5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation.

Abstract

Methylation of cytosine residues in DNA plays an important role in regulating gene expression during vertebrate embryonic development. Conversely, disruption of normal patterns of methylation is common in tumors and occurs early in progression of some human cancers. In ver-tebrates, it appears that the same DNA methyltransferase maintains preexisting patterns of methylation during DNA replication and carries out de novo methylation to create new methylation patterns. There are several indications that inherent signals in DNA structure can act in vivo to initiate or blockde novo methylation in adjacent DNA regions. To identify sequences capable of enhancing de novo methylation of DNA in vitro, we designed a series of oligodeoxyribonucleotide substrates with substrate cytosine residues in different sequence contexts. We obtained evidence that some 5-methylcytosine residues in these single-stranded DNAs can stimulate de novo methylation of adjacent sites by murine DNA 5-cytosine methyltransferase as effectively as 5-methylcytosine residues in double-stranded DNA stimulate maintenance methylation. This suggests that double-stranded DNA may not be the primary natural substrate for de novo methylation and that looped single-stranded structures formed during the normal course of DNA replication or repair serve as "nucleation" sites for de novo methylation of adjacent DNA regions.In vertebrate cells, -3% of cytosine (C) residues in DNA have a methyl group on carbon 5, and 5-methylcytosine (5MeC) is the only naturally occurring modified base detected in DNA (1). Enzymatic methylation of C residues in DNA occurs postreplicatively and primarily involves C residues in CpG dinucleotides, although methylation has been observed at C residues 5' of other nucleotides (2). The extent and pattern of methylation of genomic DNA is species-and tissue-specific (3), which implies that the pattern of methylation is faithfully inherited in all cells of common lineage within a tissue. Analysis of methylation patterns of specific genes during development suggests that patterns established in sperm and oocytes are lost during early development, that regions other than CpG islands become almost fully methylated, and that loss of methylation occurs at specific sites in tissues where a gene is expressed (4-6).Although not all genes are regulated by methylation, hypomethylation at specific sites or in specific regions in a number of genes is correlated with active transcription (7)(8)(9). DNA methylation in vitro can prevent efficient transcription of genes in cell-free systems or transient expression of transfected genes; methylation of C residues in some specific cis-regulatory regions can also block or enhance binding of transcription factors or repressors (7-11). DNA methylation is involved in inactivation of one of the two X chromosomes in female mammalian somatic cells (12), and allele-specific methylation has been proposed as a factor in genomic imprinting (13). The most direct evidence for the importance of DNA methylation in de...

Does DNA Methylation Pattern Mark Generative Development in Winter Rape?

“…Methylation patterns result from de novo methylation, demethylation and maintenance of existing methylated sites. Although not all genes are regulated by methylation, the hypomethylation at specific sites or in specific regions of a number of genes is correlated with active transcription (Christman et al, 1995).…”

“…Enzymatic methylation of C residues in the DNA occurs postreplicatively and is confined to cytosine residues, primarily CG dinucleotides and CNG trinucleotides (Lorenz and Groundine, 2001). The extent and pattern of methylation of genomic DNA are species-and tissue-specific, what implies that the pattern of methylation is faithfully inherited in all cells of common lineage within a tissue (Christman et al, 1995). Although not all genes are regulated by methylation, the hypomethylation at specific sites or in specific regions in a number of genes is correlated with active transcription (Wada et al, 2003).…”

RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation

“…In addition to maintenance methylation activity, DNMT1 can perform de novo DNA methylation as do DNMT3A and DNMT3B. [8][9][10] Dysregulated DNMT1 is capable of promoting hypermethylation or hypomethylation and, indeed, DNMT1 has been reported to be up-regulated or down-regulated in different types of cancer. [11][12][13][14] The methyltransferase activity of DNMT1 has been considered the critical effector in reprogramming cancer methylation patterns.…”

Diverse Domains of (Cytosine-5)-DNA Methyltransferases: Structural and Functional Characterization

“…Such an allosteric activation of Dnmt1 results in lowering its specificity [13,29,34,100]. This effect depends on the presence of Zn 2+ ions and seems to be provided by the binding of the Dnmt1 residues 613-748 with dimethylated DNA [13].…”

“…A similar correlation is observed for the eukaryotic enzyme Dnmt1. The Dnmt1 affinity to monomethylated 5′-CG-3′/3′-GC-5′ sites is 2-200 times higher than to unmethylated ones depending on the experimental conditions [13,[29][30][31][32][33][34][35]. Dnmt1 modifies monomethylated sites processively (more than 50 sites per one binding act on average).…”