Cis-regulatory variants affect gene expression dynamics in yeast.
1Department of Biology, University of Rochester, Rochester, United States.
Elife
|August 9, 2021
Summary
Changes in gene regulatory sequences impact gene expression timing. This study reveals cis-regulatory variants influencing allele-specific expression dynamics, crucial for understanding evolutionary processes.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Evolution of cis-regulatory sequences is driven by their impact on gene expression.
- Understanding cis-regulatory variants is key to predicting expression differences within and between species.
- Gene expression timing, in addition to expression levels, may significantly influence regulatory sequence evolution.
Purpose of the Study:
- To investigate allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift.
- To identify cis-acting variation affecting gene expression dynamics.
- To characterize cis-regulatory variants influencing expression dynamics using high-throughput reporter assays.
Main Methods:
- Analysis of allele-specific expression (ASE) dynamics during the diauxic shift in Saccharomyces species.
- Association studies linking ASE dynamics to intergenic variants, insertions, and deletions.
- High-throughput reporter assays to test promoter regions and individual cis-regulatory variants.
- Construction of chimeric promoter regions to study interspecies expression dynamics.
Main Results:
- Appreciable cis-acting variation in gene expression dynamics was observed within and between Saccharomyces species.
- Within-species ASE dynamics are associated with intergenic variants, with insertions/deletions showing stronger associations than ASE levels.
- Reporter assays identified specific cis-regulatory variants impacting expression dynamics in regions recapitulating endogenous expression.
- Chimeric promoters between species revealed novel expression patterns, suggesting constraints on the evolution of gene expression dynamics.
Conclusions:
- Cis-regulatory sequence changes can modulate gene expression dynamics.
- The interplay between expression dynamics and other expression facets is important for cis-regulatory sequence evolution.
- Understanding gene expression timing is critical for a comprehensive view of regulatory sequence evolution.
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