Enhancers as information integration hubs in development: lessons from genomics

Abstract

Transcriptional enhancers are the primary determinants of tissue-specific gene expression. Although the majority of our current knowledge of enhancer elements comes from detailed analyses of individual loci, recent progress in epigenomics has led to the development of methods for comprehensive and conservation-independent annotation of cell type-specific enhancers. Here, we discuss the advantages and limitations of different genomic approaches to enhancer mapping and summarize observations that have been afforded by the genome-wide views of enhancer landscapes, with a focus on development. We propose that enhancers serve as information integration hubs, at which instructions encoded by the genome are read in the context of a specific cellular state, signaling milieu and chromatin environment, allowing for exquisitely precise spatiotemporal control of gene expression during embryogenesis.

Figure 1

Chromatin properties at active and poised enhancers. (a) Schematic representation of proteins, histone modifications and RNA found at active (i) and poised (ii) enhancers. An active, but not poised, enhancer has the ability to drive gene expression. At both enhancer classes, multiple transcription factors (TF1 and TF2, orange), DNA-binding active signaling effectors (aSE, blue) and coactivators (p300, purple) occupy the central region of low nucleosomal density, which is hypersensitive to DNAse. In addition, active enhancers are bound by RNA-polymerase II (Pol II, light green) which produces bidirectional short RNAs called eRNAs. By contrast, poised enhancers lack Pol II, but, at least in human embryonic stem cells (hESCs), are occupied by the Polycomb repressive complex 2 (PRC2, yellow). The nucleosomes flanking enhancer regions are marked by monomethylation of histone H3 lysine 4 (H3K4me1, light blue). Lysine 27 of histone H3 is commonly acetylated at the nucleosomes flanking active enhancers (H3K27ac, dark green) but methylated at poised enhancers (H3K27me3, red). (b) Genome browser representations of select protein and histone modification enrichments at a model loci containing active (POU5F1/OCT4, left) and poised (EOMES, right) enhancers (box) in hESCs. WIG files from published data [16,80,92] for p300 (coactivator, purple), SMAD3 (active signaling effector, blue), OCT4 (TF, orange), NANOG (TF, orange), H3K4me1 (light blue), H3K27ac (green) and H3K27me3 (red) were generated using QuEST and imported into the UCSC browser. Note the tight overlap of TF (OCT4, NANOG and SMAD3) and p300 binding, and broader regions surrounding the enhancers and showing H3K4me1 enrichments. H3K27ac (green) flanks active enhancers, but is completely absent at the poised enhancer where the same lysine residue is methylated over a broader chromosomal region (red). OCT4 expression is driven by two conserved enhancers, the distal (DE) and the proximal enhancer (PE), with a distinct activity during early embryonic development; both enhancers are active in human embryonic stem cells [9,93,94].

Figure 2

Models of transcription factor (TF) involvement in enhancer priming. In the ‘placeholder’ model (a), the poised enhancer is established during development by TF1(dark green) binding to its recognition motive (RM, orange); other TFs or active signaling effectors can also be recruited in the poised state. During differentiation, TF1 is replaced by a different member of the same TF family (here TF2), which also recognizes RM. This replacement leads to the activation of the enhancer [acetylation of H3K27 (K27ac, green)] and target gene activation. (b) The ‘tug-of-war’ model proposes that, during the establishment and maintenance of the poised enhancers, TFs with opposing activities (TF3, pink and TF4, orange) are bound to the same enhancer. TF3 is able to activate the enhancer and with it the expression of the associated gene, whereas TF4 is suppressing this activation. During differentiation the expression (or chromatin association) of the opposing TF4 is diminished, allowing TF3 to activate the enhancer and transcription of the gene target. These models are not mutually exclusive; indeed, most instances of gene activation are probably tightly regulated by a combination of these models together with additional signaling effectors and TFs that become induced during the differentiation process.