The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci.
RNA-directed DNA methylation (RdDM) is required for transcriptional silencing of transposons and other DNA repeats in Arabidopsis thaliana. Although previous research has demonstrated that the SET domain-containing SU(VAR)3-9 homologs SUVH2 and SUVH9 are involved in the RdDM pathway, the underlying mechanism remains unknown. Our results indicated that SUVH2 and/or SUVH9 not only interact with the chromatin-remodeling complex termed DDR (DMS3, DRD1, and RDM1) but also with the newly characterized complex composed of two conserved Microrchidia (MORC) family proteins, MORC1 and MORC6. The effect of suvh2suvh9 on Pol IV-dependent siRNA accumulation and DNA methylation is comparable to that of the Pol V mutant nrpe1 and the DDR complex mutant dms3, suggesting that SUVH2 and SUVH9 are functionally associated with RdDM. Our CHIP assay demonstrated that SUVH2 and SUVH9 are required for the occupancy of Pol V at RdDM loci and facilitate the production of Pol V-dependent noncoding RNAs. Moreover, SUVH2 and SUVH9 are also involved in the occupancy of DMS3 at RdDM loci. The putative catalytic active site in the SET domain of SUVH2 is dispensable for the function of SUVH2 in RdDM and H3K9 dimethylation. We propose that SUVH2 and SUVH9 bind to methylated DNA and facilitate the recruitment of Pol V to RdDM loci by associating with the DDR complex and the MORC complex.
National Institute of Biological Sciences, Beijing, China.
Zhang-Wei
ZW
Liu
National Institute of Biological Sciences, Beijing, China.
Chang-Rong
CR
Shao
National Institute of Biological Sciences, Beijing, China.
Cui-Jun
CJ
Zhang
National Institute of Biological Sciences, Beijing, China.
Jin-Xing
JX
Zhou
National Institute of Biological Sciences, Beijing, China.
Su-Wei
SW
Zhang
National Institute of Biological Sciences, Beijing, China.
Lin
L
Li
National Institute of Biological Sciences, Beijing, China.
She
S
Chen
National Institute of Biological Sciences, Beijing, China.
Huan-Wei
HW
Huang
National Institute of Biological Sciences, Beijing, China.
Tao
T
Cai
National Institute of Biological Sciences, Beijing, China.
Xin-Jian
XJ
He
D000251:Adenosine Triphosphatases / Q000235:genetics / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly / Q000235:genetics*; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics; D012313:RNA / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics
D029681:Arabidopsis Proteins; D002868:Chromosomal Proteins, Non-Histone; C529025:DMS3 protein, Arabidopsis; D004268:DNA-Binding Proteins; C549271:RDM1 protein, Arabidopsis; D034741:RNA, Small Interfering; D022661:RNA, Untranslated; D012313:RNA; D011495:Histone-Lysine N-Methyltransferase; C501526:SUVH2 protein, Arabidopsis; C587137:SUVH9 protein, Arabidopsis; C538841:RNA polymerase V, Arabidopsis; D012321:DNA-Directed RNA Polymerases; D000251:Adenosine Triphosphatases; C573242:MORC1 protein, Arabidopsis; C573243:MORC6 protein, Arabidopsis