Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1 Journal Article
| Authors: | Law, J. A.; Du, J.; Hale, C. J.; Feng, S.; Krajewski, K.; Palanca, A. M. S.; Strahl, B. D.; Patel, D. J.; Jacobsen, S. E. |
| Article Title: | Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1 |
| Abstract: | DNA methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), a Pol-IV-interacting protein. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy. © 2013 Macmillan Publishers Limited. All rights reserved. |
| Keywords: | unclassified drug; methylation; mutation; protein function; mammalia; small interfering rna; rna, small interfering; homeodomain proteins; in vitro study; enzyme activity; dna methylation; methyltransferases; epigenetics; chromatin; epigenesis, genetic; binding protein; genome; models, molecular; crystallography, x-ray; protein structure, tertiary; binding sites; protein folding; histones; lysine; mutant; mitochondrial dna; dna-directed rna polymerases; nucleotidyltransferase; arabidopsis; histone modification; arabidopsis proteins; polymerase iv; rna directed dna polymerase; sawadee homeodomain homolog 1; dicotyledon |
| Journal Title: | Nature |
| Volume: | 498 |
| Issue: | 7454 |
| ISSN: | 0028-0836 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2013-06-20 |
| Start Page: | 385 |
| End Page: | 389 |
| Language: | English |
| DOI: | 10.1038/nature12178 |
| PUBMED: | 23636332 |
| PROVIDER: | scopus |
| PMCID: | PMC4119789 |
| DOI/URL: | |
| Notes: | --- - Cited By (since 1996):1 - "Export Date: 1 August 2013" - "CODEN: NATUA" - "Source: Scopus" |
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