Physiological functions of plant DNA methyltransferases

Abstract

Among factors that regulate gene expression in eukaryotes, DNA methylation, chromatin remodeling and modification of N-termini of core histones are considered to play key roles. All of these are epigenetic and recent studies have provided much information on the molecular basis of such modification and interrelationships between DNA and chromatin modification in regulation of normal development. Epigenetic modification in plants is particularly responsive to environmental stimuli. In this article, I briefly summarize current knowledge of DNA methylation in plants, and discuss its biological significance. Methylation of DNAThe most commonly modified base in DNA among the eukaryotes through animals and plants is 5-methylcytosine (m 5 C) (Yoder and Walsh et al. 1997) (Figure 1), first found in 1951 and confirmed to be a minor base in DNA (Wyatt 1951). Its proportion of the total bases varies among organisms, ranging between less than 0.25% in bacteria up to 7% in plants (Hall 1971). Initial ideas on its physiological function were focused on protection of host DNA from degradation by the so-called restriction-modification system (Kuhnlein and Arber 1972), consisting of a DNA methyltransferase and a corresponding restriction endonuclease, identified in many bacteria (Smith and Kelly 1984).In eukaryotes, m 5 C occurs in retroelements (Yoder and Walsh et al. 1997), and frequently is located in CpG islands within promoter regions of genes (reviewed in Bird 1986). Changes affect suppression of invading sequences of DNA and management of endogenous gene expression via condensation of chromatin structure. In mammals, m Abstract Epigenetic regulation is defined as mechanisms that control gene expression without altering base sequences. Cytosine methylation, chromatin remodeling, and modifications at the N-termini of core histones are key factors in this regard. Epigenetic modifications are found throughout the eukaryotes, suggesting that they developed at an early stage in biological evolution, although actual molecular mechanisms show considerable variation among species. In particular, plants are unique in establishment and maintenance of epigenetic states, as exemplified by species-specific enzymes that catalyze DNA methylation. Since the function and diversity of DNA methyltransferases in individual species are not fully understood, I here summarize recent findings in plant epigenetics, focusing on DNA methyltransferases classified into three major groups. Their possible biological functions are also discussed with reference to histone modification and chromatin remodeling. Wolffe 2001).Methylation of cytosine residues in DNA is enzymatically catalyzed by DNA methyltransferases, which transfer a methyl-group from S-adenosyl-Lmethionine (AdoMet) to the 5-position. The methylation mechanism of DNA was first determined by Holliday and Pugh (1975) and Riggs (1975) and patterns of methylated bases were proposed to be heritable, assuming that once established by a de novo DNA methyltransferase activity, methylation could b...

Size and positional effects of promoter RNA segments on virus-induced RNA-directed DNA methylation and transcriptional gene silencing

“…Methylation of plant DNA occurs in all sequence contexts (i.e., CG, CHG and CHH), whereas methylation in mammals is largely restricted to CG sites and there is no evidence for extensive methylation of asymmetric CHH sites. 42 Although Jones et al 18 and Aufsatz et al 43 suggested that methylation in the asymmetrical CHH sites cannot be maintained efficiently in the absence of RNA signals, we detected the maintenance of asymmetrical CHH methylation in the progeny plants that have no RNA trigger, even though the extent of methylation was reduced through the meiosis (Fig. 7).…”

Expression of DNA methyltransferases is involved in Quercus suber cork quality

“…Appropriate DNA methylation patterns which are established and maintained by DNA methyltransferases (DNMTs) are essential for correct development and tissue differentiation (Cao et al 2000;Finnegan and Kovac 2000;Huang et al 2010;Wada 2005). To study the involvement of DNA methylation in this process, we first characterized the structure of the four types of DNA methyltransferases (QsDNMTs) and one associated protein, DMAP1, in Q. suber.…”

“…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).…”

De novo DNA methylation of the 35S enhancer revealed by high-resolution methylation analysis of an entire T-DNA segment in transgenic gentian

“…On the other hand, the domains rearranged methyltransferase (DRM) class and the chromomethylase (CMT) class of DNA methyltransferases in Arabidopsis are involved in methylation of non-CpG sequences (Tariq M and Paszkowski 2004). DRM class methyltransferases have homology to mammalian Dnmt3 de novo methyltransferase, whereas CMT class methyltransferases are unique to plants, and maintain non-CpG (primarily CpHpG) methylation (Vaillant and Paszkowski 2007;Wada 2005). The genome-wide bisulfite sequencing study revealed that CpHpG methylation on one strand was highly correlated with CpHpG methylation on the opposing strand (Cokus et al 2008); however, the maintenance DNA methylation machinery for hemimethylated CpHpG sites is still unclear.…”