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A review of strategies used to identify transposition events in plant genomes
Transposable elements (TEs) were initially considered redundant and dubbed ‘junk DNA’. However, more recently they were recognized as an essential element of genome plasticity. In nature, they frequently become active upon exposition of the host to stress conditions. Even though most transposition e...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9751208/ https://www.ncbi.nlm.nih.gov/pubmed/36531345 http://dx.doi.org/10.3389/fpls.2022.1080993 |
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author | Bajus, Marko Macko-Podgórni, Alicja Grzebelus, Dariusz Baránek, Miroslav |
author_facet | Bajus, Marko Macko-Podgórni, Alicja Grzebelus, Dariusz Baránek, Miroslav |
author_sort | Bajus, Marko |
collection | PubMed |
description | Transposable elements (TEs) were initially considered redundant and dubbed ‘junk DNA’. However, more recently they were recognized as an essential element of genome plasticity. In nature, they frequently become active upon exposition of the host to stress conditions. Even though most transposition events are neutral or even deleterious, occasionally they may happen to be beneficial, resulting in genetic novelty providing better fitness to the host. Hence, TE mobilization may promote adaptability and, in the long run, act as a significant evolutionary force. There are many examples of TE insertions resulting in increased tolerance to stresses or in novel features of crops which are appealing to the consumer. Possibly, TE-driven de novo variability could be utilized for crop improvement. However, in order to systematically study the mechanisms of TE/host interactions, it is necessary to have suitable tools to globally monitor any ongoing TE mobilization. With the development of novel potent technologies, new high-throughput strategies for studying TE dynamics are emerging. Here, we present currently available methods applied to monitor the activity of TEs in plants. We divide them on the basis of their operational principles, the position of target molecules in the process of transposition and their ability to capture real cases of actively transposing elements. Their possible theoretical and practical drawbacks are also discussed. Finally, conceivable strategies and combinations of methods resulting in an improved performance are proposed. |
format | Online Article Text |
id | pubmed-9751208 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-97512082022-12-16 A review of strategies used to identify transposition events in plant genomes Bajus, Marko Macko-Podgórni, Alicja Grzebelus, Dariusz Baránek, Miroslav Front Plant Sci Plant Science Transposable elements (TEs) were initially considered redundant and dubbed ‘junk DNA’. However, more recently they were recognized as an essential element of genome plasticity. In nature, they frequently become active upon exposition of the host to stress conditions. Even though most transposition events are neutral or even deleterious, occasionally they may happen to be beneficial, resulting in genetic novelty providing better fitness to the host. Hence, TE mobilization may promote adaptability and, in the long run, act as a significant evolutionary force. There are many examples of TE insertions resulting in increased tolerance to stresses or in novel features of crops which are appealing to the consumer. Possibly, TE-driven de novo variability could be utilized for crop improvement. However, in order to systematically study the mechanisms of TE/host interactions, it is necessary to have suitable tools to globally monitor any ongoing TE mobilization. With the development of novel potent technologies, new high-throughput strategies for studying TE dynamics are emerging. Here, we present currently available methods applied to monitor the activity of TEs in plants. We divide them on the basis of their operational principles, the position of target molecules in the process of transposition and their ability to capture real cases of actively transposing elements. Their possible theoretical and practical drawbacks are also discussed. Finally, conceivable strategies and combinations of methods resulting in an improved performance are proposed. Frontiers Media S.A. 2022-12-01 /pmc/articles/PMC9751208/ /pubmed/36531345 http://dx.doi.org/10.3389/fpls.2022.1080993 Text en Copyright © 2022 Bajus, Macko-Podgórni, Grzebelus and Baránek https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Bajus, Marko Macko-Podgórni, Alicja Grzebelus, Dariusz Baránek, Miroslav A review of strategies used to identify transposition events in plant genomes |
title | A review of strategies used to identify transposition events in plant genomes |
title_full | A review of strategies used to identify transposition events in plant genomes |
title_fullStr | A review of strategies used to identify transposition events in plant genomes |
title_full_unstemmed | A review of strategies used to identify transposition events in plant genomes |
title_short | A review of strategies used to identify transposition events in plant genomes |
title_sort | review of strategies used to identify transposition events in plant genomes |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9751208/ https://www.ncbi.nlm.nih.gov/pubmed/36531345 http://dx.doi.org/10.3389/fpls.2022.1080993 |
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