The Role of Ctk1 Kinase in Termination of Small Non-Coding RNAs

PLoS One. 2013 Dec 4;8(12):e80495. doi: 10.1371/journal.pone.0080495. eCollection 2013.

Abstract

Transcription termination in Saccharomyces cerevisiae can be performed by at least two distinct pathways and is influenced by the phosphorylation status of the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II). Late termination of mRNAs is performed by the CPF/CF complex, the recruitment of which is dependent on CTD-Ser2 phosphorylation (Ser2P). Early termination of shorter cryptic unstable transcripts (CUTs) and small nucleolar/nuclear RNAs (sno/snRNAs) is performed by the Nrd1-Nab3-Sen1 (NNS) complex that binds phosphorylated CTD-Ser5 (Ser5P) via the CTD-interacting domain (CID) of Nrd1p. In this study, mutants of the different termination pathways were compared by genome-wide expression analysis. Surprisingly, the expression changes observed upon loss of the CTD-Ser2 kinase Ctk1p are more similar to those derived from alterations in the Ser5P-dependent NNS pathway, than from loss of CTD-Ser2P binding factors. Tiling array analysis of ctk1Δ cells reveals readthrough at snoRNAs, at many cryptic unstable transcripts (CUTs) and stable uncharacterized transcripts (SUTs), but only at some mRNAs. Despite the suggested predominant role in termination of mRNAs, we observed that a CTK1 deletion or a Pol II CTD mutant lacking all Ser2 positions does not result in a global mRNA termination defect. Rather, termination defects in these strains are widely observed at NNS-dependent genes. These results indicate that Ctk1p and Ser2 CTD phosphorylation have a wide impact in termination of small non-coding RNAs but only affect a subset of mRNA coding genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Helicases / genetics
  • DNA Helicases / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal*
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Phosphorylation
  • Protein Structure, Tertiary
  • Protein-Serine-Threonine Kinases / genetics*
  • Protein-Serine-Threonine Kinases / metabolism
  • RNA Helicases / genetics
  • RNA Helicases / metabolism
  • RNA Polymerase II / genetics*
  • RNA Polymerase II / metabolism
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • RNA, Small Nucleolar / genetics
  • RNA, Small Nucleolar / metabolism
  • RNA, Small Untranslated / genetics*
  • RNA, Small Untranslated / metabolism
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transcription, Genetic*

Substances

  • NAB3 protein, S cerevisiae
  • NRD1 protein, S cerevisiae
  • Nuclear Proteins
  • RNA, Messenger
  • RNA, Small Nucleolar
  • RNA, Small Untranslated
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • Protein-Serine-Threonine Kinases
  • RNA Polymerase II
  • SEN1 protein, S cerevisiae
  • DNA Helicases
  • RNA Helicases

Grant support

This work was supported by the Netherlands Organization of Scientific Research (NWO, http://www.nwo.nl/) grants 016108607 (FCPH), 81702015 (FCPH), 05071057 (FCPH) and 021002035 (TLL), the CNRS (http://www.cnrs.fr/)(D.L) the Danish National Research Foundation (http://dg.dk/) (DL), the ANR (http://www.agence-nationale-recherche.fr/) (ANR-08-Blan-0038-01) (DL). This research was carried out within the scope of the Associated European Laboratory LEA ‘Laboratory of Nuclear RNA Metabolism’ (DL). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.