Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.

Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter need to be biochemically compatible for promoter regulation to occur, but this compatibility has remained poorly characterised in mammalian cells. By systematic reporter assays of thousands of CRE – promoter pairs from three Mb-sized genomic regions in mouse cells, we found that CREs vary substantially in their promoter compatibility, with more than half showing significant selectivity. This selectivity does not correlate with looping interactions, suggesting that chromatin folding and compatibility are two orthogonal mechanisms of gene regulation. Overall design: 3 Biological replicates of cDNA samples for each library mix, 2 pDNA replicates for each library mix and 1 iPCR sequencing run per separate library. For cDNA samples Library mixes were transfected in mESCs and samples were collected after 24h.