Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression

• Published in: Nucleic acids research Vol. 42; no. 18; pp. 11363 - 11382
• Main Authors: Kasper, Lawryn H, Qu, Chunxu, Obenauer, John C, McGoldrick, Daniel J, Brindle, Paul K
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 13.10.2014
• Subjects: 2,2'-Dipyridyl - pharmacology; Animals; Cells, Cultured; Chromatin Immunoprecipitation; CREB-Binding Protein - genetics; CREB-Binding Protein - metabolism; Enhancer Elements, Genetic; Gene regulation, Chromatin and Epigenetics; Genome; Mice; p300-CBP Transcription Factors - genetics; p300-CBP Transcription Factors - metabolism; Promoter Regions, Genetic; Response Elements; Single-Cell Analysis; Transcription Initiation Site; Transcription, Genetic; Transcriptional Activation
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gku827

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.