Gene dosage and gene duplicability

Genetics

Volumn 179, Issue 4, 2008, Pages 2319-2324

  Qian, Wenfeng ^a   Zhang, Jianzhi ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE DOSAGE; GENE DUPLICATION; GENOME; HAPLOTYPE; HUMAN; NONHUMAN; PRIORITY JOURNAL; YEAST; FUNGAL GENE; GENETICS; MOLECULAR EVOLUTION; SACCHAROMYCES CEREVISIAE;

EVOLUTION, MOLECULAR; GENE DOSAGE; GENE DUPLICATION; GENES, FUNGAL; GENOME, FUNGAL; GENOME, HUMAN; HUMANS; SACCHAROMYCES CEREVISIAE;

EID: 55749104408     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.108.090936     Document Type: Article

References (37)

1. BINDER, G., M. BROWN and J. S. PARKS, 1996 Mechanisms responsible for dominant expression of human growth hormone gene mutations. J. Clin. Endocrinol. Metab. 81: 4047-4050.
2. CONANT, G. C., and A. WAGNER, 2002 GenomeHistory: a software tool and its application to fully sequenced genomes. Nucleic Acids Res. 30: 3378-3386.
3. DAVIS, J. C., and D. A. PETROV, 2004 Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol. 2: E55.
4. DAVIS, J. C., and D. A. PETROV, 2005 Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet. 21: 548-551.
5. DEKEL, E., and U. ALON, 2005 Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588-592.
6. DELNERI, D., D. C. HOYLE, K. GKARGKAS, E. J. CROSS, B. RASH et al., 2008 Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures. Nat. Genet. 40: 113-117.
7. DEUTSCHBAUER, A. M., D. F. JARAMILLO, M. PROCTOR, J. KUMM, M. E. HILLENMEYER et al., 2005 Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 169: 1915-1925.
8. DRAKE, J. W., B. CHARLESWORTH, D. CHARLESWORTH and J. F. CROW, 1998 Rates of spontaneous mutation. Genetics 148: 1667-1686.
9. GAO, L. Z., and H. INNAN, 2004 Very low gene duplication rate in the yeast genome. Science 306: 1367-1370.
10. GU, Z., D. NICOLAE, H. H. LU and W. H. LI, 2002 Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18: 609-613.
11. HE, X., and J. ZHANG, 2005a Gene complexity and gene duplicability. Curr. Biol. 15: 1016-1021.
12. HE, X., and J. ZHANG, 2005b Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169: 1157-1164.
13. HE, X., and J. ZHANG, 2006 Higher duplicability of less important genes in yeast genomes. Mol. Biol. Evol. 23: 144-151.
14. JIMENEZ-SANCHEZ, G., B. CHILDS and D. VALLE, 2001 Human disease genes. Nature 409: 853-855.
15. KELLIS, M., B. W. BIRREN and E. S. LANDER, 2004 Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
16. KONDRASHOV, F. A., and A. S. KONDRASHOV, 2006 Role of selection in fixation of gene duplications. J. Theor. Biol. 239: 141-151.
17. KONDRASHOV, F. A., and E. V. KOONIN, 2004 A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet. 20: 287-290.
18. KOPELMAN, N. M., D. LANCET and I. YANAI, 2005 Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nat. Genet. 37: 588-589.
19. LANG, G. I., and A. W. MURRAY, 2008 Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae. Genetics 178: 67-82.
20. LI, L., Y. HUANG, X. XIA and Z. SUN, 2006 Preferential duplication in the sparse part of yeast protein interaction network. Mol. Biol. Evol. 23: 2467-2473.
21. LIANG, H., K. R. PLAZONIC, J. CHEN, W. H. LI and A. FERNANDEZ, 2008 Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genet. 4: e11.
22. LYNCH, M., and J. S. CONERY, 2000 The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
23. LYNCH, M., and A. FORCE, 2000 The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
24. MARLAND, E., A. PRACHUMWAT, N. MALTSEV, Z. GU and W. H. LI, 2004 Higher gene duplicabilities for metabolic proteins than for nonmetabolic proteins in yeast and E. coli. J. Mol. Evol. 59: 806-814.
25. MAYO, A. E., Y. SETTY, S. SHAVIT, A. ZASLAVER and U. ALON, 2006 Plasticity of the cis-regulatory input function of a gene. PLoS Biol. 4: e45.
26. OHNO, S., 1970 Evolution by Gene Duplication. Springer-Verlag, Berlin.
27. PAPP, B., C. PAL and L. D. HURST, 2003 Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
28. PERRY, G. H., N. J. DOMINY, K. G. CLAW, A. S. LEE, H. FIEGLER et al., 2007 Diet and the evolution of human amylase gene copy number variation. Nat. Genet. 39: 1256-1260.
29. PRACHUMWAT, A., and W. H. LI, 2006 Protein function, connectivity, and duplicability in yeast. Mol. Biol. Evol. 23: 30-39.
30. SUGINO, R. P., and H. INNAN, 2006 Selection for more of the same product as a force to enhance concerted evolution of duplicated genes. Trends Genet. 22: 642-644.
31. TAKAHASHI, Y., H. KAJI, Y. OKIMURA, K. GOJI, H. ABE et al., 1996 Brief report: short stature caused by a mutant growth hormone. N. Engl. J. Med. 334: 432-436.
32. VEITIA, R. A., 2002 Exploring the etiology of haploinsufficiency. Bio-Essays 24: 175-184.
33. WAGNER, A., 2001 The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18: 1283-1292.
34. WAGNER, A., 2005 Energy constraints on the evolution of gene expression. Mol. Biol. Evol. 22: 1365-1374.
35. WOLFE, K. H., and D. C. SHIELDS, 1997 Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
36. YANG, J., R. LUSK and W. H. LI, 2003 Organismal complexity, protein complexity, and gene duplicability. Proc. Natl. Acad. Sci. USA 100: 15661-15665.
37. ZHANG, J., 2003 Evolution by gene duplication: an update. Trends Ecol. Evol. 18: 292-298.