Uncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity

Vista sencilla de ítem
dc.contributor.authorVillarroel, C.
dc.contributor.authorBastías, M.
dc.contributor.authorCanessa, P.
dc.contributor.authorCubillos, F.
dc.date.accessioned2024-09-11T23:37:11Z
dc.date.available2024-09-11T23:37:11Z
dc.date.issued2021-08
dc.descriptionTEXTO COMPLETO EN INGLÉS
dc.description.abstractHistorically, coding variants were prioritized when searching for causal mechanisms driving adaptation of natural populations to stressful environments. However, the recent focus on noncoding variants demonstrated their ubiquitous role in adaptation. ABSTRACT Saccharomyces cerevisiae rewires its transcriptional output to survive stressful environments, such as nitrogen scarcity under fermentative conditions. Although divergence in nitrogen metabolism among natural yeast populations has been reported, the impact of regulatory genetic variants modulating gene expression and nitrogen consumption remains to be investigated. Here, we employed an F1 hybrid from two contrasting S. cerevisiae strains, providing a controlled genetic environment to map cis factors involved in the divergence of gene expression regulation in response to nitrogen scarcity. We used a dual approach to obtain genome-wide allele-specific profiles of chromatin accessibility, transcription factor binding, and gene expression through ATAC-seq (assay for transposase accessible chromatin) and RNA-seq (transcriptome sequencing). We observed large variability in allele-specific expression and accessibility between the two genetic backgrounds, with a third of these differences specific to a deficient nitrogen environment. Furthermore, we discovered events of allelic bias in gene expression correlating with allelic bias in transcription factor binding solely under nitrogen scarcity, where the majority of these transcription factors orchestrates the nitrogen catabolite repression regulatory pathway and demonstrates a cis × environment-specific response. Our approach allowed us to find cis variants modulating gene expression, chromatin accessibility, and allelic differences in transcription factor binding in response to low nitrogen culture conditions. IMPORTANCE Historically, coding variants were prioritized when searching for causal mechanisms driving adaptation of natural populations to stressful environments. However, the recent focus on noncoding variants demonstrated their ubiquitous role in adaptation. Here, we performed genome-wide regulatory variation profiles between two divergent yeast strains when facing nitrogen nutritional stress. The open chromatin availability of several regulatory regions changes in response to nitrogen scarcity. Importantly, we describe regulatory events that deviate between strains. Our results demonstrate a widespread variation in gene expression regulation between naturally occurring populations in response to stressful environments.
dc.description.urihttps://www-sciencedirect-com.recursosbiblioteca.unab.cl/org/science/article/pii/S2379507721002087
dc.identifier.citationmSystems, Volume 6, Issue 4 , 17 August 2021
dc.identifier.doihttps://doi.org/10.1128/msystems.00466-21
dc.identifier.issn2379-5077
dc.identifier.urihttps://repositorio.unab.cl/handle/ria/60126
dc.language.isoen
dc.rights.licenseAttribution 4.0 International
dc.subjectyeastallele-specific
dc.subjectATAC-seqnitrogen
dc.subjectregulatory divergence
dc.subjectwinefermentation
dc.subjectgene regulation
dc.subjectgenetics
dc.subjectnatural variation
dc.titleUncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity
dc.typeArtículo
Archivos
Bloque original
Mostrando 1 - 1 de 1
No hay miniatura disponible
Nombre:
Villarroel_Uncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity.pdf
Tamaño:
1.45 MB
Formato:
Adobe Portable Document Format
Descargar
Bloque de licencias
Mostrando 1 - 1 de 1
No hay miniatura disponible
Nombre:
license.txt
Tamaño:
1.71 KB
Formato:
Item-specific license agreed upon to submission
Descripción:
Descargar
Colecciones
Fac.CV - Artículos de Revista