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The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality

Transposable elements (TEs) are major components of eukaryotic genomes and represent approximately 45% of the human genome. TEs can be important sources of novelty in genomes and there is increasing evidence that TEs contribute to the evolution of gene regulation in mammals. Gene duplication is an e...

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Autores principales: Correa, Margot, Lerat, Emmanuelle, Birmelé, Etienne, Samson, Franck, Bouillon, Bérengère, Normand, Kévin, Rizzon, Carène
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155550/
https://www.ncbi.nlm.nih.gov/pubmed/33973013
http://dx.doi.org/10.1093/gbe/evab062
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author Correa, Margot
Lerat, Emmanuelle
Birmelé, Etienne
Samson, Franck
Bouillon, Bérengère
Normand, Kévin
Rizzon, Carène
author_facet Correa, Margot
Lerat, Emmanuelle
Birmelé, Etienne
Samson, Franck
Bouillon, Bérengère
Normand, Kévin
Rizzon, Carène
author_sort Correa, Margot
collection PubMed
description Transposable elements (TEs) are major components of eukaryotic genomes and represent approximately 45% of the human genome. TEs can be important sources of novelty in genomes and there is increasing evidence that TEs contribute to the evolution of gene regulation in mammals. Gene duplication is an evolutionary mechanism that also provides new genetic material and opportunities to acquire new functions. To investigate how duplicated genes are maintained in genomes, here, we explored the TE environment of duplicated and singleton genes. We found that singleton genes have more short-interspersed nuclear elements and DNA transposons in their vicinity than duplicated genes, whereas long-interspersed nuclear elements and long-terminal repeat retrotransposons have accumulated more near duplicated genes. We also discovered that this result is highly associated with the degree of essentiality of the genes with an unexpected accumulation of short-interspersed nuclear elements and DNA transposons around the more-essential genes. Our results underline the importance of taking into account the TE environment of genes to better understand how duplicated genes are maintained in genomes.
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spelling pubmed-81555502021-05-28 The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality Correa, Margot Lerat, Emmanuelle Birmelé, Etienne Samson, Franck Bouillon, Bérengère Normand, Kévin Rizzon, Carène Genome Biol Evol Research Article Transposable elements (TEs) are major components of eukaryotic genomes and represent approximately 45% of the human genome. TEs can be important sources of novelty in genomes and there is increasing evidence that TEs contribute to the evolution of gene regulation in mammals. Gene duplication is an evolutionary mechanism that also provides new genetic material and opportunities to acquire new functions. To investigate how duplicated genes are maintained in genomes, here, we explored the TE environment of duplicated and singleton genes. We found that singleton genes have more short-interspersed nuclear elements and DNA transposons in their vicinity than duplicated genes, whereas long-interspersed nuclear elements and long-terminal repeat retrotransposons have accumulated more near duplicated genes. We also discovered that this result is highly associated with the degree of essentiality of the genes with an unexpected accumulation of short-interspersed nuclear elements and DNA transposons around the more-essential genes. Our results underline the importance of taking into account the TE environment of genes to better understand how duplicated genes are maintained in genomes. Oxford University Press 2021-04-15 /pmc/articles/PMC8155550/ /pubmed/33973013 http://dx.doi.org/10.1093/gbe/evab062 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Correa, Margot
Lerat, Emmanuelle
Birmelé, Etienne
Samson, Franck
Bouillon, Bérengère
Normand, Kévin
Rizzon, Carène
The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality
title The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality
title_full The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality
title_fullStr The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality
title_full_unstemmed The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality
title_short The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality
title_sort transposable element environment of human genes differs according to their duplication status and essentiality
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155550/
https://www.ncbi.nlm.nih.gov/pubmed/33973013
http://dx.doi.org/10.1093/gbe/evab062
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