The effect of genetic variation on promoter usage and enhancer activity

Marco Garieri, Olivier Delaneau, Federico Santoni, Richard J. Fish, David Mull, Piero Carninci, Emmanouil T. Dermitzakis, Stylianos E. Antonarakis and Alexandre Fort ()
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Marco Garieri: University of Geneva
Olivier Delaneau: University of Geneva
Federico Santoni: University of Geneva
Richard J. Fish: University of Geneva
David Mull: University of Geneva
Piero Carninci: Division of Genomic Technologies, RIKEN Center for Life Science Technologies
Emmanouil T. Dermitzakis: University of Geneva
Stylianos E. Antonarakis: University of Geneva
Alexandre Fort: University of Geneva

Nature Communications, 2017, vol. 8, issue 1, 1-9

Abstract: Abstract The identification of genetic variants affecting gene expression, namely expression quantitative trait loci (eQTLs), has contributed to the understanding of mechanisms underlying human traits and diseases. The majority of these variants map in non-coding regulatory regions of the genome and their identification remains challenging. Here, we use natural genetic variation and CAGE transcriptomes from 154 EBV-transformed lymphoblastoid cell lines, derived from unrelated individuals, to map 5376 and 110 regulatory variants associated with promoter usage (puQTLs) and enhancer activity (eaQTLs), respectively. We characterize five categories of genes associated with puQTLs, distinguishing single from multi-promoter genes. Among multi-promoter genes, we find puQTL effects either specific to a single promoter or to multiple promoters with variable effect orientations. Regulatory variants associated with opposite effects on different mRNA isoforms suggest compensatory mechanisms occurring between alternative promoters. Our analyses identify differential promoter usage and modulation of enhancer activity as molecular mechanisms underlying eQTLs related to regulatory elements.

Date: 2017
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DOI: 10.1038/s41467-017-01467-7

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