Noise-mean relationship in mutated promoters

Genome Research

Volumn 22, Issue 12, 2012, Pages 2409-2417

  Hornung, Gil ^a   Bar Ziv, Raz ^a   Rosin, Dalia ^a   Tokuriki, Nobuhiko ^a   Tawfik, Dan S ^a   Oren, Moshe ^a   Barkai, Naama ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; DOWN REGULATION; ENVIRONMENTAL STRESS; GENE EXPRESSION; GENE LIBRARY; GENE MUTATION; MOLECULE; NOISE; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; SACCHAROMYCES CEREVISIAE; TATA BOX; UPREGULATION;

BINDING SITES; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GLUCOSE TRANSPORT PROTEINS, FACILITATIVE; GLYCEROL-3-PHOSPHATE DEHYDROGENASE (NAD+); HEAT-SHOCK PROTEINS; MUTATION; NUCLEOSOMES; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TATA BOX; TRANSCRIPTION FACTORS;

EID: 84870562146     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.139378.112     Document Type: Article

References (42)

1. Acar M, Mettetal JT, van Oudenaarden A. 2008. Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40: 471-475. (Pubitemid 351450880)
2. Bar-Even A, Paulsson J, Maheshri N, Carmi M, O'Shea EK, Pilpel Y, Barkai N. 2006. Noise in protein expression scales with natural protein abundance. Nat Genet 38: 636-643. (Pubitemid 43927304)
3. Basehoar AD, Zanton SJ, Pugh BF. 2004. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116: 699-709. (Pubitemid 38326728)
4. Batada NN, Hurst LD. 2007. Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39: 945-949. (Pubitemid 47185175)
5. Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ. 2006. Phenotypic consequences of promoter-mediated transcriptional noise. Mol Cell 24: 853-865. (Pubitemid 44960090)
6. Cxaǧatay T, Turcotte M, Elowitz MB, Garcia-Ojalvo J, Süel GM. 2009. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139: 512-522.
7. Choi JK, Kim Y-J. 2008. Epigenetic regulation and the variability of gene expression. Nat Genet 40: 141-147. (Pubitemid 351171392)
8. Choi JK, Kim Y-J. 2009. Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet 41: 498-503.
9. Elowitz MB, Levine AJ, Siggia ED, Swain PS. 2002. Stochastic gene expression in a single cell. Science 297: 1183-1186. (Pubitemid 36193353)
10. Erkine AM, Adams CC, Gao M, Gross DS. 1995a. Multiple protein-DNA interactions over the yeast HSC82 heat shock gene promoter. Nucleic Acids Res 23: 1822-1829.
11. Erkine AM, Szent-Gyorgyi C, Simmons SF, Gross DS. 1995b. The upstream sequences of the HSP82 and HSC82 genes of Saccharomyces cerevisiae: Regulatory elements and nucleosome positioning motifs. Yeast 11: 573-580.
12. Erkine AM, Adams CC, Diken T, Gross DS. 1996. Heat shock factor gains access to the yeast HSC82 promoter independently of other sequence-specific factors and antagonizes nucleosomal repression of basal and induced transcription. Mol Cell Biol 16: 7004-7017. (Pubitemid 26389760)
13. Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. 2008. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 4: e1000216. doi: 10.1371/journal.pcbi.1000216.
14. Friedman N, Cai L, Xie XS. 2006. Linking stochastic dynamics to population distribution: An analytical framework of gene expression. Phys Rev Lett 97: 168302. doi: 10.1103/PhysRevLett.97.168302.
15. Jaqaman K, Danuser G. 2006. Linking data to models: Data regression. Nat Rev Mol Cell Biol 7: 813-819. (Pubitemid 44627474)
16. Kaneko K. 2007. Evolution of robustness to noise and mutation in gene expression dynamics. PLoS ONE 2: e434. doi: 10.1371/journal.pone.0000434.
17. Kussell E, Leibler S. 2005. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309: 2075-2078. (Pubitemid 41362330)
18. Lehner B. 2008. Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol 4. doi: 10.1038/msb.2008.11.
19. Lehner B. 2010. Conflict between noise and plasticity in yeast. PLoS Genet 6: e1001185. doi: 10.1371/journal.pgen.1001185.
20. Maheshri N, O'Shea EK. 2007. Living with noisy genes: How cells function reliably with inherent variability in gene expression. Annu Rev Biophys Biomol Struct 36: 413-434. (Pubitemid 46998126)
21. Meijer HA, Thomas AAM. 2002. Control of eukaryotic protein synthesis by upstream open reading frames in the 59-untranslated region of an mRNA. Biochem J 367: 1-11. (Pubitemid 35176885)
22. Mogno I, Vallania F, Mitra RD, Cohen BA. 2010. TATA is a modular component of synthetic promoters. Genome Res 20: 1391-1397.
23. Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ. 2010. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res 38: 2712-2726.
24. Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. 2006. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840-846.
25. Paulsson J. 2004. Summing up the noise in gene networks. Nature 427: 415-418. (Pubitemid 38168488)
26. Paulsson J. 2005. Models of stochastic gene expression. Phys Life Rev 2: 157-175. (Pubitemid 40792434)
27. Pedraza JM, Paulsson J. 2008. Effects of molecular memory and bursting on fluctuations in gene expression. Science 319: 339-343.
28. Raj A, van Oudenaarden A. 2008. Nature, nurture, or chance: Stochastic gene expression and its consequences. Cell 135: 216-226.
29. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. 2006. Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4: e309. doi: 10.1371/journal.pbio. 0040309.
30. Raser JM, O'Shea EK. 2004. Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814. (Pubitemid 38787899)
31. Rinott R, Jaimovich A, Friedman N. 2011. Exploring transcription regulation through cell-to-cell variability. Proc Natl Acad Sci 108: 6329-6334.
32. Sachs MS, Geballe AP. 2006. Downstream control of upstream open reading frames. Genes Dev 20: 915-921.
33. So L, Ghosh A, Zong C, Sepulveda LA, Segev R, Golding I. 2011. General properties of transcriptional time series in Escherichia coli. Nat Genet 43: 554-560.
34. Tan RZ, van Oudenaarden A. 2010. Transcript counting in single cells reveals dynamics of rDNA transcription. Mol Syst Biol 6: 358. doi: 10.1038/msb.2010.14.
35. Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, Hearn J, Emili A, Xie XS. 2010. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
36. Tawfik DS. 2010. Messy biology and the origins of evolutionary innovations. Nat Chem Biol 6: 692-696.
37. Tirosh I, Barkai N. 2008. Two strategies for gene regulation by promoter nucleosomes. Genome Res 18: 1084-1091. (Pubitemid 351931159)
38. Tsui K, Dubuis S, Gebbia M, Morse RH, Barkai N, Tirosh I, Nislow C. 2011. Evolution of nucleosome occupancy: Conservation of global properties and divergence of gene-specific patterns. Mol Cell Biol 31: 4348-4355.
39. Wang Z, Zhang J. 2011. Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci 108: E67-E76.
40. Yun Y, Adesanya TMA, Mitra RD. 2012. A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs. Genome Res 22: 1089-1097.
41. Zenklusen D, Larson DR, Singer RH. 2008. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol 15: 1263-1271.
42. Zhang Z, Qian W, Zhang J. 2009. Positive selection for elevated gene expression noise in yeast. Mol Syst Biol 5: 299. doi: 10.1038/msb.2009.58.