title: A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis.
abstract: RNA-directed DNA methylation in Arabidopsis thaliana is driven by the plant-specific RNA Polymerase IV (Pol IV). It has been assumed that a Pol IV transcript can give rise to multiple 24-nt small interfering RNAs (siRNAs) that target DNA methylation. Here, we demonstrate that Pol IV-dependent RNAs (P4RNAs) from wild-type Arabidopsis are surprisingly short in length (30 to 40 nt) and mirror 24-nt siRNAs in distribution, abundance, strand bias, and 5'-adenine preference. P4RNAs exhibit transcription start sites similar to Pol II products and are featured with 5'-monophosphates and 3'-misincorporated nucleotides. The 3'-misincorporation preferentially occurs at methylated cytosines on the template DNA strand, suggesting a co-transcriptional feedback to siRNA biogenesis by DNA methylation to reinforce silencing locally. These results highlight an unusual mechanism of Pol IV transcription and suggest a "one precursor, one siRNA" model for the biogenesis of 24-nt siRNAs in Arabidopsis.
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Jixian
authors.initials: J
authors.lastname: Zhai
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Bischof
authors.affiliation: Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China; Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.affiliation: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA.
authors.forename: Tzuu-Fen
authors.initials: TF
authors.lastname: Lee
authors.affiliation: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA.
authors.forename: Chong
authors.initials: C
authors.lastname: Teng
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Xinyuan
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Soo Young
authors.initials: SY
authors.lastname: Park
authors.affiliation: Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Linshan
authors.initials: L
authors.lastname: Liu
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA; Plant Biology Laboratory and Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Javier
authors.initials: J
authors.lastname: Gallego-Bartolome
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Wanlu
authors.initials: W
authors.lastname: Liu
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Henderson
authors.affiliation: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA.
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.affiliation: Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address: israelausin@fafu.edu.cn.
authors.forename: Israel
authors.initials: I
authors.lastname: Ausin
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA. Electronic address: jacobsen@ucla.edu.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
mesh_terms: D000225:Adenine / Q000378:metabolism; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D008954:Models, Biological; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D024363:Transcription Initiation Site
chemical_list: D018749:RNA, Plant; D034741:RNA, Small Interfering; D012321:DNA-Directed RNA Polymerases; D000225:Adenine