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Cis-regulatory variants affect gene expression dynamics in yeast

Evolution of cis-regulatory sequences depends on how they affect gene expression and motivates both the identification and prediction of cis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis-regulatory variants to...

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Autores principales: Shih, Ching-Hua, Fay, Justin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8367379/
https://www.ncbi.nlm.nih.gov/pubmed/34369376
http://dx.doi.org/10.7554/eLife.68469
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author Shih, Ching-Hua
Fay, Justin
author_facet Shih, Ching-Hua
Fay, Justin
author_sort Shih, Ching-Hua
collection PubMed
description Evolution of cis-regulatory sequences depends on how they affect gene expression and motivates both the identification and prediction of cis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis-regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of cis-regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift and found appreciable cis-acting variation in gene expression dynamics. Within-species ASE is associated with intergenic variants, and ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations, we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression, we identified and characterized cis-regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes in cis-regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects of expression is relevant to the evolution of cis-regulatory sequences.
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spelling pubmed-83673792021-08-18 Cis-regulatory variants affect gene expression dynamics in yeast Shih, Ching-Hua Fay, Justin eLife Evolutionary Biology Evolution of cis-regulatory sequences depends on how they affect gene expression and motivates both the identification and prediction of cis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis-regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of cis-regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift and found appreciable cis-acting variation in gene expression dynamics. Within-species ASE is associated with intergenic variants, and ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations, we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression, we identified and characterized cis-regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes in cis-regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects of expression is relevant to the evolution of cis-regulatory sequences. eLife Sciences Publications, Ltd 2021-08-09 /pmc/articles/PMC8367379/ /pubmed/34369376 http://dx.doi.org/10.7554/eLife.68469 Text en © 2021, Shih and Fay https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Evolutionary Biology
Shih, Ching-Hua
Fay, Justin
Cis-regulatory variants affect gene expression dynamics in yeast
title Cis-regulatory variants affect gene expression dynamics in yeast
title_full Cis-regulatory variants affect gene expression dynamics in yeast
title_fullStr Cis-regulatory variants affect gene expression dynamics in yeast
title_full_unstemmed Cis-regulatory variants affect gene expression dynamics in yeast
title_short Cis-regulatory variants affect gene expression dynamics in yeast
title_sort cis-regulatory variants affect gene expression dynamics in yeast
topic Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8367379/
https://www.ncbi.nlm.nih.gov/pubmed/34369376
http://dx.doi.org/10.7554/eLife.68469
work_keys_str_mv AT shihchinghua cisregulatoryvariantsaffectgeneexpressiondynamicsinyeast
AT fayjustin cisregulatoryvariantsaffectgeneexpressiondynamicsinyeast