Gene-specific RNA polymerase II phosphorylation and the CTD code

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      Hyunmin Kim, Benjamin Erickson, Weifei Luo, David Seward, Joel H Graber, David D Pollock, Paul C Megee & David L Bentley

    ABSTRACT

Phosphorylation of the RNA polymerase (Pol) II C-terminal domain (CTD) repeats (1-YSPTSPS-7) is coupled to transcription and may act as a 'code' that controls mRNA synthesis and processing. To examine the code in budding yeast, we mapped genome-wide CTD Ser2, Ser5 and Ser7 phosphorylations and the CTD-associated termination factors Nrd1 and Pcf11. Phospho-CTD dynamics are not scaled to gene length and are gene-specific, with highest Ser5 and Ser7 phosphorylation at the 5′ ends of well-expressed genes with nucleosome-occupied promoters. The CTD kinases Kin28 and Ctk1 markedly affect Pol II distribution in a gene-specific way. The code is therefore written differently on different genes, probably under the control of promoters. Ser7 phosphorylation is enriched on introns and at sites of Nrd1 accumulation, suggesting links to splicing and Nrd1 recruitment. Nrd1 and Pcf11 frequently colocalize, suggesting functional overlap. Unexpectedly, Pcf11 is enriched at centromeres and Pol III–transcribed genes.


[Nature Structural & Molecular Biology (2010) doi:10.1038/nsmb.1913
Received 16 June 2010 Accepted 20 August 2010 Published online 12 September 2010 ]