Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

Abstract

Background: The transcription coactivators CREB binding protein (CBP) and p300 are highly homologous acetyltransferases that mediate histone 3 lysine 27 acetylation (H3K27ac) at regulatory elements such as enhancers and promoters. Although in most cases, CBP and p300 are considered to be functionally identical, both proteins are indispensable for development and there is evidence of tissue-specific nonredundancy. However, characterization of chromatin and transcription states regulated by each protein is lacking. Results: In this study we analyze the individual contribution of p300 and CBP to the H3K27ac landscape, chromatin accessibility, and transcription in mouse embryonic stem cells (mESC). We demonstrate that p300 is the predominant H3K27 acetyltransferase in mESCs and that loss of acetylation in p300KD mESCs is more pronounced at enhancers compared to promoters. While loss of either CBP or p300 has little effect on the open state of chromatin, we observe that distinct gene sets are transcriptionally dysregulated upon depletion of p300 or CBP. Transcriptional dysregulation is generally correlated with dysregulation of promoter acetylation upon depletion of p300 (but not CBP) and appears to be relatively independent of dysregulated enhancer acetylation. Interestingly, both our transcriptional and genomic analyses demonstrate that targets of the p53 pathway are stabilized upon depletion of p300, suggesting an unappreciated view of the relationship between p300 and p53 in mESCs. Conclusions: This genomic study sheds light on distinct functions of two important transcriptional regulators in the context of a developmentally relevant cell type. Given the links to both developmental disorders and cancer, we believe that our study may promote new ways of thinking about how these proteins function in settings that lead to disease.

Short H2A histone variants are expressed in cancer

“…3b , Supplementary Data 1 ). We also examined expression of the histone chaperone NAP1 ( NAP1L1 ), which can assemble H2A.B-containing nucleosomes 15 , 21 . We detected NAP1-encoding transcripts in all TCGA cancers, with DLBCLs expressing the highest levels (Fig.…”

Planarian CREB-binding protein (CBP) gene family regulates stem cell maintenance and differentiation

“…Also, the silencing of b-catenin and Runx1 has been linked to impaired neural differentiation (Sandmann et al, 2011; Sureda-Gómez et al, 2016; Dong et al, 2018; Zou et al, 2020). Similarly, CBP/p300 interact with Smad3 and p53 to regulate cell differentiation (Jain et al, 2012; Furumatsu et al, 2005; Martire et al 2020). Finally, CBP/p300 have been shown to be required for normal epidermal regeneration through, for example, their interaction with KLF3 (Jones et al, 2020).…”

Establishment and function of chromatin modification at enhancers

“…p300 and CBP are both expressed in all tissues and required for development [138,139], but they are not interchangeable. They have distinct specificities toward each substrate lysine in vitro [140,141], and each HAT performs distinct tissue-specific roles [73,[142][143][144][145][146][147]. Strikingly, while CBP and p300 exhibit near identity of amino acid sequence in conserved domains, a much higher degree of variability exists outside of these regions, in parts of the proteins that are predicted to be unstructured.…”

“…This interpretation is supported by a recent study demonstrating little change in chromatin accessibility at enhancers in cells treated with a chemical CBP/p300 bromodomain inhibitor that results in global decreases in H3K27ac [ 71 ] and by a notable study in which mutation of endogenous H3.3K27 to H3.3K27R greatly reduced H3K27ac levels without a corresponding decrease in chromatin accessibility at enhancers [ 72 ]. Of note, we find that regions that maintain accessible chromatin when H3K27ac levels are reduced are highly enriched with lineage-specific transcription factors [ 73 ], suggesting that once established, gene regulatory networks may be self-sustaining without the need for high levels of histone acetylation [ 74 ].…”

“…However, it is also possible that the chromatin-based mechanisms that promote gene activation are different than those that are required to maintain ongoing transcription under steady state. As noted above, regions that seem impervious to loss of H3K27ac with respect to chromatin accessibility and transcriptional output tend to be highly bound by cell-type-specific transcription factors [ 73 ], and it is possible that this established state obviates the need for high activity from coactivators and high levels of acetylation [ 74 , 153 ]. Interestingly, while all of the above studies used mESCs as a model, only two used differentiation as a model to induce new transcription programmes.…”