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DNA methylation signatures of the plant chromomethyltransferases

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posted on 2022-11-22, 04:18 authored by Quentin GouilQuentin Gouil, DC Baulcombe
DNA methylation in plants is traditionally partitioned into CG, CHG and CHH contexts (with H any nucleotide but G). By investigating DNA methylation patterns in trinucleotide contexts in four angiosperm species, we show that such a representation hides spatial and functional partitioning of different methylation pathways and is incomplete. CG methylation (mCG) is largely context-independent whereas, at CHG motifs, there is under-representation of mCCG in pericentric regions of A. thaliana and tomato and throughout the chromosomes of maize and rice. In A. thaliana the biased representation of mCCG in heterochromatin is related to specificities of H3K9 methyltransferase SUVH family members. At CHH motifs there is an over-representation of different variant forms of mCHH that, similarly to mCCG hypomethylation, is partitioned into the pericentric regions of the two dicots but dispersed in the monocot chromosomes. The over-represented mCHH motifs in A. thaliana associate with specific types of transposon including both class I and II elements. At mCHH the contextual bias is due to the involvement of various chromomethyltransferases whereas the context-independent CHH methylation in A. thaliana and tomato is mediated by the RNA-directed DNA methylation process that is most active in the gene-rich euchromatin. This analysis therefore reveals that the sequence context of the methylome of plant genomes is informative about the mechanisms associated with maintenance of methylation and the overlying chromatin structure.

Funding

DCB was awarded the European Research Council (https://erc.europa.eu/) Advanced Investigator Grant ERC-2013-AdG 340642. Work in the DCB lab is supported by the Balzan Foundation. QG was supported by the Frank Smart Studentship. DCB is the Royal Society Edward Penley Abraham Research Professor. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

History

Publication Date

2016-12-20

Journal

PLoS Genetics

Volume

12

Issue

12

Article Number

e1006526

Pagination

17p.

Publisher

Public Library of Science

ISSN

1553-7390

Rights Statement

© 2016 Gouil, Baulcombe. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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