Genetic effects on promoter usage are highly context-specific and contribute to complex traits

Abstract

Genetic variants regulating RNA splicing and transcript usage have been implicated in both common and rare diseases. Although transcript usage quantitative trait loci (tuQTLs) have now been mapped in multiple cell types and conditions, the molecular mechanisms through which these variants exert their effect have remained elusive. Specifically, changes in transcript usage could arise from promoter choice, alternative splicing or 3' end choice, but current tuQTL studies have not been able to distinguish between them. Here, we performed comprehensive analysis of RNA-seq data from human macrophages exposed to a range of inflammatory stimuli (IFN{gamma}, Salmonella, IFN{gamma} + Salmonella) and a metabolic stimulus (acetylated LDL), obtained from up to 84 individuals. In addition to conventional gene-level and transcript-level analyses, we also developed an analytical approach to directly quantify promoter, internal exon and 3' end usage. We found that although naive transcript-level analysis often links single genetic variants to multiple coupled changes on the transcriptome, this appears to be an artefact of incomplete transcript annotations. Most of this coupling disappears when promoters, splicing and 3' end usage are quantified directly. Furthermore, promoter, splicing and 3' end QTLs are each enriched in distinct genomic features, suggesting that they are predominantly controlled by independent regulatory mechanisms. We also find that promoter usage QTLs are 50% more likely to be context-specific than canonical splicing QTLs and constitute 25% of the transcript-level colocalisations with complex traits. Thus, promoter usage might be a previously underappreciated molecular mechanism mediating complex trait associations in a context-specific manner.