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.
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.
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
Eerappa
E
Rajakumara
Julie A
JA
Law
Dhirendra K
DK
Simanshu
Philipp
P
Voigt
Lianna M
LM
Johnson
Danny
D
Reinberg
Dinshaw J
DJ
Patel
Steven E
SE
Jacobsen
D044503:5-Methylcytosine / Q000737:chemistry / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D002151:Calorimetry; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation; D024202:Electrophoretic Mobility Shift Assay; D006657:Histones / Q000378:metabolism*; D008780:Methyltransferases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics; D011485:Protein Binding; D017434:Protein Structure, Tertiary
D006657:Histones; D044503:5-Methylcytosine; D004247:DNA; D008780:Methyltransferases; C512047:SUVH5 protein, Arabidopsis
Nucleic Acids Res. 1982 Apr 24;10(8):2709-21
7079182
Nature. 2002 Apr 4;416(6880):556-60
11898023
Cell. 2001 May 18;105(4):487-97
11371345
Proc Natl Acad Sci U S A. 2010 May 11;107(19):8689-94
20395551
J Biol Chem. 2008 Dec 12;283(50):34490-4
18945682
PLoS Genet. 2008 Nov;4(11):e1000280
19043555
Cell Mol Life Sci. 2009 Feb;66(4):596-612
18985277
Cell. 1994 Jan 28;76(2):357-69
8293469
Chromosoma. 2004 Mar;112(6):308-15
15014946
Plant J. 2008 Dec;56(5):704-15
18643997
Nature. 2008 Oct 9;455(7214):818-21
18772891
Nature. 2007 Dec 6;450(7171):908-12
17994007
Cell. 1995 Jul 14;82(1):143-53
7606780
Plant Cell. 2006 May;18(5):1166-76
16582009
Nat Rev Genet. 2010 Mar;11(3):204-20
20142834
Curr Biol. 2007 Feb 20;17(4):379-84
17239600
Mol Cell. 2008 Feb 29;29(4):525-31
18313390
J Mol Biol. 2000 Oct 6;302(5):1023-39
11183772
PLoS One. 2008 Sep 08;3(9):e3156
18776934
Mutat Res. 2005 Sep 4;577(1-2):55-76
15941573
PLoS Genet. 2008 Aug 15;4(8):e1000156
18704160
Plant J. 2003 Feb;33(3):471-80
12581305
Nature. 2009 Nov 19;462(7271):315-22
19829295
Nature. 2007 May 24;447(7143):418-24
17522675
Cell. 2006 Sep 22;126(6):1189-201
16949657
Nature. 2007 Oct 4;449(7162):570-5
17882165
EMBO J. 2002 Dec 16;21(24):6842-52
12486005
Structure. 2008 Mar;16(3):341-50
18334209
Nat Struct Biol. 1998 Oct;5(10):872-7
9783745
Nucleic Acids Res. 1995 Apr 25;23(8):1388-95
7753630
Nature. 2008 Oct 9;455(7214):826-9
18772888
Mol Cell Biol. 2005 Dec;25(23):10507-15
16287862
Curr Biol. 2002 Aug 20;12(16):1360-7
12194816
Genes Dev. 2007 Feb 1;21(3):267-77
17242155
Science. 2007 Sep 21;317(5845):1760-4
17673620
Cell. 2006 Jul 14;126(1):93-106
16839879
Annu Rev Biochem. 2005;74:481-514
15952895
Nature. 2008 Oct 9;455(7214):822-5
18772889