Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome

Diego Garrido-Martín,Miquel Calvo,Beatrice Borsari,Roderic Guigó,Ferran Reverter

doi:10.1038/s41467-020-20578-2

Diego Garrido-Martín, Miquel Calvo + Show 3 more

Open Access

https://doi.org/10.1038/s41467-020-20578-2

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Abstract

Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We use it to analyze the GTEx dataset, generating a comprehensive catalog of sQTLs in the human genome. Downstream analysis of this catalog provides insight into the mechanisms underlying splicing regulation. We report that a core set of sQTLs is shared across multiple tissues. sQTLs often target the global splicing pattern of genes, rather than individual splicing events. Many also affect the expression of the same or other genes, uncovering regulatory loci that act through different mechanisms. sQTLs tend to be located in post-transcriptionally spliced introns, which would function as hotspots for splicing regulation. While many variants affect splicing patterns by altering the sequence of splice sites, many more modify the binding sites of RNA-binding proteins. Genetic variants affecting splicing can have a stronger phenotypic impact than those affecting gene expression.

Highlights

Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis
For sQTL mapping, we developed sQTLseekeR2, a software based on sQTLseekeR20, which identifies genetic variants associated with changes in the relative abundances of the transcript isoforms of a given gene. sQTLseekeR uses the Hellinger distance to estimate the variability of isoform abundances across observations, and Anderson’s method[21,22], a non-parametric analog to multivariate analysis of variance, to assess the significance of the associations
We extensively analyze the sQTLs identified by sqtlseeker2nf, using the expression and genotype data produced by the Genotype-Tissue Expression (GTEx) Consortium

Summary

Introduction

Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We propose an approach that takes into account the intrinsically multivariate nature of alternative splicing: variants are tested for association with a vector of AS phenotypes, such as the relative abundances of the transcript isoforms of a gene or the intron excision ratios of an intron cluster obtained by LeafCutter[18] Based on this approach, we have developed a pipeline for efficient and reproducible sQTL mapping. We have developed a pipeline for efficient and reproducible sQTL mapping We employ it to leverage the multi-tissue transcriptome data generated by the Genotype-Tissue Expression (GTEx) Consortium, producing a comprehensive catalog of genetic variants affecting splicing in the human genome. GWAS associations are strong for sQTLs altering RBP binding sites

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