Abstract
DNA methylation in plants targets cytosines in three sequence contexts, CG, CHG and CHH (H representing A, C or T). Each of these patterns has traditionally been associated with distinct DNA methylation pathways with CHH methylation being controlled by the RNA dependent DNA methylation (RdDM) pathway employing small RNAs as a guide for the de novo DOMAINS REARRANGED METHYLTRANSFERASE (DRM2), and maintenance DNA METHYLTRANSFERASE1 (MET1) being responsible for faithful propagation of CG methylation. Here we report an unusual ‘dense methylation’ pattern under the control of MET1, with methylation in all three sequence contexts. We identified epi-alleles of dense methylation at a non coding RNA locus (At4g15242) in Arabidopsis ecotypes, with distinct dense methylation and expression characteristics, which are stably maintained and transmitted in genetic crosses and which can be heritably altered by depletion of MET1. This suggests that, in addition to its classical CG maintenance function, at certain loci MET1 plays a role in creating transcriptional diversity based on the generation of independent epi-alleles. Database inspection identified several other loci with MET1-dependent dense methylation patterns. Arabidopsis ecotypes contain distinct epi-alleles of these loci with expression patterns that inversely correlate with methylation density, predominantly within the transcribed region. In Arabidopsis, dense methylation appears to be an exception as it is only found at a small number of loci. Its presence does, however, highlight the potential for MET1 as a contributor to epigenetic diversity, and it will be interesting to investigate the representation of dense methylation in other plant species.
Highlights
DNA methylation patterns in plants influence a number of molecular mechanisms, including transcription [1], repair [2] and recombination [3], with implications for plant development [4], genome structure [5] and evolution [6]
To examine which DNA methylation pathway contributed to the dense methylation pattern and if changes in DNA methylation were causal for the activation of expression, we tested the expression of At4g15242 in a met1 mutant and a drm2 mutant, both in a Columbia background
MET1 dependent Dense Methylation (MdDM) is independent of the RNA-directed DNA methylation (RdDM) pathway methyltransferase DRM1/2 but requires CMT2 for maintenance of CHH methylation marks
Summary
DNA methylation patterns in plants influence a number of molecular mechanisms, including transcription [1], repair [2] and recombination [3], with implications for plant development [4], genome structure [5] and evolution [6]. MET1 has mainly been discussed in the context of its maintenance function for CG methylation marks, providing more stable epigenetic patterns than the target loci of the RdDM pathway, which show a higher level of epigenetic variation in Arabidopsis accessions [18]. MET1 has at least an indirect role in epigenetic variation due to the responsiveness of the RdDM pathway to changes in CG methylation levels. Another indirect effect on non-CG methylation has been observed at certain loci that lose their H3K9 methylation patterns in a met mutant, which resulted in a loss of CHG and CHH methylation marks [21]. Dense methylation is MET1-dependent but independent of DRM1/2 activity, and predominantly extends throughout transcribed regions of affected genes, inversely correlating with transcript levels
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