Recent genomic studies also revealed that a variety of events may occur on enhancers when new TF-DNA interactions are introduced and demonstrated that, using a few genomic assays, it is possible to determine the status or activity of all enhancers. For example, DNaseI-Seq revealed that signal-dependent GR binding invariably increased chromatin accessibility.23
In another study, when macrophages were stimulated with lipopolysaccharide (LPS), only a subset of H3K4me1-marked enhancers near induced genes showed increased p300 binding, while levels of H3K4me1 on these locations stayed constant,31
suggesting that H3K4me1 is a stable marker for enhancers both before and after transient stimulation. Consistent with this study, two recent papers showed that during differentiation, many H3K4me1-marked enhancers in embryonic stem cells gain the H3K27 acetylation mark (presumably by recruiting HATs such as p300) while losing repressive H3K27me3 mark, suggesting a switch from “poised” to active status.32,33
These results suggest that H3K4me1 marks enhancers before they are activated. Although how this modification is catalyzed or incorporated into enhancers is still unknown, it has been shown that lineage-specific TFs can facilitate the formation of H3K4me1 on enhancers.26,31,34
In macrophages, loss of the ETS family transcription factor PU.1 leads to lower H3K4me1 levels on a subset of macrophage-specific enhancers; overexpressing this factor in fibroblasts or macrophage progenitor cells can create H3K4me1-marked enhancers.26,31
In addition, re-introduction of the B-cell specific transcription factor E2A in E2A-deficient B cells can change the abundance and pattern of the H3K4me1 mark on target enhancer regions.34
Collectively, these results confirmed the role of cell-specific TFs in establishing the enhanceosome during cell differentiation.
One unexpected phenomenon that emerged from genome-wide deep sequencing data is the finding that a significant fraction of enhancers can produce RNA, called enhancer RNA (eRNA).35,36
eRNAs are low-abundance, short, non-coding, bidirectional and non-polyadenylated RNAs, and their transcription might require the presence of a target promoter. Although production of eRNA has been shown to correlate with enhancer activity,37
it is still not clear how eRNA may regulate enhancer functions in general.