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Uniform transitions of the general RNA polymerase II transcription complex

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Abstract

We present genome-wide occupancy profiles for RNA polymerase (Pol) II, its phosphorylated forms and transcription factors in proliferating yeast. Pol II exchanges initiation factors for elongation factors during a 5′ transition that is completed 150 nucleotides downstream of the transcription start site (TSS). The resulting elongation complex is composed of all the elongation factors and shows high levels of Ser7 and Ser5 phosphorylation on the C-terminal repeat domain (CTD) of Pol II. Ser2 phosphorylation levels increase until 600–1,000 nucleotides downstream of the TSS and do not correlate with recruitment of Spt6 and Pcf11, which bind the Ser2-phosphorylated CTD in vitro. This indicates CTD-independent recruitment mechanisms and CTD masking in vivo. Elongation complexes are productive and disassemble in a two-step 3′ transition. Paf1, Spt16 (part of the FACT complex), and the CTD kinases Bur1 and Ctk1 exit upstream of the polyadenylation site, whereas Spt4, Spt5, Spt6, Spn1 (also called Iws1) and Elf1 exit downstream. Transitions are uniform and independent of gene length, type and expression.

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Figure 1: Genome-wide occupancy profiling of the Pol II machinery.
Figure 2: Statistical analysis indicates a general elongation complex.
Figure 3: Two-step 3′ transition observed at ribosomal protein (RP) genes.
Figure 4: Transcription complex composition and transitions are independent of gene length, expression and NFR size.
Figure 5: Pol II phosphorylation and factor occupancy.
Figure 6: Elongation complex occupancy predicts mRNA expression.

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Acknowledgements

We thank H. Feldmann and D. Martin for help, D. Eick (Helmholtz Zentrum München) for providing antibodies and A. Tresch for discussions. J.S. was supported by the Deutsche Forschungsgemeinschaft and SFB646. P.C. was supported by the Deutsche Forschungsgemeinschaft, the SFB646, the TR5, the Nanosystems Initiative Munich NIM, the Elitenetzwerk Bayern, the Jung-Stiftung and the Fonds der Chemischen Industrie.

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A.M. established experimental protocols; A.M., M.L. and K.L. performed experiments; M.L. and M.S. evaluated data sets; J.S. designed and supervised data evaluation; P.C. designed and supervised research and wrote the manuscript.

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Correspondence to Johannes Söding or Patrick Cramer.

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The authors declare no competing financial interests.

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Mayer, A., Lidschreiber, M., Siebert, M. et al. Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol 17, 1272–1278 (2010). https://doi.org/10.1038/nsmb.1903

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