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LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots

RNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in mammals. By contrast, long terminal repeat (LTR) retrotra...

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Autores principales: Zhu, Zhenglin, Tan, Shengjun, Zhang, Yaqiong, Zhang, Yong E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838847/
https://www.ncbi.nlm.nih.gov/pubmed/27098918
http://dx.doi.org/10.1038/srep24755
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author Zhu, Zhenglin
Tan, Shengjun
Zhang, Yaqiong
Zhang, Yong E.
author_facet Zhu, Zhenglin
Tan, Shengjun
Zhang, Yaqiong
Zhang, Yong E.
author_sort Zhu, Zhenglin
collection PubMed
description RNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in mammals. By contrast, long terminal repeat (LTR) retrotransposons appear to be the major player in plants, although an L1-like mechanism has also been hypothesized to be involved in retroposition. We tested this hypothesis by searching for young retrocopies, as these still retain the sequence features associated with the underlying retroposition mechanism. Specifically, we identified polymorphic retrocopies (retroCNVs) by analyzing public Arabidopsis (Arabidopsis thaliana) resequencing data. Furthermore, we searched for recently originated retrocopies encoded by the reference genome of Arabidopsis and Manihot esculenta. Across these two datasets, we found cases with L1-like hallmarks, namely, the expected target site sequence, a polyA tail and target site duplications. Such data suggest that an L1-like mechanism could operate in plants, especially dicots.
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spelling pubmed-48388472016-04-27 LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots Zhu, Zhenglin Tan, Shengjun Zhang, Yaqiong Zhang, Yong E. Sci Rep Article RNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in mammals. By contrast, long terminal repeat (LTR) retrotransposons appear to be the major player in plants, although an L1-like mechanism has also been hypothesized to be involved in retroposition. We tested this hypothesis by searching for young retrocopies, as these still retain the sequence features associated with the underlying retroposition mechanism. Specifically, we identified polymorphic retrocopies (retroCNVs) by analyzing public Arabidopsis (Arabidopsis thaliana) resequencing data. Furthermore, we searched for recently originated retrocopies encoded by the reference genome of Arabidopsis and Manihot esculenta. Across these two datasets, we found cases with L1-like hallmarks, namely, the expected target site sequence, a polyA tail and target site duplications. Such data suggest that an L1-like mechanism could operate in plants, especially dicots. Nature Publishing Group 2016-04-21 /pmc/articles/PMC4838847/ /pubmed/27098918 http://dx.doi.org/10.1038/srep24755 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Zhu, Zhenglin
Tan, Shengjun
Zhang, Yaqiong
Zhang, Yong E.
LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots
title LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots
title_full LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots
title_fullStr LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots
title_full_unstemmed LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots
title_short LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots
title_sort line-1-like retrotransposons contribute to rna-based gene duplication in dicots
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838847/
https://www.ncbi.nlm.nih.gov/pubmed/27098918
http://dx.doi.org/10.1038/srep24755
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