Sunday, 12 February 2012

Excited about eQTLs

During my time at the Sanger Institute I heard many talks from people in Manolis Dermitzakis' group on expressed quantitative trait loci (eQTLs). For practical purposes these eQTLs are SNPs that are strongly correlated with expression level eg. a population's genotypes at one site might be AA, AG and GG, a nearby gene might have corresponding median expression levels of 2, 4 and 6 (arbitrary units) across multiple genotyped individuals. Something I've always thought would be very interesting to look at was the functional characterisation of the sites these SNPs lie in. A recent paper by Gaffney et al entitled "Dissecting the regulatory architecture of gene expression QTLs" has made some inroads into this problem. It looks like they've focussed on the promoter regions and found that ~40% are in open chromatin structures and are enriched in transcription factor binding sites. My interests are of course more on the putative cis-regulatory elements such as structured UTR elements (eg. IREs) and microRNA binding sites that the eQTLs can presumably influence. So it looks like there are still many fun projects that these datasets can spawn.

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