Modification of enhancer chromatin: what, how, and why?

Abstract

Emergence of form and function during embryogenesis arises in large part through cell-type- and cell-state-specific variation in gene expression patterns, mediated by specialized cis-regulatory elements called enhancers. Recent large-scale epigenomic mapping revealed unexpected complexity and dynamics of enhancer utilization patterns, with 400,000 putative human enhancers annotated by the ENCODE project alone. These large-scale efforts were largely enabled through the understanding that enhancers share certain stereotypical chromatin features. However, an important question still lingers: what is the functional significance of enhancer chromatin modification? Here we give an overview of enhancer-associated modifications of histones and DNA and discuss enzymatic activities involved in their dynamic deposition and removal. We describe potential downstream effectors of these marks and propose models for exploring functions of chromatin modification in regulating enhancer activity during development.

Figure 1

Epigenetic features of active, primed and poised enhancers. (A) Schematic representation of the major chromatin features found at active enhancers. Enhancers are associated with incorporation of hypermobile nucleosomes containing H3.3/H2A.Z histone variants, which compete for DNA binding with TFs. TFs in turn recruit coactivator proteins that can modify and remodel nucleosomes. H3K4me1 and H3K27ac are the predominant histone modifications deposited at nucleosomes flanking enhancer elements. (B) Prior to activation, enhancers can exist in a primed state, characterized by the presence of H3K4me1. Other features that have been associated with enhancer priming are presence of pioneer TFs, hypermobile H3.3/H2A.Z nucleosomes, DNA 5mC hypomethylation and hydroxylation (5hmC). (C) Schematic representation of the chromatin landscape surrounding poised enhancers found in human and mouse ESC. A subset of “primed” enhancers in ESC is also marked by H3K27me3 and associated with PRC2. These enhancers are bound by TFs and coactivators and communicate with their target promoters.

Figure 2

Chromatin accessibility at enhancers (A) Cooperative binding of TFs can overcome the nucleosomal barrier and initiate regulatory events on chromatin. (B) Enhancers sites can be made available by the action of “pioneer” factors, which can directly associate with nucleosomal DNA, preceding and commonly also enabling occupancy of other TFs via recruitment of the chromatin remodeling activities. (C) Incorporation of the histone variant H2A.Z, mediated by the TIP60/p400 complex, creates domains of nucleosomal hypermobility that may facilitate initial TF binding events.

Figure 3

Methylation of H3K4 at enhancers and promoters (A) Enhancers and promoters can be distinguished by the methylation status at the histone H3 lysine 4 (H3K4). Enhancers are enriched for H3K4me1, whereas high levels of H3K4me3 predominantly mark promoters. These differences can be largely explained by the underlying differences in DNA sequence, with high CpG island density observed at most promoters, but not at enhancers. CpG-rich regions are recognized by the CxxC domain of Cfp1, a specific subunit of Set1a/b complex, allowing for its preferential binding and H3K4me3 at promoters. In contrast, other methyltransferases, such as Trr/MLL3/MLL4 complex are likely responsible for H3K4me1 at enhancers. (B) Point mutation in the CxxC motif of Cpf1, which disrupts CpG island recognition, but not the complex assembly, alters binding specificity of the Set1a/b complex, resulting in the ectopic deposition of H3K4me3 at enhancers, leading in turn to aberrantly increased transcriptional activity at the enhancer and, commonly, also at the nearby promoter. See text for details.

Figure 4

Writers, Readers and Erasers of major enhancers marks Proteins capable of adding (writers), removing (erasers) and recognizing (readers) major enhancer-associated chromatin modifications, including H3K4me1, H3K9ac, H3K27ac and 5hmC are shown. See text for details.