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Chemical-genomic dissection of the CTD code

Nature Structural & Molecular Biology volume 17, pages 1154–1161 (2010)Cite this article

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Abstract

Sequential modifications of the RNA polymerase II (Pol II) C-terminal domain (CTD) coordinate the stage-specific association and release of cellular machines during transcription. Here we examine the genome-wide distributions of the 'early' (phospho-Ser5 (Ser5-P)), 'mid' (Ser7-P) and 'late' (Ser2-P) CTD marks. We identify gene class–specific patterns and find widespread co-occurrence of the CTD marks. Contrary to its role in 3′-processing of noncoding RNA, the Ser7-P marks are placed early and retained until transcription termination at all Pol II–dependent genes. Chemical-genomic analysis reveals that the promoter-distal Ser7-P marks are not remnants of early phosphorylation but are placed anew by the CTD kinase Bur1. Consistent with the ability of Bur1 to facilitate transcription elongation and suppress cryptic transcription, high levels of Ser7-P are observed at highly transcribed genes. We propose that Ser7-P could facilitate elongation and suppress cryptic transcription.

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Figure 1: Pol II and CTD phosphorylation profiles.
Figure 2: Genome-wide Pol II and CTD phosphorylation profiles.
Figure 3: CTD phosphorylation profile for protein-coding and noncoding genes.
Figure 4: Small-molecule inhibition of CTD phosphorylation.
Figure 5: Promoter-distal Ser7-P marks are not remnants of promoter-proximal Kin28 phosphorylation.
Figure 6: Bur1 kinase directly phosphorylates Ser7.

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Acknowledgements

We thank S. Hahn (Fred Hutchinson Cancer Research Center) for sharing strains before publication and for helpful discussions, J. Nau and A. Nett for optimizing strains, E. Kanin and A. Leaf for exploratory experiments, D. Burgess and N. Thompson (Univ. of Wisconsin-Madison) for the gift of Pol II antibody (RPB3) and C. Zhang (Univ. of California, San Francisco) for providing small-molecule inhibitors and for their advice on the kinase inhibition experiments. We also gratefully acknowledge the support of the US National Science Foundation (MCB 07147), W.M. Keck, Shaw Scholar and Vilas Associate awards (to A.Z.A.). J.R.T. and J.B.R.-M. were supported by a US National Human Genome Research Institute training grant to the Genomic Sciences Training Program (5T32HG002760). D.E. was supported by Deutsche Forschungsgemeinschaft SFB/TR5 and SFB684 and S.K. was supported by HG03747 (US National Institutes of Health). M.H. was funded by a Boehringer Ingelheim Fonds travel grant.

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  1. David W Zhang, Juan B Rodríguez-Molina and Brent E White: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and The Genome Center, University of Wisconsin, Madison, Wisconsin, USA

    Joshua R Tietjen, David W Zhang, Juan B Rodríguez-Molina, Brent E White, Md Sohail Akhtar, Xin Li & Aseem Z Ansari

  2. Department of Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany

    Martin Heidemann, Rob D Chapman & Dirk Eick

  3. Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, Wisconsin, USA

    Xin Li & Sündüz Keles

  4. Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA

    Kevan Shokat

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Contributions

J.R.T., D.W.Z. and B.E.W. performed the ChIP-chip experiments in the JTY1 and Kin28as + Srb10as strains; J.B.R.-M. performed the ChIP-chip experiments with the BY4743 and Bur1as strains; J.R.T. analyzed the ChIP-chip data for all the experiments; M.S.A. and D.W.Z. performed the kinase assays; X.L. and S.K. assisted with data analysis; M.H. performed the ELISA assays; A.Z.A., R.D.C. and D.E. planned and analyzed the Ser7-P experiments; K.S. provided the unpublished small-molecule inhibitors and assisted in the planning of the kinase inhibition experiments; J.R.T., D.W.Z., J.B.R.-M. and A.Z.A. wrote the manuscript; all authors commented on the manuscript.

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Correspondence to Aseem Z Ansari.

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A.Z.A. is the proprietor of VistaMotif.

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Tietjen, J., Zhang, D., Rodríguez-Molina, J. et al. Chemical-genomic dissection of the CTD code. Nat Struct Mol Biol 17, 1154–1161 (2010). https://doi.org/10.1038/nsmb.1900

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