From Structure to Systems: High-resolution, Quantitative Genetic Analysis of RNA Polymerase II

Overview

Journal Cell

Publisher Cell Press

Specialty Cell Biology

Date 2013 Aug 13

PMID 23932120

Citations 96

Authors

Hannes Braberg

Huiyan Jin

Erica A Moehle

Yujia A Chan

Shuyi Wang

Michael Shales

Joris J Benschop

John H Morris

Chenxi Qiu

Fuqu Hu

Leung K Tang

James S Fraser

Frank C P Holstege

Philip Hieter

Christine Guthrie

Craig D Kaplan

Nevan J Krogan

Affiliations

Soon will be listed here.

Abstract

RNA polymerase II (RNAPII) lies at the core of dynamic control of gene expression. Using 53 RNAPII point mutants, we generated a point mutant epistatic miniarray profile (pE-MAP) comprising ∼60,000 quantitative genetic interactions in Saccharomyces cerevisiae. This analysis enabled functional assignment of RNAPII subdomains and uncovered connections between individual regions and other protein complexes. Using splicing microarrays and mutants that alter elongation rates in vitro, we found an inverse relationship between RNAPII speed and in vivo splicing efficiency. Furthermore, the pE-MAP classified fast and slow mutants that favor upstream and downstream start site selection, respectively. The striking coordination of polymerization rate with transcription initiation and splicing suggests that transcription rate is tuned to regulate multiple gene expression steps. The pE-MAP approach provides a powerful strategy to understand other multifunctional machines at amino acid resolution.

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References

Archambault J, Friesen J . Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev. 1993; 57(3):703-24. PMC: 372932. DOI: 10.1128/mr.57.3.703-724.1993. View

Aguilar P, Frohlich F, Rehman M, Shales M, Ulitsky I, Olivera-Couto A . A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Nat Struct Mol Biol. 2010; 17(7):901-8. PMC: 3073498. DOI: 10.1038/nsmb.1829. View

Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P . Functional organization of the S. cerevisiae phosphorylation network. Cell. 2009; 136(5):952-63. PMC: 2856666. DOI: 10.1016/j.cell.2008.12.039. View

Kettenberger H, Armache K, Cramer P . Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell. 2004; 16(6):955-65. DOI: 10.1016/j.molcel.2004.11.040. View

Collins S, Kemmeren P, Zhao X, Greenblatt J, Spencer F, Holstege F . Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics. 2007; 6(3):439-50. DOI: 10.1074/mcp.M600381-MCP200. View

Cramer P, Pesce C, Baralle F, Kornblihtt A . Functional association between promoter structure and transcript alternative splicing. Proc Natl Acad Sci U S A. 1997; 94(21):11456-60. PMC: 23504. DOI: 10.1073/pnas.94.21.11456. View

Benschop J, Brabers N, van Leenen D, Bakker L, van Deutekom H, van Berkum N . A consensus of core protein complex compositions for Saccharomyces cerevisiae. Mol Cell. 2010; 38(6):916-28. DOI: 10.1016/j.molcel.2010.06.002. View

Gnatt A, Cramer P, Fu J, Bushnell D, Kornberg R . Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science. 2001; 292(5523):1876-82. DOI: 10.1126/science.1059495. View

Schuldiner M, Collins S, Thompson N, Denic V, Bhamidipati A, Punna T . Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell. 2005; 123(3):507-19. DOI: 10.1016/j.cell.2005.08.031. View

10.

Carrozza M, Li B, Florens L, Suganuma T, Swanson S, Lee K . Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell. 2005; 123(4):581-92. DOI: 10.1016/j.cell.2005.10.023. View

11.

Laufer C, Fischer B, Billmann M, Huber W, Boutros M . Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Nat Methods. 2013; 10(5):427-31. DOI: 10.1038/nmeth.2436. View

12.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear E, Sevier C . The genetic landscape of a cell. Science. 2010; 327(5964):425-31. PMC: 5600254. DOI: 10.1126/science.1180823. View

13.

Goel S, Krishnamurthy S, Hampsey M . Mechanism of start site selection by RNA polymerase II: interplay between TFIIB and Ssl2/XPB helicase subunit of TFIIH. J Biol Chem. 2011; 287(1):557-567. PMC: 3249109. DOI: 10.1074/jbc.M111.281576. View

14.

Oesterreich F, Preibisch S, Neugebauer K . Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell. 2010; 40(4):571-81. DOI: 10.1016/j.molcel.2010.11.004. View

15.

Typas A, Nichols R, Siegele D, Shales M, Collins S, Lim B . High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods. 2009; 5(9):781-7. PMC: 2700713. DOI: 10.1038/nmeth.1240. View

16.

Spencer F, Gerring S, Connelly C, Hieter P . Mitotic chromosome transmission fidelity mutants in Saccharomyces cerevisiae. Genetics. 1990; 124(2):237-49. PMC: 1203917. DOI: 10.1093/genetics/124.2.237. View

17.

Aitken S, Alexander R, Beggs J . Modelling reveals kinetic advantages of co-transcriptional splicing. PLoS Comput Biol. 2011; 7(10):e1002215. PMC: 3192812. DOI: 10.1371/journal.pcbi.1002215. View

18.

He Y, Fang J, Taatjes D, Nogales E . Structural visualization of key steps in human transcription initiation. Nature. 2013; 495(7442):481-6. PMC: 3612373. DOI: 10.1038/nature11991. View

19.

Conesa C, Acker J . Sub1/PC4 a chromatin associated protein with multiple functions in transcription. RNA Biol. 2010; 7(3):287-90. DOI: 10.4161/rna.7.3.11491. View

20.

Howe K, Kane C, Ares Jr M . Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA. 2003; 9(8):993-1006. PMC: 1370465. DOI: 10.1261/rna.5390803. View