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Review
. 2016 Nov;13(11):1060-1067.
doi: 10.1080/15476286.2016.1218591. Epub 2016 Aug 11.

Mobile small RNAs and their role in regulating cytosine methylation of DNA

Thomas J Hardcastle  1 , Mathew G Lewsey  2
Affiliations
Review

Mobile small RNAs and their role in regulating cytosine methylation of DNA

Thomas J Hardcastle et al. RNA Biol. 2016 Nov.

Abstract

Small (s)RNAs of 21 to 24 nucleotides are associated with RNA silencing and methylation of DNA cytosine residues. All sizes can move from cell-to-cell and long distance in plants, directing RNA silencing in destination cells. Twenty-four nucleotide sRNAs are the predominant long-distance mobile species. Thousands move from shoot to root, where they target methylation of transposable elements both directly and indirectly. We derive several classes of interaction between small RNAs and methylation and use these to explore the mechanisms of methylation and gene expression that associate with mobile sRNA signaling.

Keywords: Histone modifications; RNA-directed DNA methylation; plant grafting; small RNA; transcriptional gene silencing.

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Figures

Figure 1.
Figure 1.
The 6 models of sRNA-methylome interaction investigated by grafting between shoots and roots of different Arabidopsis thaliana genotypes. The diagram represents for each model the defined combination of sRNA and cytosine DNA methylation status across roots. Graft combinations are indicated at the top; shoot above root) and model identities on the left. Loci fitting each model were identified by analyzing genome-wide sRNA-sequencing and methylC-sequencing data from roots of each graft combination. Numbers of loci identified for each methylation context (based on selection of sRNA and methylation loci exhibiting the correct behavior with an FDR< 0.05) are shown to the left of each model definition.
Figure 2.
Figure 2.
Specific RNA-directed DNA methylation mechanism components are required for mobile methylation. Methylation levels were assessed at class A, B, E and F loci in mutants of RNA silencing components. Loci are size-normalized and plotted between dotted vertical lines, with methylation of the flanking 4000 nt plotted on either side.
Figure 3.
Figure 3.
Number of overlaps per kilobase (KB) per KB between locus class types and histone peaks. Significance levels: #, 0< P < 10−5; +, 10−4 < P < 10−5; *, 10−3 < P < 10−4; !, 10−2 < P < 10−3; blue, underrepresented; red, overrepresented (relative to background).
Figure 4.
Figure 4.
Number of overlaps per megabase (MB) of mobile sRNA loci (filled red circles) between peaks of histone modification. Overlaps per MB observed in repeated block-bootstrap samplings of sRNA loci are shown as black box-and-whisker plots.
Figure 5.
Figure 5.
Fixed effect size on (log) gene expression of overlap with methylation and sRNA loci (CG, CHG, CHH, SRNA), mobile CHG and CHH methylation and sRNA loci (mCHG, mCHH and mSRNA), the effect observed in mobile samples and their interactions with mobile loci (mCHG: mobile samples, mCHH: mobile samples and mSRNA: mobile samples). Two effects are significant (< 0.0001); the overlap of genes with sRNA loci and the overlap of genes with mobile sRNA loci; no other effect is significant (after B-H correction) for a cutoff of 0.01.
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