The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation

Nucleic Acids Res. 2019 Sep 26;47(17):9024-9036. doi: 10.1093/nar/gkz615.


In plants, nuclear multisubunit RNA polymerases IV and V are RNA Polymerase II-related enzymes that synthesize non-coding RNAs for RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Here, we tested the importance of the C-terminal domain (CTD) of Pol IV's largest subunit given that the Pol II CTD mediates multiple aspects of Pol II transcription. We show that the CTD is dispensable for Pol IV catalytic activity and Pol IV termination-dependent activation of RNA-DEPENDENT RNA POLYMERASE 2, which partners with Pol IV to generate dsRNA precursors of the 24 nt siRNAs that guide RdDM. However, 24 nt siRNA levels decrease ∼80% when the CTD is deleted. RNA-dependent cytosine methylation is also reduced, but only ∼20%, suggesting that siRNA levels typically exceed the levels needed for methylation of most loci. Pol IV-dependent loci affected by loss of the CTD are primarily located in chromosome arms, similar to loci dependent CLSY1/2 or SHH1, which are proteins implicated in Pol IV recruitment. However, deletion of the CTD does not phenocopy clsy or shh1 mutants, consistent with the CTD affecting post-recruitment aspects of Pol IV activity at target loci.

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
  • Cytosine / chemistry
  • Cytosine / metabolism
  • DNA Methylation / genetics*
  • DNA-Directed RNA Polymerases / genetics*
  • DNA-Directed RNA Polymerases / metabolism
  • Gene Expression Regulation, Plant / genetics*
  • Gene Silencing
  • Genetic Loci
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism
  • Intracellular Signaling Peptides and Proteins / genetics
  • Intracellular Signaling Peptides and Proteins / metabolism
  • Methyltransferases / metabolism
  • Plants, Genetically Modified
  • Protein Domains
  • Protein Subunits / genetics
  • Protein Subunits / metabolism
  • RNA, Small Interfering / metabolism*
  • RNA-Dependent RNA Polymerase / metabolism
  • Whole Genome Sequencing


  • Arabidopsis Proteins
  • CLASSY1 protein, Arabidopsis
  • Homeodomain Proteins
  • Intracellular Signaling Peptides and Proteins
  • Protein Subunits
  • RNA, Small Interfering
  • SHH1 protein, Arabidopsis
  • Cytosine
  • Methyltransferases
  • DRM2 protein, Arabidopsis
  • RNA polymerase IV, Arabidopsis
  • RNA polymerase V, Arabidopsis
  • RDR2 protein, Arabidopsis
  • RNA-Dependent RNA Polymerase
  • DNA-Directed RNA Polymerases
  • NRPD1A protein, Arabidopsis