Linking Cis-acting Elements

Status: This talk is in preparation - details may change

Cis-acting elements (promoters, enhancers, silencers, locus control regions, boundary elements) can often be identified via their conserved, non-coding DNA sequences. In addition, when active, they may have characteristic chromatin signatures and are bound by transcription factors and polymerase II. Such features can now be identified across the entire genome by chromatin immunoprecipitation (using ChIPseq). However, cis-elements (e.g. promoters and enhancers) may be located 100s or even 1000s kb apart and therefore it is often not clear which regulatory sequence (e.g.enhancer) interacts with which promoter or additional regulatory element. The chromosome conformation capture (3C) technique was designed to analyse physical interactions between specific, previously characterised, widely separated DNA elements and it has been shown that such interactions are an inherent feature of their function. We have adapted the 3C protocol (Hughes et al Nat Genetics 2014) and developed a method which is capable of identifying all DNA elements interacting with a selected sequence (e.g. promoter) without any prior knowledge of these elements. To validate this approach, we have initially applied this method to the human  globin locus in which the interacting cis-elements have been previously characterised in detail. Further modification of the technique provides unprecedented sensitivity for analysing chromosome conformation capture and enables researchers to identify long-range cis-interactions, trans-interactions and allele-specific interactions in a manner that will help in the prioritisation of SNPs identified in GWAS studies (Davies et al in preparation).