Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance

摘要

Summary The proper location and timing of Dnmt1 activation are essential for DNA methylation maintenance. We demonstrate here that Dnmt1 utilizes two-mono-ubiquitylated histone H3 as a unique ubiquitin mark for its recruitment to and activation at DNA methylation sites. The crystal structure of the replication foci targeting sequence (RFTS) of Dnmt1 in complex with H3-K18Ub/23Ub reveals striking differences to the known ubiquitin-recognition structures. The two ubiquitins are simultaneously bound to the RFTS with a combination of canonical hydrophobic and atypical hydrophilic interactions. The C-lobe of RFTS, together with the K23Ub surface, also recognizes the N-terminal tail of H3. The binding of H3-K18Ub/23Ub results in spatial rearrangement of two lobes in the RFTS, suggesting the opening of its active site. Actually, incubation of Dnmt1 with H3-K18Ub/23Ub increases its catalytic activity in?vitro . Our results therefore shed light on the essential role of a unique ubiquitin-binding module in DNA methylation maintenance. Graphical Abstract Display Omitted Highlights ? Uhrf1 catalyzes multiple mono-ubiquitylation of H3 at K14/K18/K23 ? Crystal structure reveals a unique binding module of Dnmt1 for two-mono-Ub on H3 ? Dnmt1 recruitment to chromatin requires its two-mono-Ub-binding module ? Dnmt1 binding to two-mono-ubiquitylated H3 enhances its methyltransferase activity Ishiyama et?al. identify two-mono-ubiquitylated H3 as a specific mark for Dnmt1 recruitment to DNA replication sites. The crystal structure reveals the presence of a unique-ubiquitin binding module in Dnmt1, of which binding to the mark causes a gross structural change in entire Dnmt1, leading to its activation. ]]>