The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment

• Published in: EMBO reports 2024-11, Vol.25 (12), p.5743-5779
• Main Authors: Wapenaar, Hannah, Clifford, Gillian, Rolls, Willow, Pasquier, Moira, Burdett, Hayden, Zhang, Yujie, Deák, Gauri, Zou, Juan, Spanos, Christos, Taylor, Mark R D, Mills, Jacquie, Watson, James A, Kumar, Dhananjay, Clark, Richard, Das, Alakta, Valsakumar, Devisree, Bramham, Janice, Voigt, Philipp, Sproul, Duncan, Wilson, Marcus D
• Format: Article
• Language: English
• Subjects: Animals; Biomedical and Life Sciences; Chromatin - genetics; Chromatin - metabolism; Cryoelectron Microscopy; DNA (Cytosine-5-)-Methyltransferases - chemistry; DNA (Cytosine-5-)-Methyltransferases - genetics; DNA (Cytosine-5-)-Methyltransferases - metabolism; DNA Methylation; DNA Methyltransferase 3A - metabolism; EMBO09; EMBO40; Histones - metabolism; Humans; Life Sciences; Models, Molecular; Nucleosomes - metabolism; Protein Binding; Ubiquitination
• ISSN: 1469-3178; 1469-221X; 1469-3178
• DOI: 10.1038/s44319-024-00306-3

DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of DNMT3A1 with diverse modified nucleosomes indicative of different chromatin environments. A cryo-EM structure of the full-length DNMT3A1-DNMT3L complex with a H2AK119ub nucleosome reveals that the DNMT3A1 ubiquitin-dependent recruitment (UDR) motif interacts specifically with H2AK119ub and makes extensive contacts with the core nucleosome histone surface. This interaction facilitates robust DNMT3A1 binding to nucleosomes, and previously unexplained DNMT3A disease-associated mutations disrupt this interface. Furthermore, the UDR-nucleosome interaction synergises with other DNMT3A chromatin reading elements in the absence of histone ubiquitylation. H2AK119ub does not stimulate DNMT3A DNA methylation activity, as observed for the previously described H3K36me2 mark, which may explain low levels of DNA methylation on H2AK119ub marked facultative heterochromatin. This study highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome surface and increases our understanding of how DNMT3A1 chromatin recruitment occurs. Synopsis A UDR motif in DNMT3A acts in concert with other chromatin reading regions to promote chromatin recruitment. A cryo-EM structure reveals that DNMT3A1 binds to H2AK119ub-marked nucleosomes through its UDR motif, although this mark does not enhance DNA methylation activity. In addition to DNMT3A’s previously characterised chromatin reader domains, a UDR motif forms contacts with the nucleosome surface. These all work multivalently to ensure correct intragenic recruitment. The UDR motif interacts with multiple interfaces on the nucleosome promoting direct specific reading of H2A Lys-119 ubiquitylation. DNMT3A shows a disconnect between nucleosome recruitment and methylation activity: H2AK119ub nucleosomes bind more tightly but are less efficient substrates than H3K36me2-modified nucleosomes. A UDR motif in DNMT3A acts in concert with other chromatin reading regions to promote chromatin recruitment. A cryo-EM structure reveals that DNMT3A1 binds to H2AK119ub-marked nucleosomes through its UDR motif, although this mark does not enhance DNA methylation activity.