title: DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.
abstract: DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. DTF1 interacts directly with the chromatin remodeling protein CLASSY 1 (CLSY1), and both DTF1 and CLSY1 are associated in vivo with Pol IV but not Pol V, which functions downstream in the RdDM effector complex. DTF1 and DTF2 (a DTF1-like protein) contain a SAWADEE domain, which was found to bind specifically to histone H3 containing H3K9 methylation. Taken together, our results show that DTF1 is a core component of the RdDM pathway, and suggest that DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci.
authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
authors: Heng
authors: H
authors: Zhang
authors: Ze-Yang
authors: ZY
authors: Ma
authors: Liang
authors: L
authors: Zeng
authors: Kaori
authors: K
authors: Tanaka
authors: Cui-Jun
authors: CJ
authors: Zhang
authors: Jun
authors: J
authors: Ma
authors: Ge
authors: G
authors: Bai
authors: Pengcheng
authors: P
authors: Wang
authors: Su-Wei
authors: SW
authors: Zhang
authors: Zhang-Wei
authors: ZW
authors: Liu
authors: Tao
authors: T
authors: Cai
authors: Kai
authors: K
authors: Tang
authors: Renyi
authors: R
authors: Liu
authors: Xiaobing
authors: X
authors: Shi
authors: Xin-Jian
authors: XJ
authors: He
authors: Jian-Kang
authors: JK
authors: Zhu
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D003001:Cloning, Molecular; D019175:DNA Methylation; D019951:DNA Polymerase beta / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D020868:Gene Silencing; D006657:Histones / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism*; D009154:Mutation; D018749:RNA, Plant / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism*; D014158:Transcription, Genetic; D020798:Two-Hybrid System Techniques
chemical_list: D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; D006657:Histones; D018398:Homeodomain Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering; C568760:SHH1 protein, Arabidopsis; D012194:RNA-Directed DNA Polymerase; D019951:DNA Polymerase beta
keywords: gene silencing; histone modifications; small RNA; transposon
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