The RNA polymerase II kinase Ctk1 regulates positioning of a 5′ histone methylation boundary along genes

Tiaojiang Xiao, Yoichiro Shibata, Bhargavi Rao, Ronald Laribee, Rose O'Rourke, Michael J. Buck, Jack F. Greenblatt, Nevan J. Krogan, Jason D. Lieb, Brian D. Strahl

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

In yeast and other eukaryotes, the histone methyltransferase Set1 mediates methylation of lysine 4 on histone H3 (H3K4me). This modification marks the 5′ end of transcribed genes in a 5′-to-3′ tri- to di- to monomethyl gradient and promotes association of chromatin-remodeling and histone-modifying enzymes. Here we show that Ctk1, the serine 2 C-terminal domain (CTD) kinase for RNA polymerase II (RNAP II), regulates H3K4 methylation. We found that CTK1 deletion nearly abolished H3R4 monomethylation yet caused a significant increase in H3K4 di- and trimethylation. Both in individual genes and genome-wide, loss of CTK1 disrupted the H3K4 methylation patterns normally observed. H3K4me2 and H3K4me3 spread 3′ into the bodies of genes, while H3K4 monomethylation was diminished. These effects were dependent on the catalytic activity of Ctk1 but are independent of Set2-mediated H3K36 methylation. Furthermore, these effects are not due to spurious transcription initiation in the bodies of genes, to changes in RNAP II occupancy, to changes in serine 5 CTD phosphorylation patterns, or to "transcriptional stress." These data show that Ctk1 acts to restrict the spread of H3K4 methylation through a mechanism that is independent of a general transcription defect. The evidence presented suggests that Ctk1 controls the maintenance of suppressive chromatin in the coding regions of genes by both promoting H3K36 methylation, which leads to histone deacetylation, and preventing the 3′ spread of H3K4 trimethylation, a mark associated with transcriptional initiation.

Original languageEnglish (US)
Pages (from-to)721-731
Number of pages11
JournalMolecular and cellular biology
Volume27
Issue number2
DOIs
StatePublished - Jan 1 2007

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RNA Polymerase II
Histones
Methylation
Phosphotransferases
Genes
Serine
Chromatin Assembly and Disassembly
Eukaryota
Lysine
Chromatin
Yeasts
Maintenance
Phosphorylation
Genome
Enzymes

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Cell Biology

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The RNA polymerase II kinase Ctk1 regulates positioning of a 5′ histone methylation boundary along genes. / Xiao, Tiaojiang; Shibata, Yoichiro; Rao, Bhargavi; Laribee, Ronald; O'Rourke, Rose; Buck, Michael J.; Greenblatt, Jack F.; Krogan, Nevan J.; Lieb, Jason D.; Strahl, Brian D.

In: Molecular and cellular biology, Vol. 27, No. 2, 01.01.2007, p. 721-731.

Research output: Contribution to journalArticle

Xiao, T, Shibata, Y, Rao, B, Laribee, R, O'Rourke, R, Buck, MJ, Greenblatt, JF, Krogan, NJ, Lieb, JD & Strahl, BD 2007, 'The RNA polymerase II kinase Ctk1 regulates positioning of a 5′ histone methylation boundary along genes', Molecular and cellular biology, vol. 27, no. 2, pp. 721-731. https://doi.org/10.1128/MCB.01628-06
Xiao, Tiaojiang ; Shibata, Yoichiro ; Rao, Bhargavi ; Laribee, Ronald ; O'Rourke, Rose ; Buck, Michael J. ; Greenblatt, Jack F. ; Krogan, Nevan J. ; Lieb, Jason D. ; Strahl, Brian D. / The RNA polymerase II kinase Ctk1 regulates positioning of a 5′ histone methylation boundary along genes. In: Molecular and cellular biology. 2007 ; Vol. 27, No. 2. pp. 721-731.
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AU - Buck, Michael J.

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