Noise in Biological Systems: Pros, Cons, and Mechanisms of Control

Methods in Molecular Biology

Volumn 759, Issue , 2011, Pages 407-425

  Pilpel, Yitzhak ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

network biology; noise control mechanisms; Noise in gene expression; regulatory networks

Indexed keywords

ENVIRONMENTAL CHANGE; EUKARYOTIC CELL; GENE EXPRESSION LEVEL; GENETIC HETEROGENEITY; MICROORGANISM; NOISE; NOISE REDUCTION; NONHUMAN; PHENOTYPE; PHYSIOLOGICAL STRESS; PROBABILITY; PROTEIN EXPRESSION; SYSTEMS BIOLOGY; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELLS; CYTOLOGY; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC VARIABILITY; GENETICS; HUMAN; METABOLISM;

UNTRANSLATED RNA;

ANIMALS; CELLS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC VARIATION; HUMANS; MODELS, GENETIC; RNA, UNTRANSLATED;

EUKARYOTA;

EID: 80054752870     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-173-4_23     Document Type: Chapter

References (44)

1. Nagalakshmi, U., Wang, Z., Waern, K., et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349.
2. Shalem, O., Dahan, O., Levo, M., et al. (2008) Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol. Syst. Biol. 4, 223.
3. Ingolia, N. T., Ghaemmaghami, S., Newman, J. R., and Weissman, J. S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223.
4. Li, J. B., Levanon, E. Y., Yoon, J. K., et al. (2009) Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210–1213.
5. Balaban, N. Q., Merrin, J., Chait, R., Kowa-lik, L., and Leibler, S. (2004) Bacterial persistence as a phenotypic switch. Science 305, 1622–1625.
6. Nachman, I., Regev, A., and Ramanathan, S. (2007) Dissecting timing variability in yeast meiosis. Cell 131, 544–556.
7. Feinerman, O., Veiga, J., Dorfman, J. R., Germain, R. N., and Altan-Bonnet, G. (2008) Variability and robustness in T cell activation from regulated heterogeneity in protein levels. Science 321, 1081–1084.
8. Cohen, A. A., Geva-Zatorsky, N., Eden, E., et al. (2008) Dynamic proteomics of individual cancer cells in response to a drug. Science 322, 1511–1516.
9. Raser, J. M., and O’Shea, E. K. (2005) Noise in gene expression: origins, consequences, and control. Science 309, 2010–2013.
10. Thattai, M., and van Oudenaarden, A. (2001) Intrinsic noise in gene regulatory networks. Proc. Natl. Acad. Sci. USA 98, 8614–8619.
11. Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D., and van Oudenaarden A. (2002) Regulation of noise in the expression of a single gene. Nat. Genet. 31, 69–73.
12. Blake, W. J., Kaern, M., Cantor, C. R., and Collins, J. J. (2003) Noise in eukaryotic gene expression. Nature 422, 633–637.
13. Sigal, A., Milo, R., Cohen, A., et al. (2006) Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nat. Methods 3, 525–531.
14. Paulsson, J. (2004) Summing up the noise in gene networks. Nature 427, 415–418.
15. Cai, L., Friedman, N., and Xie, X. S. (2006) Stochastic protein expression in individual cells at the single molecule level. Nature 440, 358–362.
16. Rosenberger, R. F., and Hilton, J. (1983) The frequency of transcriptional and translational errors at nonsense codons in the lacZ gene of Escherichia coli. Mol. Gen. Genet. 191, 207–212.
17. Gordon, A. J, Halliday, J. A., Blankschien, M. D., Burns, P. A, Yatagai, F., and Herman, C. (2009) Transcriptional infidelity promotes heritable phenotypic change in a bistable gene network. PLoS Biol. 24, e44.
18. Elowitz, M. B., Levine, A. J., Siggia, E. D., and Swain, P. S. (2002) Stochastic gene expression in a single cell. Science 297, 1183– 1186.
