Mathematical Biosciences and Engineering (MBE)

Effects of elongation delay in transcription dynamics
Pages: 1431 - 1448, Issue 6, December 2014

doi:10.3934/mbe.2014.11.1431      Abstract        References        Full text (1358.5K)           Related Articles

Xuan Zhang - School of Mathematics and Systems Science, Beihang University, Beijing 100191, China (email)
Huiqin Jin - Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China (email)
Zhuoqin Yang - School of Mathematics and System Sciences and LMIB, Beihang University, Beijing, 100191, China (email)
Jinzhi Lei - Zhou Pei-Yuan Center for Applied Mathematics, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China (email)

1 M. Acar, J. T. Mettetal and A. van Oudenaarden, Stochastic switching as a survival strategy in fluctuating environments, Nat. Genet., 40 (2008), 71-475.
2 U. Alon, An Introduction to Systems Biology, Chapman & Hall/RCR, New York, 2006.       
3 I. Artsimovitch and R. Landick, The transcriptional regulator rfah stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed on template DNA strand, Cell, 109 (2002), 193-203.
4 M. J. Bailey, C. Hughes and V. Koronakis, Rfah and the ops element, components of a novel system controlling bacterial transcription elongation, Mol. Microbiol., 26 (1997), 845-851.
5 W. J. Blake, C. R. Cantor Mads Kærn and J. J. Collins, Noise in eukaryotic gene expression, Nature, 422 (2003), 633-637.
6 D. Bratsun, D. Volfson, L. S. Tsimring, and J. Hasty, Delay-induced stochastic oscillations in gene regulation, Proc. Natl. Acad. Sci. USA, 102 (2005), 14593-14598.
7 L. Cai, N. Friedman and X. S. Xie, Stochastic protein expression in individual cells at the single molecule level, Nature, 440 (2006), 358-362.
8 P. J. Choi, L. Cai, K. Frieda and X. S. Xie, A stochastic single-molecule event triggers phenotype switching of a bacterial cell, Science, 322 (2008), 442-446.
9 D. L. Cook, A. N. Gerber and S. J. Tapscott, Modeling stochastic gene expression: Implications for haploinsufficiency, Proc. Natl. Acad. Sci. USA, 95 (1998), 15641-15646.
10 X. Darzacq, Y. Shav-Tal, V. de Turris, Y. Brody, S. M. Shenoy, R. D. Phair and R. H. Singer, In vivo dynamics of RNA polymerase II transcription, Nat. Struct. Mol. Biol., 14 (2007), 796-806.
11 M. Dobrzyński and F. J. Bruggeman, Elongation dynamics shape bursty transcription and translation, Proc. Natl. Acad. Sci. USA, 106 (2009), 2583-2588.
12 A. Dvir, Promoter escape by RNA polymerase II, Biochim. Biophys. Acta., 1577 (2002), 208-223.
13 M. B. Elowitz, A. J. Levine, E. D. Siggia and P. S. Swain, Stochastic gene expression in a single cell, Science, 297 (2002), 1183-1186.
14 A. M. Femino, F. S. Fay, K. Fogarty and R. H. Singer, Visualization of single RNA transcripts in situ, Science, 280 (1998), 585-590.
15 N. Friedman, L. Cai and X. S. Xie, Linking stochastic dynamics to population distribution: an analytical framework of gene expression, Phys. Rev. Lett., 97 (2006), 168302.
16 I. Golding, J. Paulsson, S. M. Zawilski and E. C. Cox, Real-time kinetics of gene activity in individual bacteria, Cell, 123 (2005), 1025-1036.
17 S. R. Goldman, R. H. Ebright and B. E. Nickels, Direct detection of abortive RNA transcripts in vivo, Science, 324 (2009), 927-928.
18 T. Hearn, C. Haurie and M. C. Mackey, Cyclical neutropenia and the peripheral control of white blood cell production, J. Theor. Biol., 192 (1998), 167-187.
19 K. M. Herbert, A. La Porta, B. J. Wong, R. A. Mooney, K. C. Neuman, R. Landick and S. M. Block, Sequence-resolved detection of pausing by single RNA polymerase molecules, Cell, 125 (2006), 1083-1094.
20 M. Kærn, T. C. Elston, W. J. Blake and J. J. Collins, Stochasticity in gene expression expression: From theories to phenotypes, Nat. Rev. Genet., 6 (2005), 451-464.
21 M. Kerszberg, Noise, delays, robustness, canalization and all that, Curr. Opin. Genet. Dev., 14 (2004), 440-445.
22 M. L. Kireeva, B. Hancock, G. H. Cremona, W. Walter, V. M. Studitsky and M. Kashlev, Nature of the nucleosomal barrier to RNA polymerase II, Mol. Cell, 18 (2005), 97-108.
23 J. Lei, Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters, J. Theor. Biol., 256 (2009), 485-492.       
24 J. Lei, G. He, H. Liu and Q. Nie, A delay model for noise-induced bi-directional switching, Nonlinearity, 22 (2009), 2845-2859.       
25 B. Munsky, G. Neuert and A. van Oudenaarden, Using gene expression noise to understand gene regulation, Science, 336 (2012), 183-187.       
26 T. O'Brien and J. T. Lis, Rapid changes in drosophila transcription after an instantaneous heat shock, Mol. Cell. Biol., 13 (1993), 3456-3463.
27 G. Orphanides and D. Reinberg, A unified theory of gene expression, Cell, 108 (2002), 439-451.
