Small RNAs, DNA methylation and transposable elements in wheat

Dario Cantu, Leonardo S. Vanzetti, Adam Sumner, Martin Dubcovsky, Marta Matvienko, Assaf Distelfeld, Richard W Michelmore, Jorge Dubcovsky

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number408
JournalBMC Genomics
Volume11
Issue number1
DOIs
StatePublished - Jun 29 2010

Fingerprint

DNA Transposable Elements
DNA Methylation
Small Untranslated RNA
Triticum
RNA
Terminal Repeat Sequences
Mutation Rate
Genome
Transcriptional Silencer Elements
Databases
Untranslated Regions
RNA Interference

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Cantu, D., Vanzetti, L. S., Sumner, A., Dubcovsky, M., Matvienko, M., Distelfeld, A., ... Dubcovsky, J. (2010). Small RNAs, DNA methylation and transposable elements in wheat. BMC Genomics, 11(1), [408]. https://doi.org/10.1186/1471-2164-11-408

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.

In: BMC Genomics, Vol. 11, No. 1, 408, 29.06.2010.

Research output: Contribution to journalArticle

Cantu, D, Vanzetti, LS, Sumner, A, Dubcovsky, M, Matvienko, M, Distelfeld, A, Michelmore, RW & Dubcovsky, J 2010, 'Small RNAs, DNA methylation and transposable elements in wheat', BMC Genomics, vol. 11, no. 1, 408. https://doi.org/10.1186/1471-2164-11-408
Cantu D, Vanzetti LS, Sumner A, Dubcovsky M, Matvienko M, Distelfeld A et al. Small RNAs, DNA methylation and transposable elements in wheat. BMC Genomics. 2010 Jun 29;11(1). 408. https://doi.org/10.1186/1471-2164-11-408
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. In: BMC Genomics. 2010 ; Vol. 11, No. 1.
@article{f4cee3f5465349dca65491332dac2ea8,
title = "Small RNAs, DNA methylation and transposable elements in wheat",
abstract = "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.",
author = "Dario Cantu and Vanzetti, {Leonardo S.} and Adam Sumner and Martin Dubcovsky and Marta Matvienko and Assaf Distelfeld and Michelmore, {Richard W} and Jorge Dubcovsky",
year = "2010",
month = "6",
day = "29",
doi = "10.1186/1471-2164-11-408",
language = "English (US)",
volume = "11",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Small RNAs, DNA methylation and transposable elements in wheat

AU - Cantu, Dario

AU - Vanzetti, Leonardo S.

AU - Sumner, Adam

AU - Dubcovsky, Martin

AU - Matvienko, Marta

AU - Distelfeld, Assaf

AU - Michelmore, Richard W

AU - Dubcovsky, Jorge

PY - 2010/6/29

Y1 - 2010/6/29

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=77953930032&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77953930032&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-11-408

DO - 10.1186/1471-2164-11-408

M3 - Article

C2 - 20584339

AN - SCOPUS:77953930032

VL - 11

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 408

ER -