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 Journal Article
| Authors: | Eerappa, R.; Law, J. A.; Simanshu, D. K.; Voigt, P.; Johnson, L. M.; Reinberg, D.; Patel, D. J.; Jacobsen, S. E. |
| Article Title: | 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 |
| Abstract: | 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. © 2011 by Cold Spring Harbor Laboratory Press. |
| Keywords: | controlled study; gene mutation; nonhuman; in vivo study; dna methylation; dna; epigenetics; molecular recognition; crystal structure; dna binding; gel mobility shift assay; 5mc-binding pocket; dual-base flip out; h3k9 methylation; set domain; arabidopsis; calorimetry; demethylation; plant gene |
| Journal Title: | Genes and Development |
| Volume: | 25 |
| Issue: | 2 |
| ISSN: | 0890-9369 |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Date Published: | 2011-01-15 |
| Start Page: | 137 |
| End Page: | 152 |
| Language: | English |
| DOI: | 10.1101/gad.1980311 |
| PROVIDER: | scopus |
| PMCID: | PMC3022260 |
| PUBMED: | 21245167 |
| DOI/URL: | |
| Notes: | --- - "Export Date: 4 March 2011" - "CODEN: GEDEE" - "Source: Scopus" |
Altmetric
Citation Impact
BMJ Impact Analytics
Related MSK Work