Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Over half of all genes produce mRNA transcripts with varying 3' untranslated region (3'UTR) lengths.
• Current analysis methods primarily quantify mRNA abundance, neglecting transcript length variations.
• 3'UTR length is dictated by cleavage sites (CS), which are critical regulatory elements.

Purpose of the Study:

• To develop a computational pipeline for quantifying both gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data.
• To map cleavage sites (CS) across numerous human and mouse cell types and enhance existing annotations.
• To investigate the role and prevalence of 3'UTR length regulation in gene expression.

Main Methods:

• Mapping cleavage sites (CS) in over 200 primary human and mouse cell types, increasing GENCODE annotations by 40%.
• Developing scUTRquant, a computational pipeline for simultaneous quantification of gene and 3'UTR isoform expression from scRNA-seq data.
• Applying scUTRquant to analyze data from 474 cell types and 2134 perturbations.

Main Results:

• Identified that approximately half of all CS are cell-type specific, with most genes utilizing only one or two major 3' ends.
• Discovered extensive 3'UTR length changes across cell types, comparable in prevalence and coordination to gene expression changes.
• Observed that 3'UTR length alterations primarily affect different genes than those regulated by abundance changes.

Conclusions:

• mRNA abundance and mRNA length represent two largely independent regulatory axes in gene expression.
• 3'UTR length variation is a significant and widespread mechanism influencing protein synthesis.
• scUTRquant provides a novel tool for analyzing 3'UTR isoform expression in scRNA-seq data.