Histone H3 globular domain acetylation identifies a new class of enhancers

Abstract

Histone acetylation is generally associated with active chromatin, but most studies have focused on the acetylation of histone tails. Various histone H3 and H4 tail acetylations mark the promoters of active genes1. This includes acetylation of H3 on lysine 27 (H3K27ac), which blocks the deposition of polycomb mediated H3K27me32. H3K27ac is also widely used to identify active enhancers3,4, and the assumption has been that profiling of H3K27ac is a comprehensive way of cataloguing the set of active enhancers in mammalian cell types. Here we show that acetylation of lysine residues in the globular domain of H3 (H3K64ac and H3K122ac) marks active gene promoters and also a subset of active enhancers. Moreover, we find a novel class of active functional enhancers that are marked by H3K122ac but lack H3K27ac. This work suggests that, to identify enhancers, a more comprehensive analysis of histone acetylation is required than was previously considered.

CRISPR/Cas9-Based Engineering of the Epigenome

“…1A). After the initial proof-of-concept experiment (Cheng et al, 2013; Farzadfard et al, 2013; Gilbert et al, 2013; Maeder et al, 2013; Mali et al, 2013a; Perez-Pinera et al, 2013; Qi et al, 2013), numerous studies have validated this approach and further refined the experimental systems utilized (Perez-Pinera et al, 2013; Chakraborty et al, 2014; Gilbert et al, 2014; Kearns et al, 2014; Balboa et al, 2015; Kearns et al, 2015; Konermann et al, 2015; Nihongaki et al, 2015; Polstein and Gersbach, 2015; Shechner et al, 2015; Thakore et al, 2015; Zalatan et al, 2015; Black et al, 2016; Braun et al, 2016; Chavez et al, 2016; Gao et al, 2016; Garcia-Bloj et al, 2016; Genga et al, 2016; Himeda et al, 2016; Mandegar et al, 2016; Pradeepa et al, 2016; Radzisheuskaya et al, 2016; Klann et al, 2017). …”

“…The SID domain causes the recruitment of histone deacetylases via interaction with the transcriptional repressor domain PAH2. dCas9 fused to KRAB or SID has been shown to repress gene transcription by 50 to 99% in different cell lines, primary cultures and pluripotent stem cells (Gao et al, 2013; Kearns et al, 2015; Shechner et al, 2015; Thakore et al, 2015; Amabile et al, 2016; Pradeepa et al, 2016). Similarly, dCas9 has been linked to the activation domains of several transcription factors such as p65, HSF1 and MyoD, and of the viral transactivators Rta and VP16, to induce gene expression (see Supplementary Table 1).…”

“…Several studies have addressed how transactivator/repressor domains refashion the chromatin landscape (Gilbert et al, 2014; Himeda et al, 2016; Pradeepa et al, 2016; Klann et al, 2017). Although these changes are typically transient, persistent transcriptional change and cell fate conversion can occur if the newly introduced chromatin modifications are reinforced by the endogenous epigenetic machinery (Chakraborty et al, 2014; Balboa et al, 2015; Black et al, 2016).…”

“…The first approach consists of fusing the dCas9 protein to multiple copies of an effector domain, or to several effectors with similar functions in tandem. This approach dramatically increases chromatin visualization and the efficiency of transcriptional expression and repression (Balboa et al, 2015; Ma et al, 2015; Pradeepa et al, 2016). Another strategy is to use multiple gRNAs that target a discrete DNA region in order to amplify the intended effect, as well as to promote epigenetic spreading of the targeted modification to adjacent chromatin (Maeder et al, 2013; Mali et al, 2013b; Hu et al, 2014; Hilton et al, 2015; Kim et al, 2015; Liu et al, 2016; McDonald et al, 2016; Morita et al, 2016; Pradeepa et al, 2016).…”

Convergent origination of aDrosophila-like dosage compensation mechanism in a reptile lineage

“…Native ChIP-seq data generation Native chromatin immunoprecipitation (ChIP) was performed as previously described (Pradeepa et al 2016) with some modifications. Specifically, ∼20 mg of frozen brain and liver tissue sample from Anolis was ground in liquid nitrogen into fine powder.…”