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Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stre...

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Autores principales: Lopes, Fabrício R., Jjingo, Daudi, da Silva, Carlos R. M., Andrade, Alan C., Marraccini, Pierre, Teixeira, João B., Carazzolle, Marcelo F., Pereira, Gonçalo A. G., Pereira, Luiz Filipe P., Vanzela, André L. L., Wang, Lu, Jordan, I. King, Carareto, Claudia M. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3823963/
https://www.ncbi.nlm.nih.gov/pubmed/24244387
http://dx.doi.org/10.1371/journal.pone.0078931
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author Lopes, Fabrício R.
Jjingo, Daudi
da Silva, Carlos R. M.
Andrade, Alan C.
Marraccini, Pierre
Teixeira, João B.
Carazzolle, Marcelo F.
Pereira, Gonçalo A. G.
Pereira, Luiz Filipe P.
Vanzela, André L. L.
Wang, Lu
Jordan, I. King
Carareto, Claudia M. A.
author_facet Lopes, Fabrício R.
Jjingo, Daudi
da Silva, Carlos R. M.
Andrade, Alan C.
Marraccini, Pierre
Teixeira, João B.
Carazzolle, Marcelo F.
Pereira, Gonçalo A. G.
Pereira, Luiz Filipe P.
Vanzela, André L. L.
Wang, Lu
Jordan, I. King
Carareto, Claudia M. A.
author_sort Lopes, Fabrício R.
collection PubMed
description Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences.
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spelling pubmed-38239632013-11-15 Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes Lopes, Fabrício R. Jjingo, Daudi da Silva, Carlos R. M. Andrade, Alan C. Marraccini, Pierre Teixeira, João B. Carazzolle, Marcelo F. Pereira, Gonçalo A. G. Pereira, Luiz Filipe P. Vanzela, André L. L. Wang, Lu Jordan, I. King Carareto, Claudia M. A. PLoS One Research Article Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences. Public Library of Science 2013-11-11 /pmc/articles/PMC3823963/ /pubmed/24244387 http://dx.doi.org/10.1371/journal.pone.0078931 Text en © 2013 Lopes et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Lopes, Fabrício R.
Jjingo, Daudi
da Silva, Carlos R. M.
Andrade, Alan C.
Marraccini, Pierre
Teixeira, João B.
Carazzolle, Marcelo F.
Pereira, Gonçalo A. G.
Pereira, Luiz Filipe P.
Vanzela, André L. L.
Wang, Lu
Jordan, I. King
Carareto, Claudia M. A.
Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes
title Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes
title_full Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes
title_fullStr Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes
title_full_unstemmed Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes
title_short Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes
title_sort transcriptional activity, chromosomal distribution and expression effects of transposable elements in coffea genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3823963/
https://www.ncbi.nlm.nih.gov/pubmed/24244387
http://dx.doi.org/10.1371/journal.pone.0078931
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