# 3′UTR shortening alleviates miRNA repression of mRNAs critical for muscle stem cell differentiation

## TL;DR

Shortening of 3′UTRs in muscle stem cells helps mRNAs escape miRNA repression, promoting efficient muscle differentiation and regeneration.

## Contribution

The study reveals that 3′UTR shortening, via APA and reduced CFI, counteracts miRNA repression during muscle stem cell differentiation.

## Key findings

- 3′UTR shortening during muscle stem cell differentiation allows mRNAs to escape repression by myomiRs.
- Reduced CFI expression drives APA-mediated 3′UTR shortening in differentiating muscle stem cells.
- Mutating the Matr3 pA site impairs muscle regeneration in mice, highlighting its regulatory role.

## Abstract

Alternative polyadenylation (APA) modulates gene expression by altering 3′ untranslated region (3′UTR) length. Although 3′UTR lengthening typically accompanies cell differentiation, we unexpectedly observed preferential APA-mediated 3′UTR shortening events during muscle stem cell (satellite cell, SC) differentiation, coinciding with increased muscle-specific miRNAs (myomiRs) targeting at alternative 3′UTRs. Mechanistically, this shortening primarily results from reduced cleavage factor I (CFI) expression and allows transcripts to escape repression by differentiation-induced myomiRs. Interestingly, perturbation of mRNA 3′UTR shortening of multiple genes impairs myogenic differentiation. Focusing on Matr3—a gene linked to muscle disorders—we demonstrate that its APA-miRNA regulatory balance is critical for efficient SC differentiation in vitro. Genetically mutating Matr3 proximal polyadenylation site (pA site) impaired mouse muscle regeneration in vivo. Together, our findings reveal that APA-mediated 3′UTR shortening counteracts miRNA repression to orchestrate the gene expression program essential for robust muscle regeneration.

Global changes in alternative polyadenylation (APA) accompany cell differentiation, but their roles during muscle stem cell differentiation remain unclear. This study reveals a tendency toward 3′UTR shortening, which alleviates miRNA repression of mRNAs critical for differentiation, ensuring efficient muscle differentiation and regeneration.

Preferential 3′UTR shortening during stem cell differentiation occurs via CFI-mediated APA regulation.3′UTR shortening is a general strategy to escape repression by myomiRs.APA and miR-1/206 antagonistically regulate Matr3 expression for myogenesis.Mutating the proximal Matr3 polyadenylation site in mice impairs muscle regeneration.

Preferential 3′UTR shortening during stem cell differentiation occurs via CFI-mediated APA regulation.

3′UTR shortening is a general strategy to escape repression by myomiRs.

APA and miR-1/206 antagonistically regulate Matr3 expression for myogenesis.

Mutating the proximal Matr3 polyadenylation site in mice impairs muscle regeneration.

Alternative polyadenylation of myogenesis genes like Matr3 makes their 3′UTR less accessible to myomiRs during muscle regeneration.