Requirement of
            <i>CHROMOMETHYLASE3</i>
            for Maintenance of CpXpG Methylation

Lindroth, Anders M.; Cao, Xiaofeng; Jackson, James P.; Zilberman, Daniel; McCallum, Claire M.; Henikoff, Steven; Jacobsen, Steven E.

doi:10.1126/science.1059745

Cited by 811 publications

(639 citation statements)

References 21 publications

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“…CHG methylation is tightly linked to histone methylation and is maintained by a positive feedback loop. The histone methyltransferases KYP, SUVH5 and SUVH6 bind to methylated CHG and catalyze methylation on histone H3 lysine 9 (H3K9me2) [7][8][9]; the plant-specific DNA methyltransferase CMT3 binds to this mark and promotes CHG methylation [10,11]. The asymmetric CHH methylation is maintained by two different DNA methyltransferases, CMT2 and DRM2.…”

Section: Introductionmentioning

confidence: 99%

Dicer-independent RNA-directed DNA methylation in Arabidopsis

et al. 2015

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RNA-directed DNA methylation (RdDM) is an important de novo DNA methylation pathway in plants. Small interfering RNAs (siRNAs) generated by Dicers from RNA polymerase IV (Pol IV) transcripts are thought to guide sequence-specific DNA methylation. To gain insight into the mechanism of RdDM, we performed whole-genome bisulfite sequencing of a collection of Arabidopsis mutants, including plants deficient in Pol IV (nrpd1) or Dicer (dcl1/2/3/4) activity. Unexpectedly, of the RdDM target loci that required Pol IV and/or Pol V, only 16% were fully dependent on Dicer activity. DNA methylation was partly or completely independent of Dicer activity at the remaining Pol IV-and/ or Pol V-dependent loci, despite the loss of 24-nt siRNAs. Instead, DNA methylation levels correlated with the accumulation of Pol IV-dependent 25-50 nt RNAs at most loci in Dicer mutant plants. Our results suggest that RdDM in plants is largely guided by a previously unappreciated class of Dicer-independent non-coding RNAs, and that siRNAs are required to maintain DNA methylation at only a subset of loci.

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Section: Introductionmentioning

confidence: 99%

Dicer-independent RNA-directed DNA methylation in Arabidopsis

et al. 2015

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“…Arabidopsis encodes several homologs of Dnmt1, among which DNA METHYLTRANSFERASE 1 (MET1) is responsible for maintaining most CG methylation (Figure 1b;Henderson and Jacobsen, 2007). Numerous additional proteins are required for the maintenance of CG methylation (Law and Jacobsen, 2010), including the SRA-and RING-domaincontaining protein VARIANT IN METHYLATION 1 in Arabidopsis and its homolog Uhrf1 (also known as NP95) in mammals, which are thought to recruit MET1/Dnmt1 to hemi-methylated CG sites Sharif et al, 2007;Woo et al, 2007Woo et al, , 2008.Maintenance of CHG methylation is mostly effected by CHROMOMETHYLASE 3 (CMT3), a plant-specific DNA MTase (Henikoff and Comai, 1998;Lindroth et al, 2001;Cokus et al, 2008) and requires in addition SUVH4 (also known as kryptonite, KYP), the main histone methyltransferase involved in histone H3K9 dimethylation (Jackson et al, 2002;Malagnac et al, 2002). A reinforcing loop between these modifications is suggested by the fact that the chromodomain of CMT3 and the SRA domain of SUVH4 bind H3K9me2 and methylated CHG sites, respectively (Figure 1b;Lindroth et al, 2004;Johnson et al, 2007).…”

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confidence: 99%

Repeat elements and the Arabidopsis DNA methylation landscape

Teixeira

Colot

2010

Heredity

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DNA methylation is an epigenetic mark that has key roles in the control of genome activity in plants and mammals. It is critical for the stable silencing of repeat elements and is also involved in the epigenetic regulation of some genes. Despite similarities in the controlling functions of DNA methylation, its dynamics and deposition patterns differ in several respects between plants and mammals. One of the most striking differences is that plants tend to propagate pre-existing DNA methylation states across generations, whereas mammals re-establish them genome wide at every generation. Here, we review our current understanding of DNA methylation in the flowering plant Arabidopsis. We discuss in particular the role of RNAi in the incremental methylation and silencing of repeat elements over successive generations. We argue that paramutation, an epigenetic phenomenon first described in maize, is an extreme manifestation of this RNAi-dependent pathway. Heredity (2010) 105, 14-23; doi:10.1038/hdy.2010.52; published online 12 May 2010Keywords: DNA methylation; repeat elements; Arabidopsis; RNAi; paramutation Introduction DNA methylation refers to the enzymatic transfer of a methyl group to specific nucleotides within the DNA sequence. In eukaryotes, this modification almost exclusively affects cytosines. Although clearly ancestral, cytosine methylation is not universally present in the eukaryotic tree of life. Thus, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, as well as the nematode Caenorhabditis elegans have no DNA methyltransferases (DNA MTases;Goll and Bestor, 2005). Furthermore, Drosophila contains a single, enigmatic DNA MTase-like protein (Goll and Bestor, 2005) and it is unclear if this species actually methylates DNA. By contrast, DNA methylation is readily detected in plants and mammals, where it is critical for normal development and genome stability. Although numerous hypotheses have been proposed (Bird, 1995;Yoder et al., 1997;Martienssen, 1998;Regev et al., 1998;Colot and Rossignol, 1999;Suzuki and Bird, 2008), it is still a mystery as to why these organisms cannot dispense with cytosine methylation when many lower eukaryotes can.In plants and mammals, most methylated cytosines are found over repeat elements (Goll and Bestor, 2005;Suzuki and Bird, 2008;Law and Jacobsen, 2010) and loss of this modification is associated with transcriptional reactivation as well as increased mobilization of transposable elements (TEs; Slotkin and Martienssen, 2007). These observations likely reflect the ancestral role of cytosine methylation in the defence against invasive DNA. Methylation of repeat elements is also thought to have been exapted recurrently during eukaryotic evolution to exert other essential functions, notably in the epigenetic regulation of genes. Thus, genomic imprinting, which results in parent-of-origin-dependent expression, may have evolved in plants and mammals from situations in which methylation of repeat elements influences the activity of neighbouring genes (Barlow, 1993;M...

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“…Theise and Wilmut [7] point out that, during animal development, cytosine residues of the newly formed DNA strands can be left unmethylated by a passive process for physiological reasons. In plants, methyltransferase1 maintains DNA methylation on cytosine residues, whereas chromomethylase3 targets other sites [8,9]. In addition, imprinting in Arabidopsis differs from that in mammals, where the methylation of specific DNA sequences in intergenic regions of up to 100 kb (imprinting control centres) regulates the expression of a group of genes [10].…”

mentioning

confidence: 99%

Harnessing the developmental potential of nucellar cells: barriers and opportunities

Ranganath

2004

Trends in Biotechnology

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Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation

Cited by 811 publications

References 21 publications

Dicer-independent RNA-directed DNA methylation in Arabidopsis

Dicer-independent RNA-directed DNA methylation in Arabidopsis

Repeat elements and the Arabidopsis DNA methylation landscape

Harnessing the developmental potential of nucellar cells: barriers and opportunities

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