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Gene-specific RNA polymerase II phosphorylation and the CTD code

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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.

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Figure 1: Gene-specific CTD phosphorylation dynamics in yeast.
Figure 2: A 450-base interval between Ser5 and Ser2 phosphorylation at 5′ ends regardless of gene length.
Figure 3: Enrichment of Ser7P on introns and variation of CTD phosphorylation with transcription level and promoter structure.
Figure 5: Nrd1 colocalizes with Ser7P on ncRNA and mRNA genes.
Figure 4: Kin28 and Ctk1 CTD kinases affect elongation at 5′ and 3′ ends, respectively.
Figure 6: Pcf11, Nrd1 and Rat1 at 3′ end centromeres, telomeres and Pol III genes.

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Gene Expression Omnibus

Change history

  • 26 September 2010

    In the version of this article initially published online, accession code information was given incorrectly. The correct code is GEO series accession number GSE23960. The error has been corrected for the print, PDF and HTML versions of the article.

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Acknowledgements

This work was supported by US National Institutes of Health grants GM58613 to D.B., GM066213 to P.M., GM083127 to D.D.P., GM072706 to J.H.G. H.K. was supported by US National Institutes of Health American Recovery and Reinvestment Act award 3R01GM063873-06S1 to H.K. We thank S. Hahn (Fred Hutchinson Cancer Research Center) and D. Eick (CIPSM Munich) for strains and antibodies, S. Chavez (University of Seville), S. Johnson, K. Brannan and S. Kim for valuable discussions, K. Bhatta for help with figures, A. Lee (Denver School of the Arts) and A. Roth (Denver School of Science and Technology) for data analysis and C. Wang and M. Covarrubias (City of Hope Functional Genomics Core) for array hybridization.

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H.K., D.D.P., D.S. and J.H.G. wrote software and carried out data analysis; B.E., D.L.B., W.L. and P.C.M. designed and carried out experiments. D.L.B., H.K. and P.C.M. wrote the paper.

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Correspondence to David L Bentley.

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The authors declare no competing financial interests.

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Kim, H., Erickson, B., Luo, W. et al. Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat Struct Mol Biol 17, 1279–1286 (2010). https://doi.org/10.1038/nsmb.1913

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