1. Chromosomes and Gene Expression
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Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

  1. Todd Blevins
  2. Ram Podicheti
  3. Vibhor Mishra
  4. Michelle Marasco
  5. Jing Wang
  6. Douglas Rusch
  7. Haixu Tang
  8. Craig S Pikaard  Is a corresponding author
  1. Université de Strasbourg, France
  2. Indiana University, United States
  3. Howard Hughes Medical Institute, Indiana University, United States
Research Article
  • Cited 108
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Cite this article as: eLife 2015;4:e09591 doi: 10.7554/eLife.09591

Abstract

In Arabidopsis thaliana, abundant 24 nt siRNAs guide the cytosine methylation and silencing of transposons and a subset of genes. 24 nt siRNA biogenesis requires nuclear RNA Polymerase IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE3 (DCL3). However, siRNA precursors are mostly undefined. We identified Pol IV and RDR2-dependent RNAs (P4R2 RNAs) that accumulate in dcl3 mutants and are diced into 24 nt RNAs by DCL3 in vitro. P4R2 RNAs are mostly 26-45 nt and initiate with a purine adjacent to a pyrimidine, characteristics shared by Pol IV transcripts generated in vitro. RDR2 terminal transferase activity, also demonstrated in vitro, may account for occasional non-templated nucleotides at P4R2 RNA 3' termini. 24 nt siRNAs primarily correspond to the 5' or 3' ends of P4R2 RNAs, suggesting a model whereby siRNAs are generated from either end of P4R2 duplexes by single dicing events.

Article and author information

Author details

  1. Todd Blevins

    : Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Ram Podicheti

    Center for Genomics and Bioinformatics, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Vibhor Mishra

    Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Michelle Marasco

    Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jing Wang

    Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Douglas Rusch

    Center for Genomics and Bioinformatics, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Haixu Tang

    School of Informatics and Computing, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Craig S Pikaard

    Howard Hughes Medical Institute, Indiana University, Bloomington, United States
    For correspondence
    cpikaard@indiana.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Daniel Zilberman, University of California, Berkeley, United States

Publication history

  1. Received: June 21, 2015
  2. Accepted: October 1, 2015
  3. Accepted Manuscript published: October 2, 2015 (version 1)
  4. Version of Record published: December 8, 2015 (version 2)

Copyright

© 2015, Blevins et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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