scUTRquant

scUTRquant quantifies alternative 3′ untranslated region (3′UTR) isoforms from single-cell RNA sequencing (scRNA-seq) data to characterize post-transcriptional regulation and 3′ end cleavage site usage.

Key Features:

• Enhanced 3′ end cleavage site annotations: Incorporates mRNA 3′ end cleavage site (CS) annotations derived from over 200 primary human and mouse cell types, increasing CS annotations by approximately 40% compared to GENCODE.
• Precision in isoform quantification: Provides rapid, precise, and accurate quantification of gene expression and 3′UTR isoform expression at single-cell resolution using novel computational methodologies.
• Comprehensive analysis across cell types: Applied to data from 474 distinct cell types and 2,134 perturbations, revealing extensive and variable changes in 3′UTR length that are comparable in prevalence to gene expression changes.

Scientific Applications:

• Gene regulation insights: Characterizes the dual axes of gene regulation—mRNA abundance and mRNA length—to inform how these factors collectively influence protein synthesis.
• Single-cell resolution studies: Enables investigation of cell-type-specific regulatory mechanisms and the impact of perturbations on 3′UTR dynamics at single-cell resolution.
• Biomedical research applications: Maps and quantifies 3′UTR isoforms relevant to diseases where post-transcriptional regulation is critical, such as cancer and genetic disorders.

Methodology:

Integrates enhanced CS annotations with computational algorithms for isoform quantification, processes scRNA-seq data to map 3′ end cleavage sites and categorize distinct isoforms per gene, and analyzes isoform usage across cell types and conditions to identify 3′UTR length variation.