Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

Abstract

CpG islands (CGIs) represent a widespread feature of vertebrate genomes, being associated with ~70% of all gene promoters. CGIs control transcription initiation by conferring nearby promoters with unique chromatin properties. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance is barely known. Here we show that oCGIs are an essential component of poised enhancers (PEs) that augment their long-range regulatory activity and control the responsiveness of their target genes. Using a knock-in strategy in mouse embryonic stem cells (ESCs), we introduced PEs with or without oCGIs within topologically associating domains (TADs) harboring genes with different types of promoters. Analysis of the resulting cell lines revealed that oCGIs act as tethering elements that promote the physical and functional communication between PEs and distally located genes, particularly those with large CGI clusters in their promoters. Therefore, by acting as genetic determinants of gene-enhancer compatibility, CGIs can contribute to gene expression control under both physiological and potentially pathological conditions.

Metabolic and Epigenetic Regulation by Estrogen in Adipocytes

“…DNA methylation on CpG islands ( 99 ), which are present in most promoters ( 113 ), has a repressive effect on gene expression ( 114 ). This reaction can be catalyzed by two types of DNA methyltransferases (DNMTs) depending on the purpose of the methylation.…”

“…Strikingly, ERα has shown a strong preference for binding to intergenic regions ( 116 ). Interestingly, about half of the CpG islands are also found in intergenic regions, and have recently been shown to be an essential part of poised enhancers, acting as anchors between the enhancer and target promoters ( 113 ). Consequently, methylation of CpG islands plays a crucial role in determining enhancer-promoter selectivity.…”

Intragenic CpG Islands and Their Impact on Gene Regulation

“…Enhancer signatures are also found at the other type of 'orphan' CGI, intergenic CGIs. A recent study has challenged the idea that these CGIs directly serve as enhancers, and instead, boost proximal enhancer function (Pachano et al, 2021). Here, intergenic CGIs augment enhancers' ability to amplify only target genes that contain a CGI promoter themselves.…”

“…As enhancers loop to promoter CGIs, the unmethylated intergenic CGIs that are within 3 kb of the proximal enhancer bring along machinery for efficient promoter CGI transcription. These intergenic CGIs also serve to protect transcription factor binding sites (TFBS) within the proximal enhancer from repressive DNA methylation (Pachano et al, 2021). The relationship between intergenic CGIs and proximal enhancers may be reciprocal, as the TFBS within the enhancer can assist recruitment of machinery to the intergenic CGI itself.…”

Transcriptional enhancers and their communication with gene promoters

“…Promoters are also sometimes repurposed into enhancers, but at a 13-fold lower rate than enhancer-to-promoter [ 100 ]. In terms of their sequence properties, enhancers and promoters tend to differ in GC content, with many promoters and only a subset of enhancers containing CpG islands [ 74 , 249 ]. Therefore, enhancers predisposed to convert into promoters may have a particular GC sequence composition and presence of 5′ splicing regulatory motif patterns [ 100 ].…”