Predictive modeling of oocyte maternal mRNA features for five mammalian species reveals potential shared and species-restricted regulators during maturation

• Published in: Physiological genomics Vol. 56; no. 1; pp. 9 - 31
• Main Authors: Schall, Peter Z, Latham, Keith E
• Format: Journal Article
• Language: English
• Published: United States American Physiological Society 01.01.2024
• Subjects: 3' Untranslated regions; Animals; Codon bias; Female; Mammals - genetics; Mammals - metabolism; MicroRNAs - genetics; MicroRNAs - metabolism; mRNA stability; Oocytes; Oocytes - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Messenger, Stored - genetics; RNA, Messenger, Stored - metabolism; RNA-binding protein; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Species; Transcriptomes; Untranslated Regions; in silico analysis; maternal mRNA; posttranscriptional control; evolutionary conservation
• ISSN: 1094-8341; 1531-2267; 1531-2267
• DOI: 10.1152/physiolgenomics.00048.2023

Oocyte maturation is accompanied by changes in abundances of thousands of mRNAs, many degraded and many preferentially stabilized. mRNA stability can be regulated by diverse features including GC content, codon bias, and motifs within the 3'-untranslated region (UTR) interacting with RNA binding proteins (RBPs) and miRNAs. Many studies have identified factors participating in mRNA splicing, bulk mRNA storage, and translational recruitment in mammalian oocytes, but the roles of potentially hundreds of expressed factors, how they regulate cohorts of thousands of mRNAs, and to what extent their functions are conserved across species has not been determined. We performed an extensive in silico cross-species analysis of features associated with mRNAs of different stability classes during oocyte maturation (stable, moderately degraded, and highly degraded) for five mammalian species. Using publicly available RNA sequencing data for germinal vesicle (GV) and MII oocyte transcriptomes, we determined that 3'-UTR length and synonymous codon usage are positively associated with stability, while greater GC content is negatively associated with stability. By applying machine learning and feature selection strategies, we identified RBPs and miRNAs that are predictive of mRNA stability, including some across multiple species and others more species-restricted. The results provide new insight into the mechanisms regulating maternal mRNA stabilization or degradation. Conservation across species of mRNA features regulating maternal mRNA stability during mammalian oocyte maturation was analyzed. 3'-Untranslated region length and synonymous codon usage are positively associated with stability, while GC content is negatively associated. Just three RNA binding protein motifs were predicted to regulate mRNA stability across all five species examined, but associated pathways and functions are shared, indicating oocytes of different species arrive at comparable physiological destinations via different routes.