19. ′ Shea, E. K. (2004) Control of stochasticity in eukaryotic gene expression. Science 304, 1811–1814.
20. Bar-Even, A., Paulsson, J., Maheshri, N., et al. (2006) Noise in protein expression scales with natural protein abundance. Nat. Genet. 38, 636–643.
21. Newman, J. R., Ghaemmaghami, S., Ihmels, J., et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840–846.
22. Huh, W. K., Falvo, J. V., Gerke, L. C., et al. (2003) Global analysis of protein localization in budding yeast. Nature 425, 686–691.
23. Kussell, E., and Leibler, S. (2005) Phenotypic diversity, population growth, and information in fluctuating environments. Science 309, 2075–2078.
24. Pedraza, J. M., and van Oudenaarden, A. (2005) Noise propagation in gene networks. Science 307, 1965–1969.
25. Wang, Y., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D., and Brown, P. O. (2002) Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99, 5860–5865.
26. ′ Shea, E. K. (2006) Quantification of protein half-lives in the budding yeast proteome. Proc. Natl. Acad. Sci. USA 103, 13004–13009.
27. Fraser, H. B., Hirsh, A. E., Giaever, G., Kumm, J., and Eisen, M. B. (2004) Noise minimization in eukaryotic gene expression. PLoS Biol. 2, e137.
28. dos Reis, M., Savva, R., and Wernisch, L. (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32, 5036–5044.
29. Gasch, A. P., Spellman, P. T., Kao, C. M., et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 11, 4241–4257.
30. Rodríguez Martínez, M., Soriano, J., Tlusty, T., Pilpel, Y., and Furman, I. (2010) Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 81, 031924.
31. Murphy, K. F., Balázsi, G., and Collins, J. J. (2007) Combinatorial promoter design for engineering noisy gene expression. Proc. Natl. Acad. Sci. USA 104, 12726–12731.
32. Blake, W. J., Balázsi, G., Kohanski, M. A., et al. (2006). Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell 24, 853–865.
33. Segal, E., and Widom, J. (2009) What controls nucleosome positions? Trends Genet. 25, 335–343.
34. ′ Shea, E. K. (2008) A quantitative model of transcription factor-activated gene expression. Nat. Struct. Mol. Biol. 15, 1192–1198.
35. Hornung, G., and Barkai, N. (2008) Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput. Biol. 4, e8
36. Cağatay, T., Turcotte, M., Elowitz, M. B., Garcia-Ojalvo, J., and Süel GM. (2009) Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139, 512–522.
37. Kafri, R., Levy, M., and Pilpel, Y. (2006) The regulatory utilization of genetic redundancy through responsive backup circuits. Proc. Natl. Acad. Sci. USA 103, 11653– 11658.
38. Kafri, R., Springer, M., and Pilpel, Y. (2009) Genetic redundancy: new tricks for old genes. Cell 136, 389–392.
39. Hendrickson, D. G., Hogan, D. J., McCullough, H. L., et al. (2009) Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol. 7, e1000238.
40. Rinaudo, K., Bleris, L., Maddamsetti, R., Subramanian, S., Weiss, R., and Benenson, Y. (2007) A universal RNAi-based logic evalu-ator that operates in mammalian cells. Nat. Biotechnol. 25, 795–801.
41. Sniegowski, P. D., Gerrish, P. J., and Lenski, R. E. (1997) Evolution of high mutation rates in experimental populations of E. coli. Nature 387, 703–705.
42. Koonin, E. V., and Wolf, Y. I. (2009) Is evolution Darwinian or/and Lamarckian? Biol. Direct. 4, 42.
43. Acar, M., Mettetal, J. T., and van Oudenaarden, A. (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat. Genet. 40, 471–475.
44. Sigal, A., Milo, R., Cohen, A., et al. (2006) Variability and memory of protein levels in human cells. Nature 444, 643–646.