Enhancer function: mechanistic and genome-wide insights come together

Abstract

Enhancers establish spatial or temporal patterns of gene expression that are critical for development, yet our understanding of how these DNA cis-regulatory elements function from a distance to increase transcription of their target genes and shape the cellular transcriptome has been gleaned primarily from studies of individual genes or gene families. High-throughput sequencing studies place enhancer-gene interactions within the 3D context of chromosome folding, inviting a new look at enhancer function and stimulating provocative new questions. Here, we integrate these whole-genome studies with recent mechanistic studies to illuminate how enhancers physically interact with target genes, how enhancer activity is regulated during development, and the role of noncoding RNAs transcribed from enhancers in their function.

Figure 1.. Enhancers and promoters communicate by chromatin looping.

(A) Left: Two lineage specific genes and an enhancer are depicted along unfolded chromatin with neither gene being transcribed. Right: Lineage specific transcription factors mediate long range interaction between the enhancer and one of the genes through homotypic and/or heterotypic protein interaction. The gene in contact with the enhancer is activated; the other gene (inactive) is looped away from the elements that are in proximity. (B) Left: A CTCF binding site and an enhancer are depicted with an inactive gene along unfolded chromatin. Right: The gene is activated by lineage specific activators that coopt CTCF into long range interaction with the gene. (C) A non-interacting enhancer and gene. Right: The enhancer is bridged to the gene promoter by Mediator and cohesin with participation of lineage specific factors, activating the gene. (D) Left: A locus containing a gene and enhancer reside in an unfolded and inactive state. Center, Right: Enhancer-gene looping is depicted as being mediated by lineage specific activators before accumulation of Pol II and the appearance of a transcription factory, and transcription.

Figure 2.. Hallmarks of enhancers at different developmental stages.

(A) Left: Inactive ES cell enhancers have compact nucleosomes but are occupied by ELL3. Center: Poised enhancers are marked by H3K4me1, H3K27me3, PRC2, ELL3, Brg1 and p300. Right: At active enhancers, H3K27ac replaces H3K27me3 upon loss of PRC2. (B) Left: Latent macrophage enhancers lack transcription factor occupancy and enhancer-like histone modifications and contain compact nucleosomes. Center: Inactive macrophage enhancers differ from latent enhancers as they have acquired H3K4me1 and macrophage transcription factors such as PU.1. Right: Active enhancers are further marked by H3K27ac and p300 occupancy. (C) Center: In ES cells, neuroectoderm enhancers have unmethylated CpGs (white circles) and are occupied by Nanog, Sox2, and Oct4. Right: In the ectoderm, Nanog, Sox2, and Oct4 occupancy is diminished, the region remains unmethylated, and transcription of neural genes ensues. Left: Upon differentiation of ES cells to endoderm or mesoderm, Nanog, Sox2, and Oct4 occupancy is lost and the region becomes more compact and highly methylated (black circles), inactivating the enhancers.

Figure 3.. Mechanism of eRNA function

(A) To activate target genes, eRNAs can interact with Mediator and cohesin to form long range interactions between the enhancer and target genes. Loss of eRNAs or Mediator results in decreased target gene expression. (B) eRNAs can mediate target gene expression through influencing chromatin remodeling at target promoters. It is unclear if this mechanism occurs independently of chromatin looping.