A single-cell transposable element atlas of human cell identity.

Publication Type	Preprint
Authors	Reyes-Gopar H, Marston J, Singh B, Greenig M, Lin J, Ostrowski M, Randall K, Sandoval-Motta S, Dopkins N, Lawrence E, O'Mara M, Fei T, Duarte R, Powell T, Hernandez-Lemus E, Iniguez L, Nixon D, Bendall M
Journal	bioRxiv
Date Published	12/28/2023
ISSN	2692-8205
Abstract	Single cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. In both scRNA-seq and bulk tissue RNA sequencing (RNA-seq), quantification of TE expression is challenging due to repetitive sequence content and poorly characterized TE gene models. Here, we developed a tool and analysis pipeline for Single cell Transposable Element Locus Level Analysis of scRNA Sequencing (Stellarscope) that reassigns multi-mapped reads to specific genomic loci using an expectation-maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define new cell subsets not identified by standard mRNA expression profiles. Altogether, this study provides comprehensive insights into the influence of transposable elements in human biology.
DOI	10.1101/2023.12.28.573568
PubMed ID	38234829
PubMed Central ID	PMC10793444