Small RNAs, DNA methylation and transposable elements in wheat

Abstract

BackgroundMore 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.ResultsWe 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.ConclusionsOur 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.

Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs

“…CT009735), using IGB (Integrative Genome Browser), confirmed the massive reduction of small RNAs corresponding to transposons, in the polyploid compared to the parental lines ( Figure 6). Note that in the data used by Cantu et al (2010), the number of reads corresponding to Veju in natural hexaploid wheat was very low (1/400,000), similar to the data shown here for the synthetic hexaploid, but contrasting with the present data collected from natural tetraploid and diploid wheat.…”

“…Recently, small RNAs have been mapped to the repeat sequences of the Triticeae repeats database (Cantu et al 2010). This work demonstrates the changes in TE-related small RNAs following hybridization and polyploidization and confirms that TEs are targets of small RNAs, particularly at their termini.…”

“…Inversely, the relative amount of 24-nt small RNAs corresponding to transposons decreased with increased ploidy ( Figure 3). Similarly, in the work of Cantu et al (2010), the count per basepair of small RNAs corresponding to transposons was lower in hexaploid than in tetraploid wheat varieties (Cantu et al 2010). This ploidy dependence seems to be insensitive to genomic composition, but sensitive to dosage.…”

Selfish genetic elements, genetic conflict, and evolutionary innovation

“…In Drosophila melanogaster, the flamenco locus is a large genomic region containing TE insertions that is used by the piwi-interacting RNA (piRNA) pathway to suppress active TEs dispersed elsewhere in the genome. In plants, suppression of TEs can involve small noncoding RNAs that assist in transcriptional and posttranscriptional silencing and guide targeting of TEs for DNA methylation inactivation (34). By increasing rates of CG-to-TA mutation, DNA methylation of TEs also accelerates their mutational degradation.…”

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

“…These patterns may provide important clues into the interaction between TEs and the host response. To date, most studies have focused on the investigation of either consensus sequences (Cantu et al 2010;Creasey et al 2014;McCue et al 2015) or by combining exemplars from different TE orders (Wang et al 2009;Feng et al 2010;Zemach et al 2013). Although informative, these approaches often have low resolution and may not assess how siRNA and methylation levels change as a function of the age of element insertion.…”