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Genes 2019, 10(4), 258; https://doi.org/10.3390/genes10040258

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

1
CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France
2
Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
3
CNRS, IHPE UMR 5244, University of Perpignan Via Domitia, IFREMER, University Montpellier, F-66860 Perpignan, France
*
Author to whom correspondence should be addressed.
Received: 4 February 2019 / Revised: 27 March 2019 / Accepted: 27 March 2019 / Published: 31 March 2019
(This article belongs to the Special Issue Epigenetics and Adaptation)
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PDF [281 KB, uploaded 31 March 2019]

Abstract

Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so. View Full-Text
Keywords: transposable element; epigenomics; bioinformatic tools transposable element; epigenomics; bioinformatic tools
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Lerat, E.; Casacuberta, J.; Chaparro, C.; Vieira, C. On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses. Genes 2019, 10, 258.

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