Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq.

ABSTRACT: In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA) poses challenges in accurate read mapping and the interpretation of count matrices. The traditional transcriptome reference, defining the "region of interest" in bulk RNA-seq, restricts its focus to mature mRNA transcripts. This restriction leads to two problems: reads originating outside of the "region of interest" are prone to mismapping within this region, and additionally, such external reads cannot be matched to specific transcript targets. Expanding the "region of interest" to encompass both nascent and mature mRNA transcript targets provides a more comprehensive framework for RNA-seq analysis. Here, we introduce the concept of distinguishin

SUBMITTER: Sullivan DK 

PROVIDER: S-EPMC11724275 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature