Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits.

ABSTRACT: Genomic variations are associated with gene expression levels, which are called expression quantitative trait loci (eQTL). Most eQTL may affect the total gene expression levels by regulating transcriptional activities of a specific promoter. However, the direct exploration of genomic loci associated with promoter activities using RNA-seq data has been challenging because eQTL analyses treat the total expression levels estimated by summing those of all isoforms transcribed from distinct promoters. Here we propose a new method for identifying genomic loci associated with promoter activities, called promoter usage quantitative trait loci (puQTL), using conventional RNA-seq data. By leveraging public RNA-seq datasets from the lymphoblastoid cell lines of 438 individuals from the GEUVADIS proje

SUBMITTER: Kubota N 

PROVIDER: S-EPMC9462676 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature