Hyperacetylated chromatin domains mark cell type-specific genes and suggest distinct modes of enhancer function

Sierra Fox, Jacquelyn A. Myers, Christina Davidson, Michael Getman, Paul D. Kingsley, Nicholas Frankiewicz and Michael Bulger ()
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Sierra Fox: University of Rochester Medical Center
Jacquelyn A. Myers: University of Rochester Medical Center
Christina Davidson: University of Rochester Medical Center
Michael Getman: University of Rochester Medical Center
Paul D. Kingsley: University of Rochester Medical Center
Nicholas Frankiewicz: University of Rochester Medical Center
Michael Bulger: University of Rochester Medical Center

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: Abstract Stratification of enhancers by signal strength in ChIP-seq assays has resulted in the establishment of super-enhancers as a widespread and useful tool for identifying cell type-specific, highly expressed genes and associated pathways. We examine a distinct method of stratification that focuses on peak breadth, termed hyperacetylated chromatin domains (HCDs), which classifies broad regions exhibiting histone modifications associated with gene activation. We find that this analysis serves to identify genes that are both more highly expressed and more closely aligned to cell identity than super-enhancer analysis does using multiple data sets. Moreover, genetic manipulations of selected gene loci suggest that some enhancers located within HCDs work at least in part via a distinct mechanism involving the modulation of histone modifications across domains and that this activity can be imported into a heterologous gene locus. In addition, such genetic dissection reveals that the super-enhancer concept can obscure important functions of constituent elements.

Date: 2020
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DOI: 10.1038/s41467-020-18303-0

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