AUTHOR=Fumagalli Sarah E. , Smith Sean , Lin Brian , Paul Rahul , Campbell Collin , Santana-Quintero Luis , Golikov Anton , Ibla Juan , Bar Haim , Komar Anton A. , Hunt Ryan C. , DiCuccio Michael , Kimchi-Sarfaty Chava 

TITLE=Uncovering codon usage patterns during murine embryogenesis and tissue-specific developmental diseases

JOURNAL=Frontiers in Genetics

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2025.1554773

DOI=10.3389/fgene.2025.1554773

ISSN=1664-8021

ABSTRACT=IntroductionMouse models share significant genetic similarities with humans and have expanded our understanding of how embryonic tissue-specific genes influence disease states. By improved analyses of temporal, transcriptional data from these models, we can capture unique tissue codon usage patterns and determine how deviations from these patterns can influence developmental disorders.MethodsWe analyzed transcriptomic-weighted data from four mouse strains across three different germ layer tissues (liver, heart, and eye) and through embryonic stages. Applying a multifaceted approach, we calculated relative synonymous codon usage, reduced the dimensionality, and employed machine learning clustering techniques.Results and discussionThese techniques identified relative synonymous codon usage differences/similarities among strains and deviations in codon usage patterns between healthy and disease-linked genes. Original transcriptomic mouse data and RefSeq gene sequences can be found at the associated Mouse Embryo CoCoPUTs (codon and codon pair usage tables) website. Future studies can leverage this resource to uncover further insights into the dynamics of embryonic development and the corresponding codon usage biases that are paramount to understanding disease processes of embryologic origin.