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Orphan CpG islands boost the regulatory activity of poised enhancers and dictate the responsiveness of their target genes

ABSTRACT: CpG islands (CGIs) represent a unique and widespread genetic feature of vertebrate genomes, being associated with ~70% of all annotated gene promoters. CGIs have been proposed to 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 and mechanism of action are barely known. Here we show that oCGIs are an essential component of poised enhancers (PEs) that boost their long-range regulatory activity and dictate the responsiveness of their target genes. Using a CRISPR/Cas9 knock-in strategy in mESC, we introduced PEs with or without oCGIs within topological associating domains (TADs) harbouring genes with different types of promoters. By evaluating the chromatin, topological and regulatory properties of the engineered PEs, we uncovered that, rather than increasing their local activation, the oCGI boost the physical and functional communication between PEs and distally located developmental genes. Furthermore, we demonstrate that developmental genes with CpG rich promoters are particularly responsive to PEs and that such responsiveness depends on the presence of oCGI. Therefore, our work unveils a novel role for CGIs as genetic determinants of the compatibility between genes and enhancers, which has major implications for the current understanding of how developmental gene expression programs are deployed as well as for our ability to predict the pathological consequences of human structural variation.

ORGANISM(S): Mus musculus

PROVIDER: GSE156465 | GEO | 2020/08/20

REPOSITORIES: GEO

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