SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

Johnson, Lianna M.
Du, Jiamu
Hale, Christopher J.
Bischof, Sylvain
Feng, Suhua
Chodavarapu, Ramakrishna K.
Zhong, Xuehua
Marson, Giuseppe
Pellegrini, Matteo
Segal, David J.
Patel, Dinshaw J.
Jacobsen, Steven E.

¹Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
²Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
³Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
⁴Genome Center and Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California 95616, USA
⁵These authors contributed equally to this work.
⁶Present address: Wisconsin Institute for Discovery, Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA.

Received 29 May 2013; accepted 2 December 2013; Published online 22 January 2014

Nature 507(7490):p 124-128, March 6, 2014. | DOI: 10.1038/nature12931

RNA-directed DNA methylation inArabidopsis thalianadepends on the upstream synthesis of 24-nucleotide small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV)and downstream synthesis of non-coding transcripts by Pol V. Pol V transcripts are thought to interact with siRNAs which then recruit DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) to methylate DNA. The SU(VAR)3-9 homologues SUVH2 and SUVH9 act in this downstream step but the mechanism of their action is unknown. Here we show that genome-wide Pol V association with chromatin redundantly requires SUVH2 and SUVH9. Although SUVH2 and SUVH9 resemble histone methyltransferases, a crystal structure reveals that SUVH9 lacks a peptide-substrate binding cleft and lacks a properly formedS-adenosyl methionine (SAM)-binding pocket necessary for normal catalysis, consistent with a lack of methyltransferase activity for these proteins. SUVH2 and SUVH9 both contain SRA (SET- and RING-ASSOCIATED) domains capable of binding methylated DNA, suggesting that they function to recruit Pol V through DNA methylation. Consistent with this model, mutation of DNA METHYLTRANSFERASE 1 (MET1) causes loss of DNA methylation, a nearly complete loss of Pol V at its normal locations, and redistribution of Pol V to sites that become hypermethylated. Furthermore, tethering SUVH2 with a zinc finger to an unmethylated site is sufficient to recruit Pol V and establish DNA methylation and gene silencing. These results indicate that Pol V is recruited to DNA methylation through the methyl-DNA binding SUVH2 and SUVH9 proteins, and our mechanistic findings suggest a means for selectively targeting regions of plant genomes for epigenetic silencing.