Tags

Type your tag names separated by a space and hit enter

Small RNAs, DNA methylation and transposable elements in wheat.
BMC Genomics. 2010 Jun 29; 11:408.BG

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.

Authors+Show Affiliations

Department of Plant Sciences, University of California Davis, One Shields Ave, Davis, CA, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

20584339

Citation

Cantu, Dario, et al. "Small RNAs, DNA Methylation and Transposable Elements in Wheat." BMC Genomics, vol. 11, 2010, p. 408.
Cantu D, Vanzetti LS, Sumner A, et al. Small RNAs, DNA methylation and transposable elements in wheat. BMC Genomics. 2010;11:408.
Cantu, D., Vanzetti, L. S., Sumner, A., Dubcovsky, M., Matvienko, M., Distelfeld, A., Michelmore, R. W., & Dubcovsky, J. (2010). Small RNAs, DNA methylation and transposable elements in wheat. BMC Genomics, 11, 408. https://doi.org/10.1186/1471-2164-11-408
Cantu D, et al. Small RNAs, DNA Methylation and Transposable Elements in Wheat. BMC Genomics. 2010 Jun 29;11:408. PubMed PMID: 20584339.
* Article titles in AMA citation format should be in sentence-case
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, Y1 - 2010/06/29/ PY - 2010/02/18/received PY - 2010/06/29/accepted PY - 2010/6/30/entrez PY - 2010/6/30/pubmed PY - 2010/9/4/medline SP - 408 EP - 408 JF - BMC genomics JO - BMC Genomics VL - 11 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/20584339/Small_RNAs_DNA_methylation_and_transposable_elements_in_wheat_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-408 DB - PRIME DP - Unbound Medicine ER -