The influence of look-ahead on the error rate of transcription

Mathematical Modelling of Natural Phenomena

Volumn 5, Issue 3, 2010, Pages 206-227

  Yamada, Y R ^a   Peskin, C S ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

chemical master equation; elongation dynamics of transcription; error correcting mechanisms; Gillespie simulation; transcription modeling

Indexed keywords

CHEMICAL MASTER EQUATION; CORRECTION MECHANISM; COVALENT LINKAGE; DNA STRANDS; ERROR RATE; ERROR REDUCTION; ERROR-CORRECTING MECHANISMS; GILLESPIE SIMULATION; INTEGER PARAMETERS; LOOK-AHEAD; MATHEMATICAL ANALYSIS; RANDOM WALK; RIBONUCLEOSIDES; RNA POLYMERASE; RNA SYNTHESIS; WINDOW SIZE;

COMPUTER SIMULATION; ERROR CORRECTION; FUNCTIONAL POLYMERS; FUNCTIONS; HYDROLYSIS; RNA;

TRANSCRIPTION;

EID: 78349309327     PISSN: 09735348     EISSN: 17606101     Source Type: Journal    
DOI: 10.1051/mmnp/20105313     Document Type: Article

References (42)

1. A. Alon. An introduction to systems biology: design principles of biological circuits. Chapman and Hall, Boca Raton, 2007.
2. E. Abbodanzieri,W. Greenleaf, J. Shaevitz, R. Landick, S. Block. Direct observation of basepair stepping by RNA polymerase. Nature, 438 (2005), 460-465. (Pubitemid 41742012)
3. L. Bai, R. Fulbright, M. Wang. Mechanochemical kinetics of transcription elongation. Phys. Rev. Lett., 98 (2007), No. 6, 068103.
4. G. Bar-Nahum, V. Epshtein, A. Ruckenstein, R. Rafikov, A. Mustaev, E. Nudler. A ratchet mechanism of transcription elongation and its control. Cell, 120 (2005), No. 2, 183-193. (Pubitemid 40174762)
5. A. Blank, J. Gallant, R. Burgess, L. Loeb. An RNA polymerase mutant with reduced accuracy of chain elongation. Biochemistry, 25 (1986), No. 20, 5920-5928. (Pubitemid 17204024)
6. Y. Chen, D. Chafin, D. Price, A. Greenleaf. Drosophila RNA polymerase II mutants that affect transcription elongation. Jour. Biol. Chem., 271 (1996), No. 11, 5993-5999. (Pubitemid 26095400)
7. G. Eichhorn, P. Chuknyisky, J. Butzow, R. Beal, C. Garland, C. Janzen, P. Clark, E. Tarien. A structural model for fidelity in transcription. Proc. Natl. Acad. Sci., 91 (1994), No. 16, 7613-7617. (Pubitemid 24238235)
8. D. Gillespie. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comp. Phys., 22 (1976), No. 4, 403-434.
9. D. Gillespie. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem., 81 (1977), No. 25, 2340-2361.
10. S. Greive, P. von Hippel. Thinking quantitatively about transcriptional regulation. Nat. Rev. Mol. Cell Biol., 6 (2005), 221-232. (Pubitemid 40314923)
11. K. Herbert, W. Greenleaf, S. Block. Single-molecule studies of RNA polymerase: motoring along. Annu. Rev. Biochem., 77 (2008), 149-176.
12. W. Hlavacek, A. Redondo, H. Metzger, C. Wofsy, B. Goldstein. Kinetic proofreading models for cell signaling predict ways to escape kinetic proofreading. Proc. Natl. Acad. Sci., 98 (2001), No. 13, 7295-7300. (Pubitemid 32567942)
13. S. Holmes, T. Santangelo, C. Cunningham, J. Roberts, D. Erie. Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity. Jour. Biol. Chem., 281(2006), No. 27, 18677-18683. (Pubitemid 44035528)
14. J. Hopfield. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci., 71 (1974), No. 10, 4135-4139.
15. K. Howe, C. Kane, A. Ares. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in saccharomyces cerevisiae. RNA, 9 (2003), No. 8, 993-1006. (Pubitemid 36899242)
16. C. Jeon, K. Agarwal. Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc. Natl. Acad. Sci., 93 (1996), No. 24, 13677-13682. (Pubitemid 26424178)
17. M. Kireeva, Y. Nedlialkov, G. Cremona, Y. Purtov, L. Lubkowska, F. Malagon, Z. Burton, J. Strathern, M. Kashlev. Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol. Cell, 30 (2008), No. 5, 557-566. (Pubitemid 351755063)
18. R. Libby, J. Gallant. The role of RNA polymerase in transcriptional fidelity. Mol. Microbiol., 5 (1991), No. 5, 999-1004. (Pubitemid 21896125)
