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Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

Transposable elements (TEs) are mobile genetic sequences that can jump around the genome from one location to another, behaving as genomic parasites. TEs have been particularly effective in colonizing mammalian genomes, and such heavy TE load is expected to have conditioned genome evolution. Indeed,...

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Detalles Bibliográficos
Autores principales: de Souza, Flávio S.J., Franchini, Lucía F., Rubinstein, Marcelo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3649676/
https://www.ncbi.nlm.nih.gov/pubmed/23486611
http://dx.doi.org/10.1093/molbev/mst045
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author de Souza, Flávio S.J.
Franchini, Lucía F.
Rubinstein, Marcelo
author_facet de Souza, Flávio S.J.
Franchini, Lucía F.
Rubinstein, Marcelo
author_sort de Souza, Flávio S.J.
collection PubMed
description Transposable elements (TEs) are mobile genetic sequences that can jump around the genome from one location to another, behaving as genomic parasites. TEs have been particularly effective in colonizing mammalian genomes, and such heavy TE load is expected to have conditioned genome evolution. Indeed, studies conducted both at the gene and genome levels have uncovered TE insertions that seem to have been co-opted—or exapted—by providing transcription factor binding sites (TFBSs) that serve as promoters and enhancers, leading to the hypothesis that TE exaptation is a major factor in the evolution of gene regulation. Here, we critically review the evidence for exaptation of TE-derived sequences as TFBSs, promoters, enhancers, and silencers/insulators both at the gene and genome levels. We classify the functional impact attributed to TE insertions into four categories of increasing complexity and argue that so far very few studies have conclusively demonstrated exaptation of TEs as transcriptional regulatory regions. We also contend that many genome-wide studies dealing with TE exaptation in recent lineages of mammals are still inconclusive and that the hypothesis of rapid transcriptional regulatory rewiring mediated by TE mobilization must be taken with caution. Finally, we suggest experimental approaches that may help attributing higher-order functions to candidate exapted TEs.
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spelling pubmed-36496762013-05-13 Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong? de Souza, Flávio S.J. Franchini, Lucía F. Rubinstein, Marcelo Mol Biol Evol Review Transposable elements (TEs) are mobile genetic sequences that can jump around the genome from one location to another, behaving as genomic parasites. TEs have been particularly effective in colonizing mammalian genomes, and such heavy TE load is expected to have conditioned genome evolution. Indeed, studies conducted both at the gene and genome levels have uncovered TE insertions that seem to have been co-opted—or exapted—by providing transcription factor binding sites (TFBSs) that serve as promoters and enhancers, leading to the hypothesis that TE exaptation is a major factor in the evolution of gene regulation. Here, we critically review the evidence for exaptation of TE-derived sequences as TFBSs, promoters, enhancers, and silencers/insulators both at the gene and genome levels. We classify the functional impact attributed to TE insertions into four categories of increasing complexity and argue that so far very few studies have conclusively demonstrated exaptation of TEs as transcriptional regulatory regions. We also contend that many genome-wide studies dealing with TE exaptation in recent lineages of mammals are still inconclusive and that the hypothesis of rapid transcriptional regulatory rewiring mediated by TE mobilization must be taken with caution. Finally, we suggest experimental approaches that may help attributing higher-order functions to candidate exapted TEs. Oxford University Press 2013-06 2013-03-13 /pmc/articles/PMC3649676/ /pubmed/23486611 http://dx.doi.org/10.1093/molbev/mst045 Text en © The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
de Souza, Flávio S.J.
Franchini, Lucía F.
Rubinstein, Marcelo
Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
title Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
title_full Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
title_fullStr Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
title_full_unstemmed Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
title_short Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
title_sort exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3649676/
https://www.ncbi.nlm.nih.gov/pubmed/23486611
http://dx.doi.org/10.1093/molbev/mst045
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