SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression.

ABSTRACT: Transposable Elements (TEs) contribute to the repetitive fraction in almost every eukaryotic genome known to date, and their transcriptional activation can influence the expression of neighboring genes in healthy and disease states. Single cell RNA-Seq (scRNA-Seq) is a technical advance that allows the study of gene expression on a cell-by-cell basis. Although a current computational approach is available for the single cell analysis of TE expression, it omits their genomic location. Here we show SoloTE, a pipeline that outperforms the previous approach in terms of computational resources and by allowing the inclusion of locus-specific TE activity in scRNA-Seq expression matrixes. We then apply SoloTE to several datasets to reveal the repertoire of TEs that become transcriptionally active

SUBMITTER: Rodriguez-Quiroz R 

PROVIDER: S-EPMC9537157 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature