Molecular Coupling of DNA Methylation and Histone Methylation

Abstract

The combinatorial pattern of DNA and histone modifications constitutes an epigenetic ‘code’ that shapes gene-expression patterns by enabling or restricting the transcriptional potential of genomic domains. DNA methylation is associated with histone modifications, particularly the absence of histone H3 lysine 4 methylation (H3K4me0) and the presence of H3K9 methylation. This article focuses on three protein domains (ATRX–Dnmt3–Dnmt3L [ADD], Cys–X–X–Cys [CXXC] and the methyl-CpG-binding domain [MBD]) and the functional implications of domain architecture in the mechanisms linking histone methylation and DNA methylation in mammalian cells. The DNA methyltransferase DNMT3a and its accessory protein DNMT3L contain a H3K4me0-interacting ADD domain that links the DNA methylation reaction with unmodified H3K4. The H3K4 methyltransferase MLL1 contains a CpG-interacting CXXC domain that may couple the H3K4 methylation reaction to unmethylated DNA. Another H3K4 methyltransferase, SET1, although lacking an intrinsic CXXC domain, interacts directly with an accessory protein CFP1 that contains the same domain. The H3K9 methyltransferase SETDB1 contains a putative MBD that potentially links the H3K4 methylation reaction to methylated DNA or may do so through the interaction with the MBD containing protein MBD1. Finally, we consider the domain structure of the DNA methyltransferase DNMT1, its accessory protein UHRF1 and their associated proteins, and propose a mechanism by which DNA methylation and histone methylation may be coordinately maintained through mitotic cell division, allowing for the transmission of parental DNA and for the histone methylation patterns to be copied to newly replicated chromatin.

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice

“…We analyzed the expression level of de novo DNA methyltransferases; the significant increase of Dnmt3a expression was found (Supplementary Figure S27D). Changes in DNA methylation in embryonic germ cells can be associated with changes in histone epigenetic landscape since DNA methylation and histone modifications are functionally linked and can affect gene expression (104). It is also known that the somatic-to-germ line reprogramming causes the activation of retrotransposon elements (105).…”

Basic concepts of epigenetics

“…DNMTs and SETDB1 interact with MBD1, which, in turn, dock to methylated CpGs. 85 In contrast, gene expression involves the phosphorylation of H3S10, which leads to the displacement of constrictive DNA through an HMG-box, a feature that is likely to stabilize and facilitate ejection of DNA from nucleosomes. 111,115 Other identified HMG proteins include HMGN3a/3b and HMGN5, 115 which are present in euchromatin.…”

DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

“…Despite this similarity, DRM3 and Dnmt3L differ significantly in their N-terminal domains. Dnmt3L has an N-terminal ADD domain that specifically recognizes histone 3 unmethylated at lysine 4 and targets Dnmt3 to chromatin (30,31). In contrast, DRM3 has N-terminal UBA domains of unknown function (23,24).…”