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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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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. |
format | Online Article Text |
id | pubmed-7211425 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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