Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana

Abstract

BackgroundIn plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, termed Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues.ResultsWe performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). In leaves, the CRP genes are silent and their coding regions contain dense, transposon-like methylation in CG, CHG and CHH contexts, which depends partly on the Pol IV/Pol V pathway and small RNAs. Methylation in the coding region is reduced, however, in the synergid cells of the female gametophyte, where the CRP genes are specifically expressed. Further demonstrating that expressed CRP genes lack gene body methylation, a CRP4-GFP fusion gene under the control of the constitutive 35 S promoter remains unmethylated in leaves and is transcribed to produce a translatable mRNA. By contrast, a CRP4-GFP fusion gene under the control of a CRP4 promoter fragment acquires CG and non-CG methylation in the CRP coding region in leaves similar to the silent endogenous CRP4 gene.ConclusionsUnlike CG methylation in gene bodies, which does not dramatically affect Pol II transcription, combined CG and non-CG methylation in CRP coding regions is likely to contribute to gene silencing in leaves because loss of this methylation in synergid cells is associated with CRP gene expression. We discuss this unusual methylation pattern and its alteration in synergid cells as well as the possible retrogene origin and evolutionary significance of CRP genes that are methylated like transposons.

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

“…Interestingly, in the latter, more than half of the highly methylated genes that are differentially expressed are targeted by small RNAs (for example, Fig. 3e), suggesting that RdDM may have a role in the regulation of transcription of a subset of genes in diatoms, as recently inferred from studies of the atypical DNA methylation on some genes in A. thaliana 43 . Furthermore, we observed that the captured exon found in the R59 repeat is inserted in reverse orientation with respect to the PiggyBac backbone ( Supplementary Fig.…”

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

“…Plant genes, including those with presumed or demonstrated biological functions, can have methylation patterns that resemble TEs (You et al, 2012; Zemach et al, 2010a), and may therefore be regulated more like TEs than conventional genes. TEs are generally highly methylated at CG sites (Figure 6A, left panel), whereas most Arabidopsis genes have lower methylation levels, except for a distinct group that resembles TEs (Figure 6A).…”

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“…We propose that this enrichment might compensate the deprivation of maintenance DNA methyltransferases MET1 and CMT3 during female gametogenesis. In contrast with the egg cell, the central cell and the synergid cells expressed low levels of de novo DNA methyltransferases and undetectable levels of maintenance DNA methyltransferases, which likely explains why these cells express genes that are silenced by DNA methylation in vegetative tissues [14,[17][18][19].…”