Conflict between noise and plasticity in yeast

PLoS Genetics

Volumn 6, Issue 11, 2010, Pages

  Lehner, Ben ^a  

^a INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

TATA BINDING PROTEIN;

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; COST BENEFIT ANALYSIS; ESSENTIAL GENE; FUNGAL GENETICS; GENE DUPLICATION; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC TRAIT; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; PHENOTYPIC PLASTICITY; PROMOTER REGION; QUANTITATIVE ANALYSIS; TRANSCRIPTION INITIATION; YEAST CELL; BIOLOGICAL MODEL; CHROMATIN; CYTOLOGY; FUNGAL GENE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCETALES;

CHROMATIN; GENE DUPLICATION; GENE EXPRESSION REGULATION, FUNGAL; GENES, ESSENTIAL; GENES, FUNGAL; MODELS, GENETIC; PROMOTER REGIONS, GENETIC; SACCHAROMYCES CEREVISIAE;

EID: 78649708844     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1001185     Document Type: Article

References (42)

1. Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, et al. (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet 31: 370-377.
2. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840-846.
3. Choi JK, Kim YJ (2009) Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet 41: 498-503.
4. Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL (2007) Genetic properties influencing the evolvability of gene expression. Science 317: 118-121.
5. Lehner B (2008) Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol 4: 170.
6. Tirosh I, Weinberger A, Carmi M, Barkai N (2006) A genetic signature of interspecies variations in gene expression. Nat Genet 38: 830-834.
7. Tirosh I, Barkai N, Verstrepen KJ (2009) Promoter architecture and the evolvability of gene expression. J Biol 8: 95.
8. Lehner B (2010) Genes Confer Similar Robustness to Environmental, Stochastic, and Genetic Perturbations in Yeast. PLoS ONE 5: e9035. doi:10.1371/journal.pone.0009035.
9. Meiklejohn CD, Hartl DL (2002) A single mode of canalization. Trends Ecol Evoln 17: 468-473.
10. Sato K, Ito Y, Yomo T, Kaneko K (2003) On the relation between fluctuation and response in biological systems. Proc Natl Acad Sci U S A 100: 14086-14090.
11. Waddington CH (1942) Canalization of Development and the Inheritance of Acquired Characters. Nature 150: 563-565.
12. Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, et al. (2006) Phenotypic consequences of promoter-mediated transcriptional noise. Mol Cell 24: 853-865.
13. Raser JM, O'Shea EK (2005) Noise in gene expression: origins, consequences, and control. Science 309: 2010-2013.
14. Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, et al. (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 4: e1000216. doi:10.1371/journal.pcbi.1000216.
15. Tirosh I, Barkai N (2008) Two strategies for gene regulation by promoter nucleosomes. Genome Res 18: 1084-1091.
16. Pedraza JM, Paulsson J (2008) Effects of molecular memory and bursting on fluctuations in gene expression. Science 319: 339-343.
17. Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc Biol Sci 256: 119-124.
18. Des Marais DL, Rausher MD (2008) Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454: 762-765.
19. Basehoar AD, Zanton SJ, Pugh BF (2004) Identification and distinct regulation of yeast TATA box-containing genes. Cell 116: 699-709.
20. Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8: e1000414. doi:10.1371/journal.pbio.1000414.
21. Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451-464.
22. Raj A, van Oudenaarden A (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216-226.
23. Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, et al. (2007) Dynamics of replication-independent histone turnover in budding yeast. Science 315: 1405-1408.
24. Jamai A, Imoberdorf RM, Strubin M (2007) Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol Cell 25: 345-355.
25. Rufiange A, Jacques PE, Bhat W, Robert F, Nourani A (2007) Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. Mol Cell 27: 393-405.
26. Batada NN, Hurst LD (2007) Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39: 945-949.
27. Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB (2004) Noise minimization in eukaryotic gene expression. PLoS Biol 2: e137. doi:10.1371/journal.pbio.0020137.
28. Cook DL, Gerber AN, Tapscott SJ (1998) Modeling stochastic gene expression: implications for haploinsufficiency. Proc Natl Acad Sci U S A 95: 15641-15646.
29. DeLuna A, Springer M, Kirschner MW, Kishony R Need-based up-regulation of protein levels in response to deletion of their duplicate genes. PLoS Biol 8: e1000347. doi:10.1371/journal.pbio.1000347.
30. Nowak MA, Boerlijst MC, Cooke J, Smith JM (1997) Evolution of genetic redundancy. Nature 388: 167-171.
31. Vavouri T, Semple JI, Lehner B (2008) Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution. Trends Genet 24: 485-488.
32. Ha M, Kim ED, Chen ZJ (2009) Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci U S A 106: 2295-2300.
33. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
34. Acar M, Mettetal JT, van Oudenaarden A (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40: 471-475.
35. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic switch. Science 305: 1622-1625.
36. Thattai M, van Oudenaarden A (2004) Stochastic gene expression in fluctuating environments. Genetics 167: 523-530.
37. Zhang Z, Qian W, Zhang J (2009) Positive selection for elevated gene expression noise in yeast. Mol Syst Biol 5: 299.
38. Lee W, Tillo D, Bray N, Morse RH, Davis RW, et al. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244.
39. Gordon JL, Byrne KP, Wolfe KH (2009) Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet 5: e1000485. doi:10.1371/journal.pgen.1000485.
40. Wapinski I, Pfeffer A, Friedman N, Regev A (2007) Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 23: i549-558.
41. Wapinski I, Pfeffer A, Friedman N, Regev A (2007) Natural history and evolutionary principles of gene duplication in fungi. Nature 449: 54-61.
42. Byrne KP, Wolfe KH (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15: 1456-1461.