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Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans

Though sequence differences between alleles are often limited to a few polymorphisms, these differences can cause large and widespread allelic variation at the expression level. Such allele-specific expression (ASE) has been extensively explored at the level of transcription but not translation. Her...

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Autores principales: Muzzey, Dale, Sherlock, Gavin, Weissman, Jonathan S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032860/
https://www.ncbi.nlm.nih.gov/pubmed/24732588
http://dx.doi.org/10.1101/gr.166322.113
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author Muzzey, Dale
Sherlock, Gavin
Weissman, Jonathan S.
author_facet Muzzey, Dale
Sherlock, Gavin
Weissman, Jonathan S.
author_sort Muzzey, Dale
collection PubMed
description Though sequence differences between alleles are often limited to a few polymorphisms, these differences can cause large and widespread allelic variation at the expression level. Such allele-specific expression (ASE) has been extensively explored at the level of transcription but not translation. Here we measured ASE in the diploid yeast Candida albicans at both the transcriptional and translational levels using RNA-seq and ribosome profiling, respectively. Since C. albicans is an obligate diploid, our analysis isolates ASE arising from cis elements in a natural, nonhybrid organism, where allelic effects reflect evolutionary forces. Importantly, we find that ASE arising from translation is of a similar magnitude as transcriptional ASE, both in terms of the number of genes affected and the magnitude of the bias. We further observe coordination between ASE at the levels of transcription and translation for single genes. Specifically, reinforcing relationships—where transcription and translation favor the same allele—are more frequent than expected by chance, consistent with selective pressure tuning ASE at multiple regulatory steps. Finally, we parameterize alleles based on a range of properties and find that SNP location and predicted mRNA-structure stability are associated with translational ASE in cis. Since this analysis probes more than 4000 allelic pairs spanning a broad range of variations, our data provide a genome-wide view into the relative impact of cis elements that regulate translation.
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spelling pubmed-40328602014-12-01 Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans Muzzey, Dale Sherlock, Gavin Weissman, Jonathan S. Genome Res Research Though sequence differences between alleles are often limited to a few polymorphisms, these differences can cause large and widespread allelic variation at the expression level. Such allele-specific expression (ASE) has been extensively explored at the level of transcription but not translation. Here we measured ASE in the diploid yeast Candida albicans at both the transcriptional and translational levels using RNA-seq and ribosome profiling, respectively. Since C. albicans is an obligate diploid, our analysis isolates ASE arising from cis elements in a natural, nonhybrid organism, where allelic effects reflect evolutionary forces. Importantly, we find that ASE arising from translation is of a similar magnitude as transcriptional ASE, both in terms of the number of genes affected and the magnitude of the bias. We further observe coordination between ASE at the levels of transcription and translation for single genes. Specifically, reinforcing relationships—where transcription and translation favor the same allele—are more frequent than expected by chance, consistent with selective pressure tuning ASE at multiple regulatory steps. Finally, we parameterize alleles based on a range of properties and find that SNP location and predicted mRNA-structure stability are associated with translational ASE in cis. Since this analysis probes more than 4000 allelic pairs spanning a broad range of variations, our data provide a genome-wide view into the relative impact of cis elements that regulate translation. Cold Spring Harbor Laboratory Press 2014-06 /pmc/articles/PMC4032860/ /pubmed/24732588 http://dx.doi.org/10.1101/gr.166322.113 Text en © 2014 Muzzey et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Research
Muzzey, Dale
Sherlock, Gavin
Weissman, Jonathan S.
Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
title Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
title_full Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
title_fullStr Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
title_full_unstemmed Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
title_short Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
title_sort extensive and coordinated control of allele-specific expression by both transcription and translation in candida albicans
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032860/
https://www.ncbi.nlm.nih.gov/pubmed/24732588
http://dx.doi.org/10.1101/gr.166322.113
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