Small-scale copy number variation and large-scale changes in gene expression

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 43, 2008, Pages 16659-16664

  Mileyko, Yuriy ^a   Joh, Richard I ^a   Weitz, Joshua S ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Gene duplication; Gene regulation; Network motifs; Nonlinear dynamics

Indexed keywords

ARTICLE; BINDING AFFINITY; COPY NUMBER VARIATION; DEGRADATION; GENE DUPLICATION; GENE EXPRESSION; GENE INTERACTION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; POSITIVE FEEDBACK; PRIORITY JOURNAL; RNA TRANSLATION;

BIOLOGICAL CLOCKS; FEEDBACK, BIOCHEMICAL; GENE DOSAGE; GENE EXPRESSION; GENE REGULATORY NETWORKS; KINETICS; MODELS, THEORETICAL; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 55949100282     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0806239105     Document Type: Article

References (53)

1. Klappenbach JA, Dunbar JM, Schmidt TM (2000) rRNA oepron copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66:1328-1333.
2. Stevenson BS, Schmidt TM (2004) Life history implications of rRNA gene copy number in Escherichia coli. Appl Environ Microbiol 70:6670-6677.
3. Perry, G. H., et. al. (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet 39:1256-1260.
4. Deluna A, et al. (2008) Exposing the fitness contribution of duplicated genes. Nat Genet 40:676-681.
5. Kobiler O, et al. (2005) Quantitative kinetics analysis of the bacteriophage - genetic network. Proc Natl Acad Sci USA 102:4470-4475.
6. Weitz JS, Mileyko Y, Joh RI, Voit EO (2008) Collective decision making in bacterial viruses. Biophys J 95:2673-2680.
7. Ohno S (1970) Evolution by Gene Duplication (Allen and Unwin, London).
8. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
9. Li WH, Yang J, Gu X (2005) Expression divergence between duplicate genes. Trends Genet 21:602-607.
10. Korbel JO, et al. (2008) The current excitement about copy-number variation: How it relates to gene duplications and protein families. Curr Opin Struct Biol 18:366-374.
11. Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624.
12. Conrad B, Antonarakis SE (2007) Gene duplication: A drive for phenotypic diversity and cause of human disease. Annu Rev Genomics Hum Genet 8:17-35.
13. Roper RJ, Reeves RH (2006) Understanding the basis for Down Syndrome phenotypes. PLoS Genet 2:e50.
14. Pollack JR, et al. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23:41-46.
15. Pollack JR, et al. (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 99:12963-12968.
16. Beckmann JS, Estivill X, Antonarakis SE (2007) Copy number variants and genetic traits: Closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet 8:639-646.
17. Redon R, et al. (2006) Global variation in copy number variation in the human genome. Nature 444:444-454.
18. Stranger BE, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315:848-853.
19. Kidd JM, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453:56-64.
20. Cooper GM, Nickerson DA, Eichler EE (2007) Mutational and selective effects on copy-number variants in the human genome. Nat Genet 39:S22-S29.
21. Paulsson J, Ehrenberg M (2001) Noise in a minimal regulatory network: Plasmid copy number control. Q Rev Biophys 34:1-59.
22. Brookfield JFY, Badge RM (1997) Population genetics models of transposable elements. Genetica 100:281-294.
23. Guido NJ, et al. (2006) A bottom-up approach to gene regulation. Nature 439:856-860.
24. Presser A, Elowitz MB, Kellis M, Kishony R (2008) The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. Proc Natl Acad Sci USA 105:950-954.
25. Guan Y, Dunham MJ, Troyanskaya OG (2007) Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics 175:933-943.
26. Atkinson MR, Savageau MA, Myers JT, Ninfa AJ (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113:597-607.
27. Ingolia NT, Murray AW (2007) Positive-feedback loops as a flexible biological module. Curr Biol 17:668-677.
28. Milo R, et al. (2002) Network motifs: Simple building blocks of complex networks. Science 298:824-827.
29. Alon U (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman and Hall, London).
30. Ptashne M, Gann A (2002) Genes and Signals. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY).
31. Hasty J, McMillen D, Isaacs F, Collins JJ (2001) Computational studies of gene regulatory networks: In numero molecular biology. Nat Rev Genet 2:268-279.
32. Strogatz S (1994) Nonlinear Dynamics and Chaos (Addison Wesley, Reading, MA).
33. Bennett MR, Volfson D, Tsimring L, Hasty J (2007) Transient dynamics of genetic regulatory networks. Biophys J 92:3501-3512.
34. Becskei A, Seraphin B, Serrano L (2001) Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion. EMBO J 20:2528-2535.
35. Isaacs FJ, Hasty J, Cantor CR, Collins JJ (2003) Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci USA 100:7714-7719.
36. Cherry JL, Adler FR (2000) How to make a biological switch. J Theor Biol 203:117-133.
37. Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by - phage repressor. Proc Natl Acad Sci USA 79:1129-1133.
38. Rotem E, et al. (2008) Bacteriophage infection is targeted to cellular poles. Mol Microbiol 5:1107-1116.
39. Kourilsky P (1973) Lysogenization by bacteriophage-lambda 1. Multiple infection and lysogenic response. Mol Gen Genet 122:183-195.
40. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339-342.
41. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transciptional regulators. Nature 403:335-338.
42. Birchler JA, Riddle NC, Auger DL, Veitia RA (2005) Dosage balance in gene regulation: Biological implications. Trends Genet 4:219-226.
43. Griffiths AJF, Wessler SR, Lewontin RC, Carroll SB (2008) Introduction to Genetic Analysis (W. H. Freeman, New York).
44. Kollmann M, Lovdok L, Bartholome K, Timmer J, Sourjik V (2005) Design principles of a bacterial signalling network. Nature 438:504-507.
45. Pedraza JM, van Oudenaarden A (2005) Noise propagation in gene networks. Science 307:1965-1969.
46. Wagner A (2000) Robustness against mutations in genetic networks of yeast. Nat Genet 24:355-361.
47. Ciliberti S, Martin OC, Wagner A (2007) Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Comput Biol 3:e15.
48. Davidson EH, Erwin DH (2006) Gene regulatory networks and the evolution of animal body plans. Science 311:796-800.
49. Slutsky M, Mirny LA (2004) Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential. Biophys J 87:4021-4035.
50. Endy D (2005) Foundations for engineering biology. Nature 438:449-453.
51. Dean EJ, Davis JC, Davis RW, Petrov DA (2008) Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet 4:e1000113.
52. Musso G, et al. (2008) The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res 18:1092-1099.
53. Hittinger CT, Carroll SB (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449:677-681.