title: Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation.
abstract: Argonaute (AGO) family proteins are conserved key components of small RNA-induced silencing pathways. In the RNA-directed DNA methylation (RdDM) pathway in Arabidopsis, AGO6 is generally considered to be redundant with AGO4. In this report, our comprehensive, genomewide analyses of AGO4- and AGO6-dependent DNA methylation revealed that redundancy is unexpectedly negligible in the genetic interactions between AGO4 and AGO6. Immunofluorescence revealed that AGO4 and AGO6 differ in their subnuclear co-localization with RNA polymerases required for RdDM. Pol II and AGO6 are absent from perinucleolar foci, where Pol V and AGO4 are co-localized. In the nucleoplasm, AGO4 displays a strong co-localization with Pol II, whereas AGO6 co-localizes with Pol V. These patterns suggest that RdDM is mediated by distinct, spatially regulated combinations of AGO proteins and RNA polymerases. Consistently, Pol II physically interacts with AGO4 but not AGO6, and the levels of Pol V-dependent scaffold RNAs and Pol V chromatin occupancy are strongly correlated with AGO6 but not AGO4. Our results suggest that AGO4 and AGO6 mainly act sequentially in mediating small RNA-directed DNA methylation.
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Cheng-Guo
authors.initials: CG
authors.lastname: Duan
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Huiming
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Tang
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institute of Biological Sciences Chinese Academy of Sciences, Shanghai, China.
authors.forename: Weiqiang
authors.initials: W
authors.lastname: Qian
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Yueh-Ju
authors.initials: YJ
authors.lastname: Hou
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Bangshing
authors.initials: B
authors.lastname: Wang
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Zhaobo
authors.initials: Z
authors.lastname: Lang
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA Shanghai Center for Plant Stress Biology, Shanghai Institute of Biological Sciences Chinese Academy of Sciences, Shanghai, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Xingang
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
authors.forename: Pengcheng
authors.initials: P
authors.lastname: Wang
authors.affiliation: School of Life Science and Technology University of Electronic Science and Technology of China, Chengdu Sichuan, China.
authors.forename: Jianping
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Dryland Agriculture Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan Shanxi, China.
authors.forename: Gaimei
authors.initials: G
authors.lastname: Liang
authors.affiliation: Department of Horticulture, Laboratory of Genetics Resources & Functional Improvement for Horticultural Plant Zhejiang University, Hangzhou Zhejiang, China.
authors.forename: Na
authors.initials: N
authors.lastname: Liu
authors.affiliation: College of Life Sciences Nankai University, Tianjin, China.
authors.forename: Chunguo
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA Shanghai Center for Plant Stress Biology, Shanghai Institute of Biological Sciences Chinese Academy of Sciences, Shanghai, China jkzhu@purdue.edu.
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D060565:Argonaute Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D005455:Fluorescent Antibody Technique; D020868:Gene Silencing / Q000502:physiology*; D047468:Immunoprecipitation; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: C471209:AGO4 protein, Arabidopsis; C521197:AGO6 protein, Arabidopsis; D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D034741:RNA, Small Interfering; D012321:DNA-Directed RNA Polymerases
keywords: DNA methylation; RNA polymerases; RdDM; argonautes; epigenetics