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

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

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Abstract

RNA-directed DNA methylation in Arabidopsis thaliana depends 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 formed S-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.

Original languageEnglish (US)
Pages (from-to)124-128
Number of pages5
JournalNature
Volume507
Issue number7490
DOIs
StatePublished - 2014

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DNA Methylation
DNA-Directed RNA Polymerases
DNA
Small Interfering RNA
Protein Methyltransferases
RNA
Plant Genome
Zinc Fingers
Methyltransferases
Gene Silencing
Catalysis
Arabidopsis
Epigenomics
Methionine
Chromatin
Nucleotides
Protein Domains
link protein
Genome
Peptides

ASJC Scopus subject areas

  • General

Cite this

Johnson, L. M., Du, J., Hale, C. J., Bischof, S., Feng, S., Chodavarapu, R. K., ... Jacobsen, S. E. (2014). SRA-and SET-domain-containing proteins link RNA polymerase v occupancy to DNA methylation. Nature, 507(7490), 124-128. https://doi.org/10.1038/nature12931

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; Patel, Dinshaw J.; Jacobsen, Steven E.

In: Nature, Vol. 507, No. 7490, 2014, p. 124-128.

Research output: Contribution to journalArticle

Johnson, LM, Du, J, Hale, CJ, Bischof, S, Feng, S, Chodavarapu, RK, Zhong, X, Marson, G, Pellegrini, M, Segal, D, Patel, DJ & Jacobsen, SE 2014, 'SRA-and SET-domain-containing proteins link RNA polymerase v occupancy to DNA methylation', Nature, vol. 507, no. 7490, pp. 124-128. https://doi.org/10.1038/nature12931
Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK et al. SRA-and SET-domain-containing proteins link RNA polymerase v occupancy to DNA methylation. Nature. 2014;507(7490):124-128. https://doi.org/10.1038/nature12931
Johnson, Lianna M. ; Du, Jiamu ; Hale, Christopher J. ; Bischof, Sylvain ; Feng, Suhua ; Chodavarapu, Ramakrishna K. ; Zhong, Xuehua ; Marson, Giuseppe ; Pellegrini, Matteo ; Segal, David ; Patel, Dinshaw J. ; Jacobsen, Steven E. / SRA-and SET-domain-containing proteins link RNA polymerase v occupancy to DNA methylation. In: Nature. 2014 ; Vol. 507, No. 7490. pp. 124-128.
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abstract = "RNA-directed DNA methylation in Arabidopsis thaliana depends 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 formed S-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.",
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