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Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues

Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tissues, and how this varies across major vertebrate lineages. We present the first comparative analysis integrating TE expression and TE regulatory pathway a...

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Autores principales: Pasquesi, Giulia I M, Perry, Blair W, Vandewege, Mike W, Ruggiero, Robert P, Schield, Drew R, Castoe, Todd A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211425/
https://www.ncbi.nlm.nih.gov/pubmed/32271917
http://dx.doi.org/10.1093/gbe/evaa068
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author Pasquesi, Giulia I M
Perry, Blair W
Vandewege, Mike W
Ruggiero, Robert P
Schield, Drew R
Castoe, Todd A
author_facet Pasquesi, Giulia I M
Perry, Blair W
Vandewege, Mike W
Ruggiero, Robert P
Schield, Drew R
Castoe, Todd A
author_sort Pasquesi, Giulia I M
collection PubMed
description Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tissues, and how this varies across major vertebrate lineages. We present the first comparative analysis integrating TE expression and TE regulatory pathway activity in somatic and gametic tissues for a diverse set of 12 vertebrates. We conduct simultaneous gene and TE expression analyses to characterize patterns of TE expression and TE regulation across vertebrates and examine relationships between these features. We find remarkable variation in the expression of genes involved in TE negative regulation across tissues and species, yet consistently high expression in germline tissues, particularly in testes. Most vertebrates show comparably high levels of TE regulatory pathway activity across gonadal tissues except for mammals, where reduced activity of TE regulatory pathways in ovarian tissues may be the result of lower relative germ cell densities. We also find that all vertebrate lineages examined exhibit remarkably high levels of TE-derived transcripts in somatic and gametic tissues, with recently active TE families showing higher expression in gametic tissues. Although most TE-derived transcripts originate from inactive ancient TE families (and are likely incapable of transposition), such high levels of TE-derived RNA in the cytoplasm may have secondary, unappreciated biological relevance.
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spelling pubmed-72114252020-05-14 Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues Pasquesi, Giulia I M Perry, Blair W Vandewege, Mike W Ruggiero, Robert P Schield, Drew R Castoe, Todd A Genome Biol Evol Research Article Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tissues, and how this varies across major vertebrate lineages. We present the first comparative analysis integrating TE expression and TE regulatory pathway activity in somatic and gametic tissues for a diverse set of 12 vertebrates. We conduct simultaneous gene and TE expression analyses to characterize patterns of TE expression and TE regulation across vertebrates and examine relationships between these features. We find remarkable variation in the expression of genes involved in TE negative regulation across tissues and species, yet consistently high expression in germline tissues, particularly in testes. Most vertebrates show comparably high levels of TE regulatory pathway activity across gonadal tissues except for mammals, where reduced activity of TE regulatory pathways in ovarian tissues may be the result of lower relative germ cell densities. We also find that all vertebrate lineages examined exhibit remarkably high levels of TE-derived transcripts in somatic and gametic tissues, with recently active TE families showing higher expression in gametic tissues. Although most TE-derived transcripts originate from inactive ancient TE families (and are likely incapable of transposition), such high levels of TE-derived RNA in the cytoplasm may have secondary, unappreciated biological relevance. Oxford University Press 2020-04-09 /pmc/articles/PMC7211425/ /pubmed/32271917 http://dx.doi.org/10.1093/gbe/evaa068 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Pasquesi, Giulia I M
Perry, Blair W
Vandewege, Mike W
Ruggiero, Robert P
Schield, Drew R
Castoe, Todd A
Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
title Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
title_full Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
title_fullStr Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
title_full_unstemmed Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
title_short Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
title_sort vertebrate lineages exhibit diverse patterns of transposable element regulation and expression across tissues
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211425/
https://www.ncbi.nlm.nih.gov/pubmed/32271917
http://dx.doi.org/10.1093/gbe/evaa068
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