Noncanonical CTD kinases regulate RNA polymerase II in a gene-class-specific manner

Abstract

Phosphorylation of the carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) governs stage-specific interactions with different cellular machines. The CTD consists of Y1S2P3T4S5P6S7 heptad repeats and sequential phosphorylations of Ser7, Ser5 and Ser2 occur universally at Pol II-transcribed genes. Phosphorylation of Thr4, however, appears to selectively modulate transcription of specific classes of genes. Here, we identify ten new Thr4 kinases from different kinase structural groups. Irreversible chemical inhibition of the most active Thr4 kinase, Hrr25, reveals a novel role for this kinase in transcription termination of specific class of noncoding snoRNA genes. Genome-wide profiles of Hrr25 reveal a selective enrichment at 3ʹ regions of noncoding genes that display termination defects. Importantly, phospho-Thr4 marks placed by Hrr25 are recognized by Rtt103, a key component of the termination machinery. Our results suggest that these uncommon CTD kinases place phospho-Thr4 marks to regulate expression of targeted genes.

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Fig. 1: Yeast kinases phosphorylate Thr4 in vitro.
Fig. 2: Yeast kinases phosphorylate Thr4 in vivo.
Fig. 3: Irreversible inhibition of Hrr25.
Fig. 4: Hrr25-dependent Thr4 phosphorylation is required for snoRNA termination.
Fig. 5: Hrr25 profiles correlate with Pol II at protein-coding genes.
Fig. 6: Hrr25-dependent Thr4 phosphorylation recruits RTT103.

Data availability

All ChIP and RNA-seq data are available at the Gene Expression Omnibus under the accession number: GSE107166.

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Acknowledgements

We thank K. Moeller for preliminary data, and Professors J. Corden (Johns Hopkins School of Medicine), E. Hurt (University of Heidelberg), B. Andrews (University of Toronto), A. Greenleaf (Duke University), S. Hahn (Fred Hutchinson Cancer Research, M. Stark (University of Dundee), and M. Webb (The Francis Crick Institute) for plasmids and strains. We thank members of the Ansari lab, especially J. Rodríguez-Molina, for thoughtful comments, suggestions, and advice. This work was funded by NSF MCB1413547 and NIH GM117362 to A.Z.A., NIH R01 GM083989 to A.P.G., Deutsche Forschungsgemeinschaft, SFB1064, Chromatin Dynamics to DE, The Department of Biotechnology, Government of India (GAP0103) to M.S.A. A.A. and M.F.A. are supported by an Indo-US postdoctoral fellowship from SERB, Government of India.

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C.M.N., A.K.S., and K.J.R. purified yeast kinases and performed in vitro kinase assays. M.S.A. guided A.K.S. and provided in vitro kinase data. C.M.N. tested analog-sensitive and irreversibly sensitive kinases in vivo. K.S. and M.F.A. performed inhibition time course and collected IC50 data. R.K.K. worked with K.S. to generate the Kin28is strain. A.A. docked CMK and 3-MB-PP1 into structures of Hrr25. C.M.N. purified RNA and performed northern blot analysis. Y.-H.H. and A.P.G. performed analysis of hrr25as RNA-seq. S.C.T. prepared hrr25is RNA-seq libraries, and S.C.T. and C.M.N. analyzed hrr25is RNA-seq data. ChIP-chip experiments were performed by C.M.N., and ChIP-qPCR was performed by A.K.S. C.M.N. and K.S. performed binding experiments. C.H. and D.E. provided antibodies and shared data, protocols, and insights to facilitate this project. C.M.N. and A.Z.A. conceived the project and wrote the manuscript, with input from all authors.

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Correspondence to Aseem Z. Ansari.

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A.Z.A. is the sole member of VistaMotif, LLC and founder of the educational US nonprofit WINStep Forward.

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Nemec, C.M., Singh, A.K., Ali, A. et al. Noncanonical CTD kinases regulate RNA polymerase II in a gene-class-specific manner. Nat Chem Biol 15, 123–131 (2019). https://doi.org/10.1038/s41589-018-0194-1

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