Chapter 29

Where to Start

Liu, X., Bushnell, D. A., and Kornberg, R. D. 2013. RNA polymerase II transcription: Structure and mechanism. Biochim. Biophys. Acta 1829:2–8.

Kornberg, R. D. 2007. The molecular basis of eukaryotic transcription. Proc. Natl. Acad. Sci. U.S.A. 104:12955–12961.

Woychik, N. A. 1998. Fractions to functions: RNA polymerase II thirty years later. Cold Spring Harbor Symp. Quant. Biol. 63:311–317.

Losick, R. 1998. Summary: Three decades after sigma. Cold Spring Harbor Symp. Quant. Biol. 63:653–666.

Sharp, P. A. 1994. Split genes and RNA splicing (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 33:1229–1240.

Cech, T. R. 1990. Nobel lecture: Self-splicing and enzymatic activity of an intervening sequence RNA from Tetrahymena. Biosci. Rep. 10:239–261.

Villa, T., Pleiss, J. A., and Guthrie, C. 2002. Spliceosomal snRNAs: Mg2+ dependent chemistry at the catalytic core? Cell 109: 149–152.

Books

Krebs, J. E., and Goldstein, E. S. 2012. Lewin’s Genes XI (11th ed.). Jones and Bartlett.

Kornberg, A., and Baker, T. A. 1992. DNA Replication (2d ed.). W. H. Freeman and Company.

Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Bretscher, A., Ploegh, H., Amon, A., and Scott, M. P. 2012. Molecular Cell Biology (7th ed.). W. H. Freeman and Company.

Watson, J. D., Baker, T. A., Bell, S. P., Gann, A., Levine, M., and Losick, R. 2013. Molecular Biology of the Gene (7th ed.). Benjamin Cummings.

Gesteland, R. F., Cech, T., and Atkins, J. F. 2006. The RNA World: The Nature of Modern RNA Suggests a Prebiotic RNA (3d ed.). Cold Spring Harbor Laboratory Press.

RNA Polymerases

Liu, X., Bushnell, D. A., Wang, D., Calero, G., and Kornberg, R. D. 2010. Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 327:206–209.

Wang, D., Bushnell, D. A., Huang, X., Westover, K. D., Levitt, M., and Kornberg, R. D. 2009. Structural basis of transcription: Backtracked RNA polymerase II at 3.4 Å resolution. Science 324:1203–1206.

Darst, S. A. 2001. Bacterial RNA polymerase. Curr. Opin. Struct. Biol. 11:155–162.

Ross, W., Gosink, K. K., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., Severinov, K., and Gourse, R. L. 1993. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:1407–1413.

Cramer, P., Bushnell, D. A., and Kornberg, R. D. 2001. Structural basis of transcription: RNA polymerase II at 2.8 Å resolution. Science 292:1863–1875.

Gnatt, A. L., Cramer, P., Fu, J., Bushnell, D. A., and Kornberg, R. D. 2001. Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 Å resolution. Science 292:1876–1882.

Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K., and Darst, S. A. 1999. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98:811–824.

B33

Campbell, E. A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., and Darst, S. A. 2001. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 104:901–912.

Darst, S. A. 2004. New inhibitors targeting bacterial RNA polymerase. Trends Biochem. Sci. 29:159–160.

Cheetham, G. M., and Steitz, T. A. 1999. Structure of a transcribing T7 RNA polymerase initiation complex. Science 286:2305–2309.

Ebright, R. H. 2000. RNA polymerase: Structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 304:687–698.

Paule, M. R., and White, R. J. 2000. Survey and summary: Transcription by RNA polymerases I and III. Nucleic Acids Res. 28:1283–1298.

Initiation and Elongation

Murakami, K. S., and Darst, S. A. 2003. Bacterial RNA polymerases: The whole story. Curr. Opin. Struct. Biol. 13:31–39.

Buratowski, S. 2000. Snapshots of RNA polymerase II transcription initiation. Curr. Opin. Cell Biol. 12:320–325.

Conaway, J. W., and Conaway, R. C. 1999. Transcription elongation and human disease. Annu. Rev. Biochem. 68:301–319.

