Our aim is to map promoter-enhancer interactions particularly in human complex disease context. We developed HiCap by combining 4-cutter Hi-C with sequence capture targeting promoters (Sahlén P et al 2015). We now improved our capture design to target promoters more efficiently with fewer amounts of probes making the method cost-effective.
Promoters are central players in regulating expression levels of genes. However it is through their interactions with distal acting enhancers, that they achieve specific patterns of expression in different cells, tissues and developmental stages. In general, regulatory mutations (e.g. those in promoters and enhancers) carry lower burdens for the fitness of individuals than those of protein-coding mutations. Indeed, around 93% of complex disease-associated variants from genome-wide association studies (GWAS) lie within noncoding sequences and 77% of those are strong candidates for enhancers (Maurano MT et al, 2012). Therefore it is of paramount importance to know the target genes of such regions to understand their functional implications in disease.
We currently apply HiCap in cardiovascular disease context to map interactions of associated regions to find their target genes. We also apply HiCap for soft-tissue sarcoma and normal samples taken from patients to identify any possible disease associanted regulatory miswiring.
Rapolas Spalinskas, Post doc
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