A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation

Elife. 2022 Jan 31:11:e73260. doi: 10.7554/eLife.73260.

Abstract

In plants, selfish genetic elements, including retrotransposons and DNA viruses, are transcriptionally silenced by RNA-directed DNA methylation. Guiding the process are short interfering RNAs (siRNAs) cut by DICER-LIKE 3 (DCL3) from double-stranded precursors of ~30 bp that are synthesized by NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). We show that Pol IV's choice of initiating nucleotide, RDR2's initiation 1-2 nt internal to Pol IV transcript ends and RDR2's terminal transferase activity collectively yield a code that influences which precursor end is diced and whether 24 or 23 nt siRNAs are produced. By diversifying the size, sequence, and strand specificity of siRNAs derived from a given precursor, alternative patterns of DCL3 dicing allow for maximal siRNA coverage at methylated target loci.

Keywords: A. thaliana; RNA polymerase; RNA silencing; RNA-directed DNA methylation; chromosomes; dicer endonuclease; dicer-like 3; gene expression; genetics; genomics; siRNA biogenesis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Gene Expression Regulation, Plant*
  • RNA, Small Interfering / genetics*
  • RNA, Small Interfering / metabolism*
  • RNA-Dependent RNA Polymerase
  • Ribonuclease III / genetics*
  • Ribonuclease III / metabolism
  • Transcription, Genetic*

Substances

  • Arabidopsis Proteins
  • RNA, Small Interfering
  • RNA-Dependent RNA Polymerase
  • DCL3 protein, Arabidopsis
  • Ribonuclease III