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Small RNAs, DNA methylation and transposable elements in wheat
BACKGROUND: More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppressed in the genome via small non-coding RNAs (sRNAs). sRNAs guide silencing of TE...
Autores principales: | , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996936/ https://www.ncbi.nlm.nih.gov/pubmed/20584339 http://dx.doi.org/10.1186/1471-2164-11-408 |
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author | Cantu, Dario Vanzetti, Leonardo S Sumner, Adam Dubcovsky, Martin Matvienko, Marta Distelfeld, Assaf Michelmore, Richard W Dubcovsky, Jorge |
author_facet | Cantu, Dario Vanzetti, Leonardo S Sumner, Adam Dubcovsky, Martin Matvienko, Marta Distelfeld, Assaf Michelmore, Richard W Dubcovsky, Jorge |
author_sort | Cantu, Dario |
collection | PubMed |
description | BACKGROUND: More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppressed in the genome via small non-coding RNAs (sRNAs). sRNAs guide silencing of TEs at the transcriptional (mainly 24-nt sRNAs) and post-transcriptional (mainly 21-nt sRNAs) levels. In this study, we report the distribution of these two types of sRNAs among the different classes of wheat TEs, the regions targeted within the TEs, and their impact on the methylation patterns of the targeted regions. RESULTS: We constructed an sRNA library from hexaploid wheat and developed a database that included our library and three other publicly available sRNA libraries from wheat. For five completely-sequenced wheat BAC contigs, most perfectly matching sRNAs represented TE sequences, suggesting that a large fraction of the wheat sRNAs originated from TEs. An analysis of all wheat TEs present in the Triticeae Repeat Sequence database showed that sRNA abundance was correlated with the estimated number of TEs within each class. Most of the sRNAs perfectly matching miniature inverted repeat transposable elements (MITEs) belonged to the 21-nt class and were mainly targeted to the terminal inverted repeats (TIRs). In contrast, most of the sRNAs matching class I and class II TEs belonged to the 24-nt class and were mainly targeted to the long terminal repeats (LTRs) in the class I TEs and to the terminal repeats in CACTA transposons. An analysis of the mutation frequency in potentially methylated sites revealed a three-fold increase in TE mutation frequency relative to intron and untranslated genic regions. This increase is consistent with wheat TEs being preferentially methylated, likely by sRNA targeting. CONCLUSIONS: Our study examines the wheat epigenome in relation to known TEs. sRNA-directed transcriptional and post-transcriptional silencing plays important roles in the short-term suppression of TEs in the wheat genome, whereas DNA methylation and increased mutation rates may provide a long-term mechanism to inactivate TEs. |
format | Text |
id | pubmed-2996936 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-29969362010-12-07 Small RNAs, DNA methylation and transposable elements in wheat Cantu, Dario Vanzetti, Leonardo S Sumner, Adam Dubcovsky, Martin Matvienko, Marta Distelfeld, Assaf Michelmore, Richard W Dubcovsky, Jorge BMC Genomics Research Article BACKGROUND: More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppressed in the genome via small non-coding RNAs (sRNAs). sRNAs guide silencing of TEs at the transcriptional (mainly 24-nt sRNAs) and post-transcriptional (mainly 21-nt sRNAs) levels. In this study, we report the distribution of these two types of sRNAs among the different classes of wheat TEs, the regions targeted within the TEs, and their impact on the methylation patterns of the targeted regions. RESULTS: We constructed an sRNA library from hexaploid wheat and developed a database that included our library and three other publicly available sRNA libraries from wheat. For five completely-sequenced wheat BAC contigs, most perfectly matching sRNAs represented TE sequences, suggesting that a large fraction of the wheat sRNAs originated from TEs. An analysis of all wheat TEs present in the Triticeae Repeat Sequence database showed that sRNA abundance was correlated with the estimated number of TEs within each class. Most of the sRNAs perfectly matching miniature inverted repeat transposable elements (MITEs) belonged to the 21-nt class and were mainly targeted to the terminal inverted repeats (TIRs). In contrast, most of the sRNAs matching class I and class II TEs belonged to the 24-nt class and were mainly targeted to the long terminal repeats (LTRs) in the class I TEs and to the terminal repeats in CACTA transposons. An analysis of the mutation frequency in potentially methylated sites revealed a three-fold increase in TE mutation frequency relative to intron and untranslated genic regions. This increase is consistent with wheat TEs being preferentially methylated, likely by sRNA targeting. CONCLUSIONS: Our study examines the wheat epigenome in relation to known TEs. sRNA-directed transcriptional and post-transcriptional silencing plays important roles in the short-term suppression of TEs in the wheat genome, whereas DNA methylation and increased mutation rates may provide a long-term mechanism to inactivate TEs. BioMed Central 2010-06-29 /pmc/articles/PMC2996936/ /pubmed/20584339 http://dx.doi.org/10.1186/1471-2164-11-408 Text en Copyright ©2010 Cantu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Cantu, Dario Vanzetti, Leonardo S Sumner, Adam Dubcovsky, Martin Matvienko, Marta Distelfeld, Assaf Michelmore, Richard W Dubcovsky, Jorge Small RNAs, DNA methylation and transposable elements in wheat |
title | Small RNAs, DNA methylation and transposable elements in wheat |
title_full | Small RNAs, DNA methylation and transposable elements in wheat |
title_fullStr | Small RNAs, DNA methylation and transposable elements in wheat |
title_full_unstemmed | Small RNAs, DNA methylation and transposable elements in wheat |
title_short | Small RNAs, DNA methylation and transposable elements in wheat |
title_sort | small rnas, dna methylation and transposable elements in wheat |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996936/ https://www.ncbi.nlm.nih.gov/pubmed/20584339 http://dx.doi.org/10.1186/1471-2164-11-408 |
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