28 E. M. Ozbudak, M. Thattai, I. Kurtser, A. D. Grossman and A. van Oudenaarden, Regulation of noise in the expression of a single gene, Nat. Genet., 31 (2002), 69-73.
29 J. Paulsson, Summing up the noise in gene networks, Nature, 427 (2004), 415-418.
30 J. Paulsson, Models of stochastic gene expression, Phys. Life Rev., 2 (2005), 157-175.
31 J. M. Pedraza and J. Paulsson, Effects of molecular memory and bursting on fluctuations in gene expression, Science, 319 (2008), 339-343.
32 S. Proshkin, A. R. Rahmouni, A. Mironov and E. Nudler, Cooperation between translating ribosomes and RNA polymerase in transcription elongation, Science, 328 (2010), 504-508.
33 N. J. Proudfoot, A. Furger and M. J. Dye, Integrating mRNA processing with transcription, Cell, 108 (2002), 501-572.
34 T. Rajala, A. Häkkinen, S. Healy, O. Yli-Harja and A. S. Ribeiro, Effects of transcriptional pausing on gene expression dynamics, PLoS Comp. Biol., 6 (2010), e1000704.       
35 D. B. Renner, Y. Yamaguchi, T. Wada, H. Handa and D. H. Price, A highly purified RNA polymerase II elongation control system, J. Biol. Chem., 276 (2001), 42601-42609.
36 A. S. Ribeiro, Stochastic and delayed stochastic models of gene expression and regulation, Math. Biosci., 223 (2010), 1-11.       
37 A. S. Ribeiro, O-P. Smolander, T. Rajala, A. Häkkinen and O. Yli-Harja, Delayed stochastic model of transcription at the single nucleotide level, J. Comput. Biol., 16 (2009), 539-553.
38 M. R. Roussel and R. Zhu, Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression, Phys. Biol., 3 (2006), 274-284.
39 V. Shahrezaei, J. F. Ollivier and P. S. Swain, Colored extrinsic fluctuations and stochastic gene expression, Mol. Syst. Biol., 4 (2008), 196.
40 V. Shahrezaei and P. S. Swain, Analytical distributions for stochastic gene expression, Proc. Natl. Acad. Sci. USA, 105 (2008), 17256-17261.
41 A. Shundrovsky, T. J. Santangelo, J. W. Roberts and M. D. Wang, A single-molecule technique to study sequence-dependent transcription pausing, Biophy. J., 87 (2004), 3945-3953.
42 J. Sticker, S. Cookson, M. R. Bennett, W. H. Mather, L. S. Tsimring and J. Hasty, A fast, robust and tunable synthetic gene oscillator, Nature, 456 (2008), 516-519.
43 G. M. Süel, J. Garcia-Ojalvo, L. M. Liberman and M. B. Elowitz, An excitable gene regulatory circuit induces transient cellular differentiation, Nature, 440 (2006), 545-550.
44 P. S. Swain, M. B. Elowitz and E. D. Siggia, Intrinsic and extrinsic contributions to stochasticity in gene expression, Proc. Natl. Acad. Sci. USA, 99 (2002), 12795-12800.
45 I. A. Swinburne and P. A. Silver, Intron delays and transcriptional timing during development, Dev. Cell, 14 (2008), 324-330.
46 C. N. Tennyson, H. J. Klamut and R. G. Worton, The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced, Nat. Genet., 9 (1995), 184-190.
47 T. Tian, K. Burrage, P. M. Burrage and M. Carletti, Stochastic delay differential equation for genetic regulatory networks, J. Comput. Appl. Math., 205 (2007), 696-707.       
48 M. Tigges, T. T. Marquez-Lago, J. Stelling, and M. Fussenegger, A tunable synthetic mammalian oscillator, Nature, 457 (2009), 309-312.
49 T-L. To and N. Maheshri, Noise can induce bimodality in positive transcriptional feedback loops without bistability, Science, 327 (2010), 1142-1145.
50 S. X. Xie, Paul J. Choi, G-W. Li, N. K. Lee and G. Lia, Single-molecule approach to molecular biology in living bacterial cells, Ann. Rev. Biophy., 37 (2008), 417-444.
51 M. Yonaha and N. J. Proudfoot, Specific transcriptional pausing activates polyadenylation in a coupled in vitro system, Mol. Cell, 3 (1999), 593-600.
52 R. Yvinec, C. j. Zhuge, J. Lei and M. C. Mackey, Adiabatic reduction of a model of stochastic gene expression with jump markov process, J. Math. Biol., 68 (2014), 1051-1070.       
53 E. Zavala and T. T. Marquez-Lago, Delays induce novel stochastic effects in negative feedback gene circuits, Biophy. J., 106 (2014), 467-478.
54 J. Zhang, L. Chen and T. Zhou, Analytical distribution and tunability of noise in a model of promoter progress, Biophy. J., 102 (2012), 1247-1257.
55 J. Zhang and T. Zhou, Promoter-mediated transcriptional dynamics, Biophy. J., 106 (2014), 479-488.
56 L. Zhang, K. Radtke, L. Zheng, A. Q. Cai, T. F. Schilling and Q. Nie, Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain, Mol. Syst. Biol., 8 (2012), 613.
57 R. Zhu, A. S. Ribeiro, D. Salahub and S. A. Kauffman, Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models, J. Theor. Biol., 246 (2007), 725-745.       
58 R. Zhu and D. Salahub, Delay stochastic simulation of sinlge-gene expression reveals a detailed relationship between protein noise and mean abundance, FEBS Lett., 582 (2008), 2905-2910.

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