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.

KEYWORDS::

• ADD
• CpG-binding domain
• CXXC
• H3K4me0-binding domain
• hemi-methyl-CpG-binding domain
• MBD
• methyl-CpG-binding domain
• SRA

Financial & competing interests disclosure

The work in the authors‘ laboratories is currently supported by the US NIH (GM049245-17, GM068680-06 and GM092035-01 to Xiaodong Cheng, and CA077337-10 and CA132065-02 to Paula M Vertino). Xiaodong Cheng is a Georgia Research Alliance Eminent Scholar and Paula M Vertino is a Georgia Cancer Coalition Distinguished Scholar. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

The work in the authors‘ laboratories is currently supported by the US NIH (GM049245-17, GM068680-06 and GM092035-01 to Xiaodong Cheng, and CA077337-10 and CA132065-02 to Paula M Vertino). Xiaodong Cheng is a Georgia Research Alliance Eminent Scholar and Paula M Vertino is a Georgia Cancer Coalition Distinguished Scholar. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.