Conaway, J. W., Shilatifard, A., Dvir, A., and Conaway, R. C. 2000. Control of elongation by RNA polymerase II. Trends Biochem. Sci. 25:375–380.

Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A., and Darst, S. A. 2000. A structural model of transcription elongation. Science 289:619–625.

Reines, D., Conaway, R. C., and Conaway, J. W. 1999. Mechanism and regulation of transcriptional elongation by RNA polymerase II. Curr. Opin. Cell Biol. 11:342–346.

Promoters, Enhancers, and Transcription Factors

Merika, M., and Thanos, D. 2001. Enhanceosomes. Curr. Opin. Genet. Dev. 11:205–208.

Park, J. M., Gim, B. S., Kim, J. M., Yoon, J. H., Kim, H. S., Kang, J. G., and Kim, Y. J. 2001. Drosophila mediator complex is broadly utilized by diverse gene-specific transcription factors at different types of core promoters. Mol. Cell. Biol. 21:2312–2323.

Smale, S. T., and Kadonaga, J. T. 2003. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72:449–479.

Gourse, R. L., Ross, W., and Gaal, T. 2000. Ups and downs in bacterial transcription initiation: The role of the alpha subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 37:687– 695.

Fiering, S., Whitelaw, E., and Martin, D. I. 2000. To be or not to be active: The stochastic nature of enhancer action. BioEssays 22:381–387.

Hampsey, M., and Reinberg, D. 1999. RNA polymerase II as a control panel for multiple coactivator complexes. Curr. Opin. Genet. Dev. 9:132–139.

Chen, L. 1999. Combinatorial gene regulation by eukaryotic transcription factors. Curr. Opin. Struct. Biol. 9:48–55.

Muller, C. W. 2001. Transcription factors: Global and detailed views. Curr. Opin. Struct. Biol. 11:26–32.

Reese, J. C. 2003. Basal transcription factors. Curr. Opin. Genet. Dev. 13:114–118.

Kadonaga, J. T. 2004. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 116:247–257.

Harrison, S. C. 1991. A structural taxonomy of DNA-binding domains. Nature 353:715–719.

Sakurai, H., and Fukasawa, T. 2000. Functional connections between mediator components and general transcription factors of Saccharomyces cerevisiae. J. Biol. Chem. 275:37251–37256.

Droge, P., and Muller-Hill, B. 2001. High local protein concentrations at promoters: Strategies in prokaryotic and eukaryotic cells. Bioessays 23:179–183.

Smale, S. T., Jain, A., Kaufmann, J., Emami, K. H., Lo, K., and Garraway, I. P. 1998. The initiator element: A paradigm for core promoter heterogeneity within metazoan protein-coding genes. Cold Spring Harbor Symp. Quant. Biol. 63:21–31.

Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B., 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature 365:512–520.

Kim, J. L., Nikolov, D. B., and Burley, S. K., 1993. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:520–527.

White, R. J., and Jackson, S. P., 1992. The TATA-binding protein: A central role in transcription by RNA polymerases I, II and III. Trends Genet. 8:284–288.

Martinez, E. 2002. Multi-protein complexes in eukaryotic gene transcription. Plant Mol. Biol. 50:925–947.

Meinhart, A., Kamenski, T., Hoeppner, S., Baumli, S., and Cramer, P. 2005. A structural perspective of CTD function. Genes Dev. 19: 1401–1415.

Palancade, B., and Bensaude, O. 2003. Investigating RNA polymerase II carboxyl-terminal domain (CTD) phosphorylation. Eur. J. Biochem. 270:3859–3870.

Termination

Burgess, B. R., and Richardson, J. P. 2001. RNA passes through the hole of the protein hexamer in the complex with Escherichia coli Rho factor. J. Biol. Chem. 276:4182–4189.

Yu, X., Horiguchi, T., Shigesada, K., and Egelman, E. H. 2000. Three-dimensional reconstruction of transcription termination factor rho: Orientation of the N-terminal domain and visualization of an RNA-binding site. J. Mol. Biol. 299:1279–1287.

