The gene balance hypothesis: From classical genetics to modern genomics

Plant Cell

Volumn 19, Issue 2, 2007, Pages 395-402

  Birchler, James A ^a   Veitia, Reiner A ^b  

^a UNIVERSITY OF MISSOURI   (United States)

^b INSTITUT COCHIN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34250632677     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.106.049338     Document Type: Article

References (70)

1. Aury, J.-M., et al. (2006). Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178.
2. Belling, J., and Blakeslee, A.F. (1924). The configurations and sizes of the chromosomes in trivalents of 25-chromosome Daturas. Proc. Natl. Acad. Sci. USA 10: 116-120.
3. Birchler, J.A. (1979). A study of enzyme activities in a dosage series of the long arm of chromosome one in maize. Genetics 92: 1211-1229.
4. Birchler, J.A. (1981). The genetic basis of dosage compensation of Alcohol dehydrogenase-1 in maize. Genetics 97: 625-637.
5. Birchler, J.A., Bhadra, U., Pal-Bhadra, M., and Auger, D.L. (2001). Dosage dependent gene regulation in higher eukaryotes: Implications for dosage compensation, aneuploid syndromes and quantitative traits. Dev. Biol. 234: 275-288.
6. Birchler, J.A., Fernandez, H., and Kavi, H.H. (2006). Commonalities in compensation. Bioessays 28: 565-568.
7. Birchler, J.A., Hiebert, J.C., and Paigen, K. (1990). Analysis of autosomal dosage compensation involving the Alcohol dehydrogenase locus in Drosophila melanogaster. Genetics 124: 677-686.
8. Birchler, J.A., and Newton, K.J. (1981). Modulation of protein levels in chromosomal dosage series of maize: The biochemical basis of aneuploid syndromes. Genetics 99: 247-266.
9. Birchler, J.A., Riddle, N.C., Auger, D.L., and Veitia, R.A. (2005). Dosage balance in gene regulation: Biological implications. Trends Genet. 21: 219-226.
10. Blakeslee, A.F. (1921). Types of mutations and their possible significance in evolution. Am. Nat. 5: 254-267.
11. Blakeslee, A.F. (1934). New Jimson weeds from old chromosomes. J. Hered. 25: 80-108.
12. Blakeslee, A.F., and Avery, B.T. (1919). Mutations in the Jimson weed. J. Hered. 10: 111-120.
13. Blakeslee, A.F., Belling, J., and Farnham, M.E. (1920). Chromosomal duplication and Mendelian phenomena in Datura mutants. Science 52: 388-390.
14. Blanc, G., and Wolfe, K.H. (2004). Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691.
15. Bowers, J.E., Chapman, B.A., Rong, J., and Paterson, A.H. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
16. Bridges, C.B. (1925). Sex in relation to chromosomes and genes. Am. Nat. 59: 127-137.
17. Burke, J.M., Tang, S., Knapp, S.J., and Rieseberg, L.H. (2002). Genetic analysis of sunflower domestication. Genetics 161: 1257-1267.
18. Carlson, P.S. (1972). Locating genetic loci with aneuploids. Mol. Gen. Genet. 114: 273-280.
19. Chapman, B.A., Bowers, J.E., Feltus, F.A., and Paterson, A.H. (2006). Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc. Natl. Acad. Sci. USA 103: 2730-2735.
20. Chen, K.C., Calzone, L., Csikasz-Nagy, A., Cross, F.R., Novak, B., and Tyson, J.J. (2004). Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell 15: 3841-3862.
21. Crow, J.F. (1997). Birth defects, Jimson weeds and bell curves. Genetics 147: 1-6.
22. Dellaporta, S.L., and Calderon-Urrea, A. (1993). Sex determination in flowering plants. Plant Cell 5: 1241-1251.
23. Davis, J.C., and Petrov, D.A. (2005). Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet. 21: 548-551.
24. Derti, A., Roth, F.P., Church, G.M., and Wu, C.T. (2006). Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nat. Genet. 38: 1216-1220.
25. Devlin, R.H., Holm, D.G., and Grigliatti, T.A. (1982). Autosomal dosage compensation in Drosophila melanogaster strains trisomic for the left arm of chromosome 2. Proc. Natl. Acad. Sci. USA 79: 1200-1204.
26. Devlin, R.H., Holm, D.G., and Grigliatti, T.A. (1988). The influence of whole-arm trisomy on gene expression in Drosophila. Genetics 118: 87-101.
27. deVries, H. (1901). Die Mutationstheorie. Bd. 1. Die Entstehung der Arten durch Mutation, Vol. 1. (Leipzig, Germany: Veit & Co.).
28. Dobzhansky, T. (1937). Genetics and the Origin of Species. (New York: Columbia University Press).
29. Emerson, S.H., and Sturtevant, A.H. (1931). Genetic and cytological studies of Oenothera. III. The translocation interpretation. Z. Indukt. Abstammungs-Vererbungl. 59: 395-419.
30. Erickson, J.W., and Cline, T.W. (1993). A bZIP protein, sisterless-a, collaborates with bHLH transcription factors in Drosophila development to determine sex. Genes Dev. 7: 1688-1702.
31. FitzPatrick, D.R., Ramsay, J., McGill, N.I., Shