title: A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis.
abstract: DNA methylation directed by 24-nucleotide (nt) small interfering RNAs (siRNAs) plays critical roles in gene regulation and transposon silencing in Arabidopsis. 24-nt siRNAs are known to be processed from double-stranded RNAs by Dicer-like 3 (DCL3) and loaded into the effector Argonaute 4 (AGO4). Here we report a distinct class of siRNAs independent of DCLs (sidRNAs). sidRNAs are present as ladders of ∼ 20-60 nt in length, often having the same 5' ends but differing in 3' ends by 1-nt steps. We further show that sidRNAs are associated with AGO4 and capable of directing DNA methylation. Finally we show that sidRNA production depends on distributive 3'-5' exonucleases. Our findings suggest an alternative route for siRNA biogenesis. Precursor transcripts are bound by AGO4 and subsequently subjected to 3'-5' exonucleolytic trimming for maturation. We propose that sidRNAs generated through this route are the initial triggers of de novo DNA methylation.
authors.affiliation: Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Ye
authors.affiliation: Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Peking University, Beijing 100871, China; National Institute of Biological Sciences, Beijing 102206, China.
authors.forename: Zulong
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Bi
authors.initials: B
authors.lastname: Lian
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: M Jordan
authors.initials: MJ
authors.lastname: Rowley
authors.affiliation: Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Xia
authors.affiliation: Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Jijie
authors.initials: J
authors.lastname: Chai
authors.affiliation: Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: National Institute of Biological Sciences, Beijing 102206, China.
authors.forename: Xin-Jian
authors.initials: XJ
authors.lastname: He
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Andrzej T
authors.initials: AT
authors.lastname: Wierzbicki
authors.affiliation: Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China. Electronic address: qiyijun@tsinghua.edu.cn.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Qi
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D060565:Argonaute Proteins / Q000378:metabolism; D001483:Base Sequence; D019175:DNA Methylation; D018745:Genome, Plant; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000096:biosynthesis*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D036226:Seedlings / Q000235:genetics
chemical_list: C471209:AGO4 protein, Arabidopsis; D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering; C519655:RDR2 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase