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Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids

Transposable element (TE) insertions are a source of structural variation and can cause genetic instability and gene expression changes. A host can limit the spread of TEs with various repression mechanisms. Many examples of plant and animal interspecific hybrids show disrupted TE repression leading...

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Autores principales: Drouin, Marika, Hénault, Mathieu, Hallin, Johan, Landry, Christian R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512236/
https://www.ncbi.nlm.nih.gov/pubmed/37744137
http://dx.doi.org/10.3389/ffunb.2021.729264
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author Drouin, Marika
Hénault, Mathieu
Hallin, Johan
Landry, Christian R.
author_facet Drouin, Marika
Hénault, Mathieu
Hallin, Johan
Landry, Christian R.
author_sort Drouin, Marika
collection PubMed
description Transposable element (TE) insertions are a source of structural variation and can cause genetic instability and gene expression changes. A host can limit the spread of TEs with various repression mechanisms. Many examples of plant and animal interspecific hybrids show disrupted TE repression leading to TE propagation. Recent studies in yeast did not find any increase in transposition rate in hybrids. However, this does not rule out the possibility that the transcriptional or translational activity of TEs increases following hybridization because of a disruption of the host TE control mechanisms. Thus, whether total expression of a TE family is higher in hybrids than in their parental species remains to be examined. We leveraged publically available RNA-seq and ribosomal profiling data on yeast artificial hybrids of the Saccharomyces genus and performed differential expression analysis of their LTR retrotransposons (Ty elements). Our analyses of total mRNA levels show that Ty elements are generally not differentially expressed in hybrids, even when the hybrids are exposed to a low temperature stress condition. Overall, only 2/26 Ty families show significantly higher expression in the S. cerevisiae × S. uvarum hybrids while there are 3/26 showing significantly lower expression in the S. cerevisiae x S. paradoxus hybrids. Our analysis of ribosome profiling data of S. cerevisiae × S. paradoxus hybrids shows similar translation efficiency of Ty in both parents and hybrids, except for Ty1_cer showing higher translation efficiency. Overall, our results do not support the hypothesis that hybridization could act as a systematic trigger of TE expression in yeast and suggest that the impact of hybridization on TE activity is strain and TE specific.
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spelling pubmed-105122362023-09-22 Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids Drouin, Marika Hénault, Mathieu Hallin, Johan Landry, Christian R. Front Fungal Biol Fungal Biology Transposable element (TE) insertions are a source of structural variation and can cause genetic instability and gene expression changes. A host can limit the spread of TEs with various repression mechanisms. Many examples of plant and animal interspecific hybrids show disrupted TE repression leading to TE propagation. Recent studies in yeast did not find any increase in transposition rate in hybrids. However, this does not rule out the possibility that the transcriptional or translational activity of TEs increases following hybridization because of a disruption of the host TE control mechanisms. Thus, whether total expression of a TE family is higher in hybrids than in their parental species remains to be examined. We leveraged publically available RNA-seq and ribosomal profiling data on yeast artificial hybrids of the Saccharomyces genus and performed differential expression analysis of their LTR retrotransposons (Ty elements). Our analyses of total mRNA levels show that Ty elements are generally not differentially expressed in hybrids, even when the hybrids are exposed to a low temperature stress condition. Overall, only 2/26 Ty families show significantly higher expression in the S. cerevisiae × S. uvarum hybrids while there are 3/26 showing significantly lower expression in the S. cerevisiae x S. paradoxus hybrids. Our analysis of ribosome profiling data of S. cerevisiae × S. paradoxus hybrids shows similar translation efficiency of Ty in both parents and hybrids, except for Ty1_cer showing higher translation efficiency. Overall, our results do not support the hypothesis that hybridization could act as a systematic trigger of TE expression in yeast and suggest that the impact of hybridization on TE activity is strain and TE specific. Frontiers Media S.A. 2021-08-23 /pmc/articles/PMC10512236/ /pubmed/37744137 http://dx.doi.org/10.3389/ffunb.2021.729264 Text en Copyright © 2021 Drouin, Hénault, Hallin and Landry. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Fungal Biology
Drouin, Marika
Hénault, Mathieu
Hallin, Johan
Landry, Christian R.
Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids
title Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids
title_full Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids
title_fullStr Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids
title_full_unstemmed Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids
title_short Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids
title_sort testing the genomic shock hypothesis using transposable element expression in yeast hybrids
topic Fungal Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512236/
https://www.ncbi.nlm.nih.gov/pubmed/37744137
http://dx.doi.org/10.3389/ffunb.2021.729264
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