title: DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons.
abstract: The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1, the largest catalytic subunit of Pol V. We found that Pol V is enriched at promoters and evolutionarily recent transposons. This localization pattern is highly correlated with Pol V-dependent DNA methylation and small RNA accumulation. We also show that genome-wide chromatin association of Pol V is dependent on all members of a putative chromatin-remodeling complex termed DDR. Our study presents a genome-wide view of Pol V occupancy and sheds light on the mechanistic basis of Pol V localization. Furthermore, these findings suggest a role for Pol V and RNA-directed DNA methylation in genome surveillance and in responding to genome evolution.
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA.
authors.forename: Xuehua
authors.initials: X
authors.lastname: Zhong
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Hale
authors.forename: Julie A
authors.initials: JA
authors.lastname: Law
authors.forename: Lianna M
authors.initials: LM
authors.lastname: Johnson
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.forename: Andy
authors.initials: A
authors.lastname: Tu
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism*; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D009154:Mutation; D011401:Promoter Regions, Genetic; D021122:Protein Subunits / Q000032:analysis / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; C529025:DMS3 protein, Arabidopsis; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; D021122:Protein Subunits; C549271:RDM1 protein, Arabidopsis; C538841:RNA polymerase V, Arabidopsis; D012321:DNA-Directed RNA Polymerases; C504888:DRD1 protein, Arabidopsis