19. R. Libby, J Gallant. Phosphorolytic error correction during transcription. Mol. Microbiol., 12 (1994), No. 1, 121-129. (Pubitemid 24197450)
20. R. Libby, L. Nelson, J. Calvo, J. Gallant. Transcriptional proofreading in escherichia coli. EMBO Jour., 8 (1989), No. 10, 3153-3158. (Pubitemid 19275018)
21. F. Malagon, M. Kireeva, B. Shafer, L. Lubkowska, M. Kashlev, J. Strathern. Mutations in the saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-Azauracil. Genetics, 172 (2006), No. 4, 2201-2209.
22. P. Mason, K. Struhl. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell, 17 (2005), No. 6, 831-840. (Pubitemid 40386944)
23. M. de la Mata, C. Alonso, S. Kadener, J. Fededa, M. Blaustein, J. Pelisch, P. Cramer, D. Bentley, A. Kornblihtt. A Slow RNA Polymerase II Affects Alternative Splicing in Vivo. Mol. Cell, 12 (2003), No. 2, 525-532. (Pubitemid 37238937)
24. T. McKeithan. Kinetic proofreading in T-cell receptor signal transduction. Proc. Natl. Acad. Sci., 92 (1995), No. 11, 5042-5046.
25. J. Ninio. Kinetic amplification of enzyme discrimination. Biochimie, 57 (1975), No. 5, 587-595.
26. J. Roberts, S. Shankar, J. Filter. RNA polymerase elongation Ffactors. Annu. Rev. Microbiol., 62 (2008), 211-233.
27. J. Roussel, R. Zhu. Stochastic kinetics description of a simple transcription model. Bull. Math. Biol., 68 (2006), No. 7, 1681-1713. (Pubitemid 44392965)
28. J. Shaevitz, E. Abbondanzieri, R. Landick, S. Block . Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature, 426 (2003), 684-687. (Pubitemid 38009379)
29. R. Sims, R. Belotserkovskaya, D. Reinberg. Elongation by RNA polymerase II: the short and long of it. Genes Dev., 18 (2004), 2437-2468. (Pubitemid 39362887)
30. C. Springgate, L. Loeb. On the fidelity of transcription by escherichia coli ribonucleic acid polymerase. J. Mol. Biol., 97 (1975), No. 4, 577-591.
31. E. Stepanova, J. Lee, M. Ozerova, E. Semenova, K. Datsenko, B. Wanner, K. Severinov, S. Borukhov. Analysis of promoter targets for Escheichia coli transcription elongation factor GreA in vivo and in vitro. J. Bateriol., 189 (2007), No. 24, 8772-8785.
32. P. Swain, E. Siggia. The role of proofreading in signal transduction specifity. Biophys. J., 82 (2007), No. 6, 2928-2933.
33. V. Tadigotla, D. O'Maoileidigh, A. Sengupta, V. Epshtein, R. Ebright, E. Nudler, A. Ruckenstein. Thermodynamic and kinetic modeling of transcriptional pausing. Prof. Natl. Acad. Sci.,103 (2006), No. 12, 4439-4444.
34. J. Thomas, A. Platas, D. Hawley. Transcriptional fidelity and proofreading by RNA polymerase II Cell, 93 (1998), No. 4, 627-637. (Pubitemid 28240723)
35. T. Tlusty, R. Bar-Ziv, A. Libchaber. High-fidelity DNA sensing by protein binding fluctuations. Phys. Rev. Lett., 93 (2004), No. 25, 2581031.
36. U. Vogel, K. Jensen. The RNA chain elongation rate in escherichia coli depends on the growth rate. J. Bacteriol., 176 (1994), No. 10, 2807-2813. (Pubitemid 24152923)
37. M. Voliotis, N. Cohen, C. Molina-Paris, T. Liverpool. Fluctuations, pauses, and backtracking in DNA transcription. Biophys. J., 94 (2008), No. 2, 334-348.
38. M. Voliotis, N. Cohen, C. Molina-Paris, T. Liverpool. Backtracking and error correction in DNA transcription in The Art and Science of Statistical Bioinformatics. 104-107, Leeds University Press, Leeds, 2008.
39. P. Xie. A dynamic model for transcription elongation and sequence-dependent short pauses by RNA polymerase. BioSystems, 93 (2008), 199-210.
40. Y. Yamada, C. Peskin. A chemical kinetic model of transcriptional elongation. LANL ArXiv (2006), q-bio.BM/0603012.
41. Y. Yamada, C. Peskin. A look-ahead model for the elongation dynamics of transcription. Biophys. J., 96 (2009), No. 8, 3015-3031.
42. N. Zenkin, Y. Yuzenkova, K. Severinov. Transcript-assisted transcriptional proofreading. Science, 313 (2006), No. 5786, 518-520. (Pubitemid 44148455)