Improved detection of genetic effects on promoter usage with augmented transcript annotations

Abstract

Disease-associated non-coding variants can modulate their target genes by disrupting multiple mechanisms, including regulating total gene expression level, splicing, alternative polyadenylation or promoter usage. Quantifying promoter usage from standard RNA sequencing data is challenging due to incomplete reference transcriptome annotations and low read coverage observed at the ends of transcripts. We previously developed the txrevise tool (https://github.com/kauralasoo/txrevise) to quantify promoter usage events from RNA-seq data using reference transcriptome annotations. Here, we augment the txrevise promoter event annotations with experimentally identified Cap Analysis of Gene Expression (CAGE) promoters from the FANTOM5 project. Applying the new annotations to RNA-seq data from 358 individuals, we found that augmented promoter event annotations increased the power to detect promoter usage quantitative trait loci (puQTLs) by ~30%. However, concordance between puQTLs inferred from RNA-seq data and those directly measured using CAGE remained low, suggesting that additional experimental and computational improvements are needed to capture the full range of regulatory effects of non-coding variants.

eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs

“…In addition to these four, we have now also implemented LeafCutter [ 27 ] to directly quantify the usage of splice junctions (Fig A in S1 Text ). We have also augmented the txrevise promoter annotations with experimentally determined promoters from the FANTOM5 project [ 28 ]. Finally, we have updated the reference transcriptome annotations to Ensembl version 105 and GENCODE version 39.…”

“…For transcript quantification, we used the GENCODE V39 (GRCh38.p13) reference transcript sequences (fasta) file to build the Salmon index. For transcriptional event usage, we downloaded pre-computed txrevise [ 5 , 28 ] alternative promoter, splicing and alternative 3′ end annotations corresponding to Ensembl version 105 from Zenodo ( https://doi.org/10.5281/zenodo.6499127 ) in GFF format. These annotations had been augmented with additional experimentally derived promoter annotations from the FANTOM5 consortium [ 77 , 78 ].…”

Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci

“…In addition to these four, we have now also implemented LeafCutter (Li et al, 2018) to directly quantify the usage of splice junctions (Supplementary Figure 1). We have also augmented the txrevise promoter annotations with experimentally determined promoters from the FANTOM5 project (Vija and Alasoo, 2022). Finally, we have updated the reference transcriptome annotations to Ensembl version 105 and GENCODE version 39.…”

“…For transcript quantification, we used the GENCODE V39 (GRCh38.p13) reference transcript sequences (fasta) file to build the Salmon index. For transcriptional event usage, we downloaded pre-computed txrevise (Alasoo et al, 2019;Vija and Alasoo, 2022) alternative promoter, splicing and alternative 3ʹ end annotations corresponding to Ensembl version 105 from Zenodo (https://doi.org/10.5281/zenodo.6499127) in GFF format. These annotations had been augmented with additional experimentally derived promoter annotations from the FANTOM5 consortium (Abugessaisa et al, 2017;FANTOM Consortium and the RIKEN PMI and CLST et al, 2014).…”