ENAGenomicsMultiomicsMichael R. Green, Molecular, Cell and Cancer Biology, University of Massachusetts Medical Schoolhttps://www.ebi.ac.uk/ena/browser/view/PRJNA170540Homo sapiensxref:PubMed:23150797The general transcription factor TFIID is composed of the TATA-box-binding protein (TBP) and approximately 14 TBP-associated factors (TAFs). Here we find, unexpectedly, that undifferentiated human embryonic stem cells (hESCs) contain only six TAFs (TAFs 2, 3, 5, 6, 7 and 11), whereas following differentiation all TAFs are expressed. Directed and global chromatin immunoprecipitation analyses reveal an unprecedented promoter occupancy pattern: most active genes are bound by only TAFs 3 and 5 along with TBP, whereas the remaining active genes are bound by TBP and all six hESC TAFs. Consistent with these results, hESCs contain a previously undescribed complex containing TAFs 2, 6, 7, 11 and TBP. Altering the composition of hESC TAFs, either by depletion of TAFs that are present or ectopic expression of TAFs that are absent, results in misregulation of pluripotency gene expression and induction of differentiation. Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew. ChIP-chip was used in this study to assess the global pattern of TAF recruitment at a gene promoters, to verify the existence of two classes of genes which differentially recruit and use TAF proteins for transcription initiation. Overall design: Comparison of recruitment of 4 TAFs (TAF3, TAF5, TAF7 and TAf11) with the recruitment of TBP and RNA Polymerase II in wild-type H9 embryonic stem cells from replicate experimentsENAphosphoric acid tributyl ester, TAF47, dTAF[[II]]155, dTAFII30beta, PRO214, GTF2D, ChIP-Chip, Chromatin Immuno-precipitation, TAFII100, TAF40, AI115401, CLIP-Seq, Assay for Transposase-Accessible Chromatin Using Sequencing, CG7704, DmelCG4079, RBP, dTAF[[II]]30., dmTAF3, dmTaf5, 140kDa, TAFII28, dmTAF5, TAF2I, Chromatin Immunoprecipitation Sequencing-Chip, 1110038O14Rik, DmTAF3, TAF2F, Gtf2d, TAF2D, TAF[II]80, TBP38, ChIA-PET, Chromatin Immunoprecipitation Sequencing Chip, DmelCG9874, TAF67, Chromatin Immuno precipitation Sequencing, HDL4, TAF[[II]]155, ChIP, dTAF[[II]]30beta, Chromatin Immunoprecipitation Paired End Tag, Chromatin Immuno Precipitation Paired End Tag, SPAC30.12, Cross-Linking and Immunoprecipitation Followed by Deep Sequencing, bip-II, Taf[[II]]80, TFIID 28 beta, dTAFII85, dTAFii80, TBP-associated factor 7, 4933439M23Rik, taf2d, TBP-associated factor 5, Sequencing, d80, taf2f, TAF140, Chromatin Immunoprecipitation Paired-End Tag, Taf2f, TAFII80, TF2D, F21J6.5, TAFII85, SCA17, DNA Dependent RNA Polymerase II, TAFII155, p85, dBIP2, TAF80/85, GTF2D1, ATAC-Seq, Chromatin Immunoprecipitation Sequencing-Chips, AI607308, TAF155, Bip2, BIP2, BB007175, TFIIDtau, TAF, TAF[[II]]80/85, TAF[II]30beta, serum total protein, CG2009, TFIID-p28beta, HITS-CLIP, High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, TAFII140, i31, TAF30b, taf7, taf5, Taf[[II]]30beta, Cross Linking and Immunoprecipitation Followed by Deep Sequencing, TAF80, dTBP, dTbp, tri-(n-butyl )-phosphate, ChIP Sequencing, tafii100, i163, CG4079, 28kDa, ChIP-PET, TAF[[II]]80, TAF[[II]]85, TfIID, ChIP-Exo, taf5l, TBP, taf72, dTAFII3, AW552398, DmelCG7704, 55kDa, F7A10.3, dTAFII30 beta, AW539625, TFIID, AV117817, MGC:15243, High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, TAF[[II]]30beta, AL024207, MGC - 15243, TAFII-140, F7A10_3, dTAF[[II]]80, tbp, tri-n-butyl phosphate, tributylphosphate, DmelCG2009, TAFII55, RNA Pol II, tdf1, tri-n-butylphosphate, Chromatin Immunoprecipitation, Chromatin Immuno-precipitation Sequencing, ChIP Exonuclease, ChIP-Seq, TAF[[II]], Taf30beta, Assay for Transposase Accessible Chromatin Using Sequencing, TFIID 85, TAF11, dTAF5, TAF30beta, dTFIID, Chromatin Immuno-Precipitation Paired-End Tag, TAF90, dtbp, RNA Polymerase B, DNA-Dependent RNA Polymerase II, mTAFII140, CG9874, d30beta, ChIP-Exonuclease, dTAFII30, Taf85, TAF5, Taf80, TAF3, 6330528C20RikHuman, Modern., human being, Man (Taxonomy), Homo sapiens, man, Man, human, Modern ManfalseHomo sapiensChIP-chip from H9 hESCs for RNA Polymerase II, TBP, TAF3, TAF5, TAF7, and TAF112025-09-242014-02-11PRJNA170540GSE39312960623150797