Abstract
DNA methylation is a type of epigenetic marking that strongly influences chromatin structure and gene expression in plants and mammals. Over the past decade, DNA methylation has been intensively investigated in order to elucidate its control mechanisms. These studies have shown that small RNAs are involved in the induction of DNA methylation, that there is a relationship between DNA methylation and histone methylation, and that the base excision repair pathway has an important role in DNA demethylation. Some aspects of DNA methylation have also been shown to be shared with mammals, suggesting that the regulatory pathways are, in part at least, evolutionarily conserved. Considerable progress has been made in elucidating the mechanisms that control DNA methylation; however, many aspects of the mechanisms that read the information encoded by DNA methylation and mediate this into downstream regulation remain uncertain, although some candidate proteins have been identified. DNA methylation has a vital role in the inactivation of transposons, suggesting that DNA methylation is a key factor in the evolution and adaptation of plants.
Highlights
Gene expression in eukaryotes is highly influenced by chromatin structure
CLASSY 1 (CLSY1), the SWI2/SNF2-like chromatin remodeling factor, may have a function at some point in the early stages of siRNA biogenesis (Smith et al 2007). This double-stranded RNA (dsRNA) is chopped into 24 nt siRNAs by DICER-LIKE 3 (DCL3) (Xie et al 2004); in turn, these siRNAs undergo a ‘maturation’ process mediated by HUA ENHANCER 1 (HEN1) in which a methyl group is added to their 30 end (Yu et al 2005)
These proteins include the subunits of DNA-dependent RNA (Pol) V (Kanno et al 2005, Onodera et al 2005, Pontier et al 2005, He et al 2009a, Lahmy et al 2009), SUPPRESSOR OF TY INSERTION 5-LIKE (SPT5L)/KOW DOMAIN-CONTAINING TRANSCRIPTION FACTOR 1 (KTF1) (Bies-Etheve et al 2009, He et al 2009a, Huang et al 2009), DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1) (Kanno et al 2004), DEFECTIVE IN MERISTEM SILENCING 3 (DMS3)/INVOLVED IN DE NOVO 1 (IDN1) (Kanno et al 2008, Ausin et al 2009), RNA-DIRECTED DNA METHYLATION 1 (RDM1) (Gao et al 2010), DEFECTIVE
Summary
Gene expression in eukaryotes is highly influenced by chromatin structure. For example, gene expression is inactivated in compact chromatin which consists of highly packed nucleosomes (heterochromatin) but is active in less condensed chromatin (euchromatin). A decrease in the DNA methylation level influences the rates of infection by bacterial pathogens (Pavet et al 2006) In this issue, Mittelesten-Scheid and Pecinka have reviewed epigenetic regulation including DNA methylation under stress adaptation. Many of the advances in this field have derived from studies using Arabidopsis mutants, which have enabled identification of many factors involved in DNA methylation and have demonstrated that some mechanisms are conserved and shared with mammals. In this comprehensive review we briefly describe the achievements of these studies and outline the regulatory mechanisms of DNA methylation. We will discuss the current understanding of the roles of DNA methylation in transposon regulation
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