Enhancer regions show high histone H3.3 turnover that changes during differentiation

Deaton, Aimee M; Gómez-Rodríguez, Mariluz; Mieczkowski, Jakub; Tolstorukov, Michael Y; Kundu, Sharmistha; Sadreyev, Ruslan I; Jansen, Lars ET; Kingston, Robert E

http://hdl.handle.net/10400.7/747

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Authors

Deaton, Aimee M

Gómez-Rodríguez, Mariluz

Mieczkowski, Jakub

Tolstorukov, Michael Y

Abstract(s)

The organization of DNA into chromatin is dynamic; nucleosomes are frequently displaced to facilitate the ability of regulatory proteins to access specific DNA elements. To gain insight into nucleosome dynamics, and to follow how dynamics change during differentiation, we used a technique called time-ChIP to quantitatively assess histone H3.3 turnover genome-wide during differentiation of mouse ESCs. We found that, without prior assumptions, high turnover could be used to identify regions involved in gene regulation. High turnover was seen at enhancers, as observed previously, with particularly high turnover at super-enhancers. In contrast, regions associated with the repressive Polycomb-Group showed low turnover in ESCs. Turnover correlated with DNA accessibility. Upon differentiation, numerous changes in H3.3 turnover rates were observed, the majority of which occurred at enhancers. Thus, time-ChIP measurement of histone turnover shows that active enhancers are unusually dynamic in ESCs and changes in highly dynamic nucleosomes predominate at enhancers during differentiation.

Description

Data availability - High throughput sequencing data has been deposited in GEO and is accessible using the following links: Time-ChIP: GSE78876 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78876 ChIP-seq: GSE78899 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78899 MNase titration and RNA-seq: GSE78984 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78984