A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
Genes & development (Impact Factor: 10.8). 01/2011; 25(2):137-52. DOI: 10.1101/gad.1980311
Source: PubMed


Cytosine DNA methylation is evolutionarily ancient, and in eukaryotes this epigenetic modification is associated with gene silencing. Proteins with SRA (SET- or RING-associated) methyl-binding domains are required for the establishment and/or maintenance of DNA methylation in both plants and mammals. The 5-methyl-cytosine (5mC)-binding specificity of several SRA domains have been characterized, and each one has a preference for DNA methylation in different sequence contexts. Here we demonstrate through mobility shift assays and calorimetric measurements that the SU(VAR)3-9 HOMOLOG 5 (SUVH5) SRA domain differs from other SRA domains in that it can bind methylated DNA in all contexts to similar extents. Crystal structures of the SUVH5 SRA domain bound to 5mC-containing DNA in either the fully or hemimethylated CG context or the methylated CHH context revealed a dual flip-out mechanism where both the 5mC and a base (5mC, C, or G, respectively) from the partner strand are simultaneously extruded from the DNA duplex and positioned within binding pockets of individual SRA domains. Our structure-based in vivo studies suggest that a functional SUVH5 SRA domain is required for both DNA methylation and accumulation of the H3K9 dimethyl modification in vivo, suggesting a role for the SRA domain in recruitment of SUVH5 to genomic loci.

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Available from: Julie A Law, Nov 21, 2014
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    • "Most algal KMT1 proteins show high sequence similarity to land plant KMT1 polypeptides, both within the SET domain and in the surrounding regions known as the Pre-SET and Post-SET motifs (Fig. 1). Additionally, all algal sequences contain an SRA (SET and RING associated) domain (Fig. 1), which recognizes the methylation status of CG and CHH DNA sequences (where H = A, T, or C) (Rajakumara et al., 2011). Land plant KMT1 proteins have been reported to fall into several distinct subgroups, indicative of functional diversification (Casas-Mollano et al., 2007; Huang et al., 2011). "
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    Full-text · Article · Oct 2014 · Bioresource Technology
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    • "VAST and DALI searches also revealed that the C-terminal domain of AbaSI is structurally similar to the SET and RING-finger associated (SRA) domains of Arabidopsis SUVH5 (44), human and mouse UHRF1 (45–47), and the N-terminal DNA-binding domain of MspJI (48) (Supplementary Figure S5). In AbaSI, this domain contains eight β-strands (in the order 10, 11, 12, 15, 14, 13, 9 and 8) that together roughly form one twisted β-sheet resembling an arch (the ‘beta-arch’). "
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    • "In this complex, both 5hmC and the unmethylated cytosine located on the opposite strands flip out of the duplex, and both flipped-out bases were bound by UHRF2-SRA (Figure 4B). This binding feature closely resembles that observed in the complex of the SRA domain of Arabidopsis SUVH5 with hemimethylated CG DNA, where both methylated and unmethylated cytosines on the opposite strands flip out and each base was bound to an SRA domain (Rajakumara et al., 2011). Superimposing UHRF1-SRA with the two UHRF2-SRA molecules in the present structure reveals steric clashes between the NKR loops of the two superimposed UHRF1-SRA molecules (Figure 4B). "
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