Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA.
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA.
Nat Commun. 2022 Jul 22;13(1):4249. doi: 10.1038/s41467-022-31933-w.
DNA methyltransferase DNMT3B plays an essential role in establishment of DNA methylation during embryogenesis. Mutations of DNMT3B are associated with human diseases, notably the immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome. How ICF mutations affect DNMT3B activity is not fully understood. Here we report the homo-oligomeric structure of DNMT3B methyltransferase domain, providing insight into DNMT3B-mediated DNA methylation in embryonic stem cells where the functional regulator DNMT3L is dispensable. The interplay between one of the oligomer interfaces (FF interface) and the catalytic loop renders DNMT3B homo-oligomer a conformation and activity distinct from the DNMT3B-DNMT3L heterotetramer, and a greater vulnerability to certain ICF mutations. Biochemical and cellular analyses further reveal that the ICF mutations of FF interface impair the DNA binding and heterochromatin targeting of DNMT3B, leading to reduced DNA methylation in cells. Together, this study provides a mechanistic understanding of DNMT3B-mediated DNA methylation and its dysregulation in disease.
DNA 甲基转移酶 DNMT3B 在胚胎发生过程中 DNA 甲基化的建立中发挥着重要作用。DNMT3B 的突变与人类疾病有关，特别是免疫缺陷、着丝粒不稳定和面部异常（ICF）综合征。ICF 突变如何影响 DNMT3B 的活性还不完全清楚。在这里，我们报告了 DNMT3B 甲基转移酶结构域的同寡聚体结构，深入了解了在胚胎干细胞中 DNMT3B 介导的 DNA 甲基化，其中功能性调节剂 DNMT3L 是可有可无的。寡聚体界面之一（FF 界面）和催化环之间的相互作用使 DNMT3B 同寡聚体呈现出与 DNMT3B-DNMT3L 异四聚体不同的构象和活性，并且对某些 ICF 突变更为脆弱。生化和细胞分析进一步表明，FF 界面的 ICF 突变会损害 DNMT3B 的 DNA 结合和异染色质靶向，导致细胞中 DNA 甲基化减少。总之，这项研究提供了对 DNMT3B 介导的 DNA 甲基化及其在疾病中失调的机制理解。
