Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

Abstract

Transcriptional enhancers are critical for maintaining cell-type-specific gene expression and driving cell fate changes during development. Highly transcribed genes are often associated with a cluster of individual enhancers such as those found in locus control regions. Recently, these have been termed stretch enhancers or super-enhancers, which have been predicted to regulate critical cell identity genes. We employed a CRISPR/Cas9-mediated deletion approach to study the function of several enhancer clusters (ECs) and isolated enhancers in mouse embryonic stem (ES) cells. Our results reveal that the effect of deleting ECs, also classified as ES cell super-enhancers, is highly variable, resulting in target gene expression reductions ranging from 12% to as much as 92%. Partial deletions of these ECs which removed only one enhancer or a subcluster of enhancers revealed partially redundant control of the regulated gene by multiple enhancers within the larger cluster. Many highly transcribed genes in ES cells are not associated with a super-enhancer; furthermore, super-enhancer predictions ignore 81% of the potentially active regulatory elements predicted by cobinding of five or more pluripotency-associated transcription factors. Deletion of these additional enhancer regions revealed their robust regulatory role in gene transcription. In addition, select super-enhancers and enhancers were identified that regulated clusters of paralogous genes. We conclude that, whereas robust transcriptional output can be achieved by an isolated enhancer, clusters of enhancers acting on a common target gene act in a partially redundant manner to fine tune transcriptional output of their target genes.

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation

“…In contrast, the Esrrb enhancer (Festuccia et al , 2012; Moorthy et al , 2017), which is active in ESCs but inactive in primed pluripotent cells, becomes completely methylated as cells commit to differentiate. Our results build on previous reports that accumulation of DNA methylation at the regulatory regions of pluripotency genes accompanies loss of naïve pluripotency (Ficz et al , 2013; Habibi et al , 2013; Hackett et al , 2013; Leitch et al , 2013).…”

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

“…We examined whether super-enhancers and enhancers exhibit structural variations in 3D genome maps. To this end, we selected a list of candidates whose enhancer function has been validated (22). Both super-enhancers and enhancers are linked to their promoter by similar architectural stripes, with no significant difference between them in terms of chromatin conformation and interaction intensity.…”

Hyperacetylated Chromatin Domains Mark Cell Type-Specific Genes and Suggest Distinct Modes of Enhancer Function

“…An additional concern is the "stitching" step of super-enhancer analysis, in which putative enhancer regions located within a specific distance of each other (the default in the ROSE algorithm is 12.5 kb, and so this is most often used) are considered as a single element, under the assumption that closely-spaced enhancers work together in activation of the same gene or genes [6][7][8] . Some studies have questioned the general validity of this assumption 10,31 , and our own analysis of the Tspan32 locus presents a clear example of how the superenhancer concept tends to oversimplify more complex patterns of gene regulation. We found that the Tspan32 super-enhancer, comprised of three distinct candidate enhancer regions, is in fact involved in the regulation of two additional genes as well as Tspan32.…”