Full-length transcriptomic profiling reveals age-associated isoform remodeling and altered coding potential in the...

Area of Science:

• Reproductive biology
• Genomics
• Molecular biology

Background:

• Ovarian aging leads to decreased oocyte quality and quantity, impacting female fertility and causing reproductive disorders.
• The precise transcript-level molecular mechanisms driving ovarian aging are not fully understood.

Purpose of the Study:

• To investigate age-associated transcriptomic alterations in mouse ovarian cells using long-read RNA sequencing.
• To identify novel transcript isoforms and differential expression patterns related to ovarian aging.

Main Methods:

• Oxford Nanopore long-read and Illumina short-read RNA sequencing of mouse granulosa cells and oocytes from young and aged mice.
• Transcript annotation, differential expression analysis, alternative polyadenylation (APA) analysis, and weighted gene co-expression network analysis (WGCNA).

Main Results:

• Comprehensive annotation identified over 100,000 novel isoforms, with aging associated with a shift towards isoforms of lower coding potential.
• Age-related 3'UTR shortening was observed via APA analysis, alongside 795 significant transcript isoform switching events.
• WGCNA highlighted aging-associated gene modules, including an Esr1-derived transcript linked to ovarian function and disease.

Conclusions:

• Long-read sequencing enhances the resolution of ovarian transcriptomic diversity at the isoform level.
• Identified candidate transcript alterations associated with ovarian aging may contribute to reproductive decline.
• Cell-type-specific isoform usage in disease-associated genes, including novel isoforms, underscores the complexity of aging transcriptomes.