On how mammalian transcription factors recognize methylated DNA

Abstract

DNA methylation is an epigenetic mark that is essential for the development of mammals; it is frequently altered in diseases ranging from cancer to psychiatric disorders. The presence of DNA methylation attracts specialized methyl-DNA binding factors that can then recruit chromatin modifiers. These methyl-CpG binding proteins (MBPs) have key biological roles and can be classified into three structural families: methyl-CpG binding domain (MBD), zinc finger, and SET and RING finger-associated (SRA) domain. The structures of MBD and SRA proteins bound to methylated DNA have been previously determined and shown to exhibit two very different modes of methylated DNA recognition. The last piece of the puzzle has been recently revealed by the structural resolution of two different zinc finger proteins, Kaiso and ZFP57, in complex with methylated DNA. These structures show that the two methyl-CpG binding zinc finger proteins adopt differential methyl-CpG binding modes. Nonetheless, there are similarities with the MBD proteins suggesting some commonalities in methyl-CpG recognition across the various MBP domains. These fresh insights have consequences for the analysis of the many other zinc finger proteins present in the genome, and for the biology of methyl-CpG binding zinc finger proteins.

Keywords: DNA methylation; Kaiso; MBD; SRA domain; ZFP57; methyl-CpG binding proteins; protein structure; zinc finger.

Figure 1. The three families of MBPs and their known targets. Left panels: schematic representation of the human proteins known to bind methylated DNA. Some of their structural domains are indicated: MBD, methyl-binding domain; CXXC, CXXC-type zinc finger; Ubl, ubiquitin-like domain; TTD, tandem tudor domain; PHD, plant homeo domain; SRA, SET and RING-finger associated domain; RING, really interesting new gene domain; BTB/POZ, broad complex, Tramtrack and Bric-à-brac/POx virus and Zinc finger Domain; ZF, Cys₂His₂ zinc finger domain; KRAB, Krüppel-associated box. The zinc fingers that are necessary for methylated DNA recognition are underlined. Right panel: some of the high-affinity DNA targets identified in vitro. The list is not exhaustive. M represents 5-methylcytosine. H represents 5-hydroxymethylcytosine. N is any nucleotide.

Figure 2. Representative structures for each MBP family. (A) Crystal structure of the MBD of human MeCP2 in complex with a methylated DNA consensus site derived from the brain-derived neurotrophic factor (BDNF) promoter (PDB 3C2I). (B) Crystal structure of the SRA domain of human UHRF1 in complex with hemimethylated DNA (PDB 3CLZ). (C) Crystal structure of the mouse Cys₂His₂ zinc finger protein ZFP57 in complex with a methylated DNA target known to be localized in imprinting control regions (PDB 4GZN). (D) Crystal structure of the human Cys₂His₂ zinc finger protein Kaiso in complex with a methylated DNA consensus site derived from the E-cadherin (CDH1) promoter (PDB 4F6N). Pink spheres represent methyl groups in the methylated cytosines.