Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1

Abstract

DNA methylation is a key epigenetic process and the faithful maintenance of DNA methylation patterns is essential to the wellbeing of mammalian cells. This means that cells need a mechanism to identify the partially methylated version of CpG once a new DNA strand has been replicated or repaired, so that it can be further methylated by the DNA methyltransferase, DNMT1. As part of this process the protein UHRF1 (or Np95/ICBP90) facilitates the loading of DNMT1 onto the hemimethylated CpG sequences during DNA replication. Three papers in this issue describe crystal structures of the SRA domain of UHRF1 bound to DNA containing a hemi-methylated CpG site. The structures show that methyl-cytosine is flipped out of the DNA helix and inserted into a binding pocket on the SRA domain. Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development1,2. UHRF1 (also known as ICBP90 in humans and Np95 in mouse)3 is an E3 ligase important for the maintenance of global and local DNA methylation in vivo4,5. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain6 and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code4,5,7. Here we report the 1.7 Å crystal structure of the apo SRA domain of human UHRF1 and a 2.2 Å structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA–DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.