title: Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression.
abstract: Genome-wide distribution of histone H3K18 and H3K27 acetyltransferases, CBP (CREBBP) and p300 (EP300), is used to map enhancers and promoters, but whether these elements functionally require CBP/p300 remains largely uncertain. Here we compared global CBP recruitment with gene expression in wild-type and CBP/p300 double-knockout (dKO) fibroblasts. ChIP-seq using CBP-null cells as a control revealed nearby CBP recruitment for 20% of constitutively-expressed genes, but surprisingly, three-quarters of these genes were unaffected or slightly activated in dKO cells. Computationally defined enhancer-promoter-units (EPUs) having a CBP peak near the enhancer-like element were more predictive, with CBP/p300 deletion attenuating expression of 40% of such constitutively-expressed genes. Examining signal-responsive (Hypoxia Inducible Factor) genes showed that 97% were within 50 kilobases of an inducible CBP peak, and 70% of these required CBP/p300 for full induction. Unexpectedly, most inducible CBP peaks occurred near signal-nonresponsive genes. Finally, single-cell expression analysis revealed additional context dependence where some signal-responsive genes were not uniformly dependent on CBP/p300 in individual cells. While CBP/p300 was needed for full induction of some genes in single-cells, for other genes CBP/p300 increased the probability of maximal expression. Thus, target gene context influences the transcriptional requirement for CBP/p300, possibly by multiple mechanisms.
authors.affiliation: Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA lawryn.kasper@stjude.org.
authors.forename: Lawryn H
authors.initials: LH
authors.lastname: Kasper
authors.affiliation: Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
authors.forename: Chunxu
authors.initials: C
authors.lastname: Qu
authors.affiliation: Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Obenauer
authors.affiliation: Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: McGoldrick
authors.affiliation: Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
authors.forename: Paul K
authors.initials: PK
authors.lastname: Brindle
mesh_terms: D015082:2,2'-Dipyridyl / Q000494:pharmacology; D000818:Animals; D050882:CREB-Binding Protein / Q000235:genetics / Q000378:metabolism*; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D004742:Enhancer Elements, Genetic; D016678:Genome; D051379:Mice; D011401:Promoter Regions, Genetic; D020218:Response Elements; D059010:Single-Cell Analysis; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D015533:Transcriptional Activation; D050880:p300-CBP Transcription Factors / Q000235:genetics / Q000378:metabolism; D000099224:p300-CBP-Associated Factor
chemical_list: D015082:2,2'-Dipyridyl; D050882:CREB-Binding Protein; D050880:p300-CBP Transcription Factors; D000099224:p300-CBP-Associated Factor; C494364:Crebbp protein, mouse