Stitt, B. L. 2001. Escherichia coli transcription termination factor Rho binds and hydrolyzes ATP using a single class of three sites. Biochemistry 40:2276–2281.

Henkin, T. M. 2000. Transcription termination control in bacteria. Curr. Opin. Microbiol. 3:149–153.

Gusarov, I., and Nudler, E. 1999. The mechanism of intrinsic transcription termination. Mol. Cell 3:495–504.

Riboswitches

Barrick, J. E., and Breaker, R. R. 2007. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol. 8:R239.

Cheah, M. T., Wachter, A., Sudarsan, N., and Breaker, R. R. 2007. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497–500.

Serganov, A., Huang, L., and Patel, D. J. 2009. Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature 458:233–237.

Noncoding RNA

Cech, T. R. and Steitz, J. A. 2014. The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157:77–94.

Peculis, B. A. 2002. Ribosome biogenesis: Ribosomal RNA synthesis as a package deal. Curr. Biol. 12:R623–R624.

Decatur, W. A., and Fournier, M. J. 2002. rRNA modifications and ribosome function. Trends Biochem. Sci. 27:344–351.

Hopper, A. K., and Phizicky, E. M. 2003. tRNA transfers to the limelight. Genes Dev. 17:162–180.

Weiner, A. M. 2004. tRNA maturation: RNA polymerization without a nucleic acid template. Curr. Biol. 14:R883–R885.

5’-Cap Formation and Polyadenylation

Shatkin, A. J., and Manley, J. L. 2000. The ends of the affair: Capping and polyadenylation. Nat. Struct. Biol. 7:838–842.

Bentley, D. L. 2005. Rules of engagement: Co-transcriptional recruitment of pre-mRNA processing factors. Curr. Opin. Cell Biol. 17:251–256.

Aguilera, A. 2005. Cotranscriptional mRNP assembly: From the DNA to the nuclear pore. Curr. Opin. Cell Biol. 17:242–250.

B34

Ro-Choi, T. S. 1999. Nuclear snRNA and nuclear function (discovery of 5′ cap structures in RNA). Crit. Rev. Eukaryotic Gene Expr. 9:107–158.

Bard, J., Zhelkovsky, A. M., Helmling, S., Earnest, T. N., Moore, C. L., and Bohm, A. 2000. Structure of yeast poly(A) polymerase alone and in complex with 3′-dATP. Science 289:1346–1349.

Martin, G., Keller, W., and Doublie, S. 2000. Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. EMBO J. 19:4193–4203.

Zhao, J., Hyman, L., and Moore, C. 1999. Formation of mRNA 3′ ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63:405–445.

Minvielle-Sebastia, L., and Keller, W. 1999. mRNA polyadenylation and its coupling to other RNA processing reactions and to transcription. Curr. Opin. Cell Biol. 11:352–357.

Small Regulatory RNAs

Winter, J., Jung, S., Keller, S., Gregory, R. I., and Diederichs, S. 2009. Many roads to maturity: MicroRNA biogenesis pathways and their regulation. Nat. Cell Biol. 11:228–234.

Ruvkun, G., Wightman, B., and Ha, I. 2004. The 20 years it took to recognize the importance of tiny RNAs. Cell 116:S93–S96.

RNA Editing

Gott, J. M., and Emeson, R. B. 2000. Functions and mechanisms of RNA editing. Annu. Rev. Genet. 34:499–531.

Simpson, L., Thiemann, O. H., Savill, N. J., Alfonzo, J. D., and Maslov, D. A. 2000. Evolution of RNA editing in trypanosome mitochondria. Proc. Natl. Acad. Sci. U.S.A. 97:6986–6993.

Chester, A., Scott, J., Anant, S., and Navaratnam, N. 2000. RNA editing: Cytidine to uridine conversion in apolipoprotein B mRNA. Biochim. Biophys. Acta 1494:1–3.

Maas, S., and Rich, A. 2000. Changing genetic information through RNA editing. BioEssays 22:790–802.

Splicing of mRNA Precursors

Caceres, J. F., and Kornblihtt, A. R. 2002. Alternative splicing: Multiple control mechanisms and involvement in human disease. Trends Genet. 18:186–193.

