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Gardening the genome: DNA methylation in Arabidopsis thaliana

An Erratum to this article was published on 01 July 2005

Key Points

  • DNA methylation is a conserved epigenetic modification of the genome that serves the dual roles of gene regulation and control of repetitive elements, such as transposons.

  • The genome of Arabidopsis thaliana contains extensive DNA methylation and encodes four classes of cytosine methyltransferase (three of which are found in mammals). Genetic and genomic approaches in this species are providing the means to analyse the control of DNA methylation patterns.

  • Cytosine methylation can occur in symmetric (CG) or non-symmetric (CNG or CHH) contexts. The establishment and maintenance of methylation in these contexts has different characteristics and uses different genetic pathways.

  • Recent work has identified RNA as guiding much of DNA methylation. Components of the RNA-interference pathway produce siRNAs, which are able to target cytosine methyltransferases to homologous sequences.

  • Histone modification is also a key process involved in maintaining patterns of DNA methylation.

  • A new class of enzymes that function in a demethylation pathway has also been characterized, and has roles in gene silencing and imprinting.

Abstract

DNA methylation has two essential roles in plants and animals — defending the genome against transposons and regulating gene expression. Recent experiments in Arabidopsis thaliana have begun to address crucial questions about how DNA methylation is established and maintained. One cardinal insight has been the discovery that DNA methylation can be guided by small RNAs produced through RNA-interference pathways. Plants and mammals use a similar suite of DNA methyltransferases to propagate DNA methylation, but plants have also developed a glycosylase-based mechanism for removing DNA methylation, and there are hints that similar processes function in other organisms.

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Figure 1: Four classes of DNA methyltransferase in Arabidopsis thaliana.
Figure 2: Mechanisms for maintenance of CG and asymmetric methylation.
Figure 3: Establishment and maintenance of DNA methylation in Arabidopsis thaliana.
Figure 4: Mechanism of DNA demethylation by a DNA glycosylase/lyase.

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Acknowledgements

We apologize to the many authors whose work was not cited because of space limitations. DNA-methylation studies in our laboratory have been supported by Searle Scholar, Beckman Young Investigator and National Institutes of Health grants to S.E.J. S.W.-L.C. is a DoE Energy Biosciences fellow of the Life Sciences Research Foundation. I.R.H. is supported by an EMBO postdoctoral fellowship.

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Correspondence to Steven E. Jacobsen.

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DATABASES

The Arabidopsis Information Resource

AG

AGO4

BAL

CMT3

DCL3

DDM1

DRM1

DRM2

FWA

HDA6

HDT1

KYP

LHP1

MEDEA

MET1

PAI1

PAI2

PAI4

RDR2

ROS1

RPD1

SUP

FURTHER INFORMATION

Jacobsen laboratory home page

Glossary

ENDOSPERM

The triploid seed tissue, which often provides nutrition to the developing embryo. It is formed by the fertilization of the embryo sac central cell (diploid) by a sperm nucleus (haploid) from the pollen.

ACCESSION

A homozygous line of Arabidopsis thaliana collected from a natural population at a specific location.

VIROID

An infectious agent of plants that consists of ssRNA but that lacks the protein component that is typical of viruses.

EPIMUTATION

A heritable change in gene expression but not gene sequence. This usually takes place by an abnormal increase or decrease in the methylation status of a gene. This can then be heritable for many generations.

GAMETOPHYTIC STAGE

The haploid phase of the plant life-cycle, in which a post-meiotic cell undergoes 2–3 mitoses. In flowering plants, the embryo sac comprises the female structure and the male form is the pollen grain.

CHROMODOMAIN

A protein domain shared by several regulators of chromatin structure. Different classes of chromodomains have been implicated in binding histones, RNA and DNA.

POLYCOMB GROUP (PcG).

Genes in this group were identified as mutations in Drosophila melanogaster, which caused homeotic transformations. PcG proteins modify chromatin and maintain transcriptional decisions required for correct development.

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Chan, SL., Henderson, I. & Jacobsen, S. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6, 351–360 (2005). https://doi.org/10.1038/nrg1601

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  • DOI: https://doi.org/10.1038/nrg1601

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