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Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice
Sylvia M Durkin1, Mallory A Ballinger1, Michael W Nachman1
1Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America.
Plos Genetics
|February 2, 2024
Summary
Adaptive evolution in mice shows parallel gene expression changes driven by cis-regulatory alterations in tissue-specific genes. These findings illuminate early-stage gene regulatory evolution during divergence.
Area of Science:
- Evolutionary biology
- Genomics
- Molecular biology
Background:
- Gene regulation changes are key to adaptive evolution.
- The roles of cis- and trans-acting factors in short-term evolution are not fully understood.
- Studying parallel evolution can reveal mechanisms of divergence.
Purpose of the Study:
- To investigate gene expression patterns in mice adapted to different climates.
- To determine the relative contributions of cis- and trans-acting changes in early adaptive evolution.
- To assess the role of tissue-specific and cis-regulated genes in parallel evolution.
Main Methods:
- Comparative gene expression analysis in liver and brown adipose tissue of warm- and cold-adapted mouse strains.
- Allele-specific expression analysis in F1 hybrids.
- Integration of expression data with population genetic scans for selection.
Main Results:
- Parallel gene expression changes were observed more frequently than expected by chance.
- Expression evolution was predominantly linked to tissue-specific and cis-regulated genes.
- Genes under selection in natural populations showed parallelism and were enriched for cis-regulation, impacting traits like body size and immunity.
Conclusions:
- Parallel gene expression evolution in independently adapting mouse populations is largely driven by cis-regulatory changes.
- Tissue-specific regulation plays a significant role in early adaptive divergence.
- Cis-regulatory changes under selection influence key adaptive phenotypes.
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