Faustino, N. A., and Cooper, T. A. 2003. Pre-mRNA splicing and human disease. Genes Dev. 17:419–437.

Lou, H., and Gagel, R. F. 1998. Alternative RNA processing: Its role in regulating expression of calcitonin/calcitonin gene-related peptide. J. Endocrinol. 156:401–405.

Matlin, A. J., Clark, F., and Smith, C. W. 2005. Understanding alternative splicing: Towards a cellular code. Nat. Rev. Mol. Cell Biol. 6:386–398.

McKie, A. B., McHale, J. C., Keen, T. J., Tarttelin, E. E., Goliath, R., van Lith-Verhoeven, J. J., Greenberg, J., Ramesar, R. S., Hoyng, C. B., Cremers, F. P., et al. 2001. Mutations in the pre-mRNA splicing factor gene PRPC8 in autosomal dominant retinitis pigmentosa (RP13). Hum. Mol. Genet. 10:1555–1562.

Nilsen, T. W. 2003. The spliceosome: The most complex macromolecular machine in the cell? BioEssays 25:1147–1149.

Rund, D., and Rachmilewitz, E. 2005. β-Thalassemia. New Engl. J. Med. 353:1135–1146.

Patel, A. A., and Steitz, J. A. 2003. Splicing double: Insights from the second spliceosome. Nat. Rev. Mol. Cell Biol. 4:960–970.

Sharp, P. A. 2005. The discovery of split genes and RNA splicing. Trends Biochem. Sci. 30:279–281.

Valadkhan, S., and Manley, J. L. 2001. Splicing-related catalysis by protein-free snRNAs. Nature 413:701–707.

Zhou, Z., Licklider, L. J., Gygi, S. P., and Reed, R. 2002. Comprehensive proteomic analysis of the human spliceosome. Nature 419: 182–185.

Stark, H., Dube, P., Luhrmann, R., and Kastner, B. 2001. Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. Nature 409:539–542.

Strehler, E. E., and Zacharias, D. A. 2001. Role of alternative splicing in generating isoform diversity among plasma membrane calcium pumps. Physiol. Rev. 81:21–50.

Graveley, B. R. 2001. Alternative splicing: Increasing diversity in the proteomic world. Trends Genet. 17:100–107.

Newman, A. 1998. RNA splicing. Curr. Biol. 8:R903–R905.

Reed, R. 2000. Mechanisms of fidelity in pre-mRNA splicing. Curr. Opin. Cell Biol. 12:340–345.

Sleeman, J. E., and Lamond, A. I. 1999. Nuclear organization of pre-mRNA splicing factors. Curr. Opin. Cell Biol. 11:372–377.

Black, D. L. 2000. Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell 103:367–370.

Collins, C. A., and Guthrie, C. 2000. The question remains: Is the spliceosome a ribozyme? Nat. Struct. Biol. 7:850–854.

Self-Splicing and RNA Catalysis

Adams, P. L., Stanley, M. R., Kosek, A. B., Wang, J., and Strobel, S. A. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature 430:45–50.

Adams, P. L., Stanley, M. R., Gill, M. L., Kosek, A. B., Wang, J., and Strobel, S. A. 2004. Crystal structure of a group I intron splicing intermediate. RNA 10:1867–1887.

Stahley, M. R., and Strobel, S. A. 2005. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science 309:1587–1590.

Carola, C., and Eckstein, F. 1999. Nucleic acid enzymes. Curr. Opin. Chem. Biol. 3:274–283.

Doherty, E. A., and Doudna, J. A. 2000. Ribozyme structures and mechanisms. Annu. Rev. Biochem. 69:597–615.

Fedor, M. J. 2000. Structure and function of the hairpin ribozyme. J. Mol. Biol. 297:269–291.

Hanna, R., and Doudna, J. A. 2000. Metal ions in ribozyme folding and catalysis. Curr. Opin. Chem. Biol. 4:166–170.

Scott, W. G. 1998. RNA catalysis. Curr. Opin. Struct. Biol. 8:720–726.