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Ferreira, P.G.* ; Oti, M.* ; Barann, M.* ; Wieland, T. ; Ezquina, S.* ; Friedländer, M.R.* ; Rivas, M.A.* ; Esteve-Codina, A.* ; Rosenstiel, P.* ; Strom, T.M. ; Lappalainen, T.* ; Guigo, R.* ; Sammeth, M.*

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.

Sci. Rep. 6, 32406 (2016)

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Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.

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