Plant DNA methyltransferases

Finnegan, E. Jean; Kovac, Kathryn A.

doi:10.1007/978-94-011-4183-3_5

Cited by 106 publications

(131 citation statements)

References 74 publications

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“…Alternatively, non-CG methylation may be important to gene silencing (Martienssen and Colot 2001;Jackson et al 2002) because MET1 is essential for the maintenance of methylation in symmetrical CG dinucleotides in A. thaliana (Finnegan and Kovac 2000). It is also likely that RNAi does not completely knock out MET1 expression such that residual methylation remains in the genome.…”

Section: Discussionmentioning

confidence: 99%

RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids

Chen

Lackey

et al. 2008

Genetics

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Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant A. thaliana and A. arenosa genomes that are homeologous in the allotetraploid. Here we report that RNAi of met1 reduced DNA methylation and altered the expression of $200 genes, many of which encode transposons, predicted proteins, and centromeric and heterochromatic RNAs. Reduced DNA methylation occurred frequently in promoter regions of the upregulated genes, and an En/Spm-like transposon was reactivated in met1-RNAi A. suecica lines. Derepression of transposons, heterochromatic repeats, and centromeric small RNAs was primarily derived from the A. thaliana genome, and A. arenosa homeologous loci were less affected by methylation defects. A high level of A. thaliana centromeric small RNA accumulation was correlated with hypermethylation of A. thaliana centromeres. The greater effects of reduced DNA methylation on transposons and centromeric repeats in A. thaliana than in A. arenosa are consistent with the repression of many genes that are expressed at higher levels in A. thaliana than in A. arenosa in the resynthesized allotetraploids. Moreover, non-CG (CC) methylation in the promoter region of A. thaliana At2g23810 remained in the resynthesized allotetraploids, and the methylation spread within the promoter region in natural A. suecica, leading to silencing of At2g23810. At2g23810 was demethylated and reactivated in met1-RNAi A. suecica lines. We suggest that many A. thaliana genes are transcriptionally repressed in resynthesized allotetraploids, and a subset of A. thaliana loci including transposons and centromeric repeats are heavily methylated and subjected to homeologous genome-specific RNA-mediated DNA methylation in natural allopolyploids.

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Section: Discussionmentioning

confidence: 99%

RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids

Chen

Lackey

et al. 2008

Genetics

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“…The importance of the epigenetic regulation of plant developmental steps is widely recognized (Finnegan and Kovac 2000;Huang et al 2010;Wada 2005). Epigenetic phenomena are associated with several chromatin modifications being DNA methylation, a heritable DNA modification, the best studied (Martienssen and Colot 2001).…”

Section: Communicated By D Nealementioning

confidence: 99%

“…Epigenetic phenomena are associated with several chromatin modifications being DNA methylation, a heritable DNA modification, the best studied (Martienssen and Colot 2001). The DNA methylation mark is imposed through the activity of DNA methyltransferases (DNMTs) which add a methyl group to the fifth carbon of a cytosine from the cofactor S -adenosyl-L -methionine (SAM) (Cao et al 2000;Finnegan and Kovac 2000;Genger et al 1999). In plants, there are three DNMT classes which play a role in different DNA sequence contexts and in different developmental situations: METHYLTRANSFERASE I (MET1), DOMAIN REARRANGED METHYLTRANSFERASE (DRM1/2), and CHROMOMETHYLTRANSFERASE 3 (CMT3).…”

Section: Communicated By D Nealementioning

confidence: 99%

Expression of DNA methyltransferases is involved in Quercus suber cork quality

Ramos¹,

Rocheta²,

Carvalho³

et al. 2013

Tree Genetics & Genomes

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Cork oak (Quercus suber ) is an important Portuguese species, mainly due to the economic value of the cork it produces. Cork results from phellogen, a meristematic tissue, which can locally produce lenticels or have discontinuities, originating "defects": pores and nail inclusions that are detrimental to cork industrial use. Epigenetic processes control plant development and its deregulation can lead to altered phenotypes; therefore, the study of epigenetic players in the phellogen is important to understand the emergence of cork's defects. DNA methyltransferases (DNMTs) and one protein associated to MET1 (DMAP1) were characterized in Q. suber, and their gene expression was analyzed in phellogen and contiguous differentiating cell layers of trees producing high and low quality cork, after the evaluation of their defects by physical and image analysis methods. All classes of DNMTs (MET, DRM, and CMT) with the respective canonical motifs were identified in Q. suber. The expression analyses of these genes showed that QsDRM2 was the most active methyltransferases in the cells analyzed, and that all the genes were differentially expressed in trees with distinct cork quality, with a tendency for higher expression levels in low quality producers. Interestingly, the global methylation level was higher in cells with low expression of DNA methyltransferases. A positive and significant correlation was obtained between QsDMAP1 gene expression and the percentage of cork defects. This work provides the first evidence that cork quality in Q. suber is likely influenced by epigenetic mechanisms.

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“…To understand the mechanism of DNA methylation under environmental stresses in rice, we analyzed the activities of MTases under 2 major abiotic stresses (salt and osmotic) separately and by dividing the plant into root and shoot. In rice, there are 4 basic subfamilies of DNA MTases to begin (de novo methylation) and to continue (maintenance methylation) DNA methylation: DNA methyltransferase 1 (MET1), DNA methyltransferase 2 (DNMT2), chromomethyltransferase (CMT), and domains rearranged methyltransferase (DRM) (Henikoff and Comai, 1998;Finnegan and Kovac, 2000;Cao and Südhof, 2001). OsMET1 and OsCMT3 mainly function in maintaining DNA hypermethylation at CG and CHG sites (where H is A, T, or C) during DNA duplication.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.)

Ahmad¹,

Huang²,

Lan³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Cytosine DNA methylation is a conserved epigenetic regulatory mechanism in both plants and animals. DNA methyltransferases (DNA MTases) not only initiate (de novo) but also maintain the process of DNA methylation. Here, we characterized the genome-wide expression profiles of 10 cytosine DNA MTase genes belonging to 4 subfamilies, MET1, CMT, DNMT2, and DRM, in rice. Tissue-specific gene expression analysis showed that all family members varied widely in their expression and specificities and might be involved in some basic metabolic pathways. Similarly, the expression of all rice cytosine DNA MTase genes was not regulated by plant hormones except OsDRM1a and OsDRM1b, which were downregulated by jasmonic acid. The transcription level of 10 genes in rice shoots and roots was also measured under salt and osmotic stress. Meanwhile, quantitative polymerase chain reaction data of the japonica and indica rice cultivars revealed that there is large variation in the expression activities of all genes. The results provide a foundation to further explore the roles of DNA MTases and the epigenetic regulation of abiotic stress responses in rice.

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Plant DNA methyltransferases

Cited by 106 publications

References 74 publications

RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids

RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids

Expression of DNA methyltransferases is involved in Quercus suber cork quality

Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.)

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