Fig. 1. A structural framework for understanding the H3K9me2-directed CHG methylation maintenance by ZMET2.

a In vitro DNA methylation assay of ZMET2 on an 18-mer DNA duplex containing single CAG or hmCAG site, in the presence or absence of histone peptide (H3_1–17K9me2 or H3_1–32K9me2). Data are mean ± s.d. (n = 3 biological replicates). Statistical analysis of the presence vs absence of peptide conditions used two-tailed Student’s t test. ns, not significant; *p = 0.01; ***p = 0.0008; ****p < 0.0001. b Crystal structure of ZMET2 in complex with an 18-mer hmCAG and the H3_1–32Kc9me2 peptide, with the active site harboring the target cytosine fC10 shown in the expanded view. ZMET2, DNA, and H3_1–32Kc9me2 peptides are colored in aquamarine, lemon, and yellow, respectively. The hmCAG site is colored in purple (for fC10) or yellow-orange. The SAH molecule is shown in sphere representation. The secondary structures of ZMET2 are labeled numerically for helices and alphabetically for β-strands. The disordered regions of ZMET2 and H3 peptides are depicted as dashed lines. c Fo-Fc omit map (violet; 2.0σ contour) and cartoon representation of the DNA bound to ZMET2, with the nucleotides at the CHG site labeled. d Electrostatic surface view of ZMET2 bound to DNA and H3_1–32K9me2 peptides, with the Fo-Fc omit maps (violet; 2σ contour) of the H3 peptides (residues labeled; stick representation) are highlighted in the expanded views. The same color scheme in b is applied to all the subsequent figures unless indicated otherwise. Source data are provided as a Source Data file.