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The establishment of cell type specific gene expression programs during vertebrate development is largely dependent on distal cis-regulatory sequences known as enhancers. An important question in enhancer biology is to understand how activating regulatory cues from enhancers are communicated specifically to their correct target gene and not others. It is widely assume that insulator elements can regulate enhancer specificity by restricting their search space to regions located within their same topological associated domain (TAD). However, recent evidences have identified examples in which genes do not respond to enhancers placed into their same TAD. Therefore, we hypothesize that genetic and/or biochemical compatibilities must further regulate how promoters respond to enhancers. Here, we uncover a novel role for CpG islands (CGIs) in dictating the compatibility between genes and distal enhancers. By using a CRISPR/Cas9 knockin strategy, we inserted poised enhancers (PEs) within topological associated domains (TADs) containing genes with different promoter types. Analysis of the resulting cell lines revealed that developmental genes with CGI-rich promoters are particularly responsive to PEs, and that such responsiveness depends on the presence of an orphan CGI in proximity to the PE sequence. We report here that CGIs can amplify the regulatory activity of PEs by conferring them a permissive topological configuration that increases the responsiveness of target genes with CGI-associated promoters. Our results provide major insights into fundamental and unresolved questions of cisregulatory control during cell differentiation including: (i) the genetic factors controlling the topological features of enhancers; (ii) the regulatory rules dictating the compatibility and responsiveness between genes and enhancers. Moreover, our data will help to understand the pathomechanisms of human congenital diseases involving structural variants. |
