTAF1, Taf230, Drosophila melangaster, Nuclear Hormone Receptor Co Repressors, Projections and Predictions, Animal, Catalogs, TAF250, Genomes., Corepressor Protein, study, Transcription, Taf200, dTAF[[II]]250, Genetic, cell, ligand, Nuclear Receptor Co-Repressors, Double Stranded, Taf1p, Deoxyribonucleic acid, metazoa, Nuclear Receptor Corepressors, Nuclear Hormone Receptor Co-Repressors, dTAF250, DmelCG4216, d-smurf, (Deoxyribonucleotide)m, methyltransferase activity, elements, TAF, BACTS2, atom, Autoregulation, Co Repressor, ahl4, TAF[[II]]250, body, DNAn+1, l(3)84Ab, whole body, Factor, BG:DS00004.13, Dsmurf, Corepressor Proteins, Cistrons, D. melanogaster, ZAC1, Cell, dTAF230, development, dSmurf, p230, Smurf ubiquitin ligase, Nuclear Receptor Co-Repressor, Metazoa, Protein, G9A, TAF[[II]]250/230, TFIID, atomus, Nuclear, ds-DNA, INSDC_feature:regulatory, Taf[[II]]250, TAF[[II]]230, Corepressor, Co Repressor Protein, G9a, postnatal growth, CG4216, TAF[II]250, Ng36, Understanding, multicellular animals, activation of homeostatic process, DmelCG17603, Co-Repressor, SOCS, Drosophila melanogasters, Desoxyribonukleinsaeure, NG36, Suppressor of cytokine signaling, Co-Repressors, Future, growth, ZAC, TAF1falseA genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repressionDifferential gene transcription enables development and homeostasis in all animals and is regulated by two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers. While enhancers have been thoroughly characterized, the properties and mechansisms of silencers remain largely unknown. By an unbiased genome-wide functional screen in Drosophila melanogaster S2 cells, we discover a class of silencers that bind one of three transcription factors (TFs) and are generally not included in chromatin-defined CRE catalogs, as they mostly lack detectable DNA accessibility. The silencer-binding TF CG11247, which we term Saft, safeguards cell fate decisions in vivo and functions via a highly-conserved domain we term ZAC and the corepressor G9a, independently of G9a’s H3K9-methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanisms has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.2024-11-132023-12-20PXD047987NEWT:330879NEWT:377960NEWT:1131NEWT:35795NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NEWT:1334565NEWT:625351NEWT:258594NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:247480NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:2315688NEWT:592321NEWT:1073882NEWT:6819NEWT:112509NEWT:475174NEWT:111205NEWT:1599NEWT:428386NEWT:1117NEWT:498257NEWT:10036NEWT:32264NEWT:12215NEWT:1590NEWT:10034NEWT:33114NEWT:1596NEWT:661410NEWT:638632NEWT:224326NEWT:376619NEWT:1748418NCBITaxon:79857NEWT:1096976NEWT:3765NEWT:3767NEWT:1589NEWT:1907535NEWT:135622NEWT:4615NEWT:672127NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:656064NEWT:1582NEWT:3760NEWT:1584NEWT:2086595NEWT:36630NEWT:1585NEWT:383379NEWT:381198NEWT:418106NCBITaxon:12721NEWT:10029NEWT:913645NEWT:2492962NEWT:641809NEWT:1392488NEWT:38815NEWT:317447NEWT:4688NEWT:3357NEWT:111225NEWT:7719NEWT:5530NEWT:868565NEWT:135674NEWT:1562698NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:49928NEWT:3349NEWT:160621NEWT:2502409NEWT:212790NEWT:110368NEWT:55350NEWT:1916073NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:1912919NEWT:410658NEWT:5516NEWT:44688NEWT:44689NEWT:370038NEWT:498211NEWT:345076NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:1310173NEWT:200795NEWT:37919NEWT:2579791NEWT:44685NEWT:161934NEWT:156587NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:260499NEWT:410661NEWT:329854NEWT:1140NCBITaxon:2157NEWT:2066563NEWT:2649329NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:150808NEWT:1182590NEWT:3712NEWT:3711NEWT:3714NCBITaxon:37162NEWT:270643NEWT:3715NEWT:1538NEWT:2065263NEWT:177437NEWT:717966NEWT:10891NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:28174NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:3704NEWT:244366NEWT:1246791NEWT:176597NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:9006NEWT:33548NEWT:52299NEWT:8165NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:926571NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:2714896NEWT:1424507NEWT:1194599NEWT:272844NEWT:1348799NEWT:1608994NEWT:33995NEWT:55784NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2709072NEWT:2499525NEWT:2853422NEWT:1122984NEWT:487NEWT:1538553NEWT:1679718NEWT:480NEWT:67767NEWT:45972NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:294607NEWT:1502NEWT:128017NEWT:2836NEWT:376686NEWT:237610NEWT:95486EFO:0001352NEWT:119562NEWT:1883446NEWT:1233435NEWT:118223NEWT:11757NEWT:987059NEWT:109760NEWT:29031NEWT:317047NEWT:1509NEWT:491NEWT:460523NEWT:45954NEWT:235443NEWT:1579NEWT:1757312NEWT:85694NEWT:109786NEWT:1922344NEWT:108458NEWT:5936NEWT:85692NEWT:321967NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:279010NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:415978NEWT:1255228NEWT:410289NEWT:191701NEWT:373153NEWT:1640278NEWT:9054NEWT:472NEWT:940825NEWT:29459NEWT:529507NEWT:1071661NEWT:28128NEWT:470NEWT:41122NEWT:5911NEWT:1328300NEWT:748693NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:11723NEWT:445NEWT:153009NEWT:261756NEWT:166314NEWT:166313NEWT:63366NEWT:63367NEWT:29488NEWT:215402NEWT:1547NEWT:1290454NEWT:3726NEWT:906914NEWT:81231006NEWT:30455NEWT:28141NEWT:9031NEWT:27292NEWT:1050722NEWT:3728NEWT:108931NEWT:1293497NEWT:1055524NEWT:548NEWT:150475NEWT:267872NEWT:381666NEWT:172269NEWT:9534NEWT:2126348NEWT:5180NEWT:256737NEWT:299467NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:542NEWT:2903NEWT:185579NEWT:872227NEWT:13076NEWT:2587410NEWT:207340NEWT:1006581NEWT:8673NEWT:33940NEWT:2126337NEWT:550NEWT:10804NEWT:33941NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:42410NEWT:36185NEWT:1054211NEWT:1225786NEWT:771870NEWT:51338NEWT:9995NEWT:575412NEWT:28112NEWT:49012NEWT:28110NEWT:6493NEWT:10832NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:64657NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:40697NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:9983NEWT:8655NEWT:5147NEWT:595495NEWT:28108NEWT:28104NEWT:1114957NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:1613NEWT:8247NEWT:8245NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:353153NEWT:227377NEWT:1774284NEWT:27689NEWT:40674NEWT:1194669NEWT:51329NEWT:8236NEWT:74426NEWT:204274NEWT:443906NEWT:13037NEWT:519NEWT:30871NEWT:2510939NEWT:7394NEWT:6063NEWT:8240NEWT:1328388NEWT:105487NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:475932NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:204232NEWT:214053NEWT:28550NEWT:80863NEWT:90675NEWT:52639NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:861109NEWT:8695NEWT:75736NEWT:884204NEWT:510516NEWT:1045775NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:30850NEWT:83906NEWT:99488NEWT:1134506NEWT:25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