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

Ferreira, Pedro G
Oti, Martin
Barann, Matthias
Wieland, Thomas
Ezquina, Suzana
Friedländer, Marc R
Rivas, Manuel A
Esteve-Codina, Anna
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Published in Scientific reports. 2016, vol. 6, 32406
Abstract 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.
PMID: 27617755
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Research group Pathologie Moléculaire de la Trisomie 21 et le Génome Humain (248)
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FERREIRA, Pedro G et al. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. In: Scientific reports, 2016, vol. 6, p. 32406. doi: 10.1038/srep32406 https://archive-ouverte.unige.ch/unige:88981

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Deposited on : 2016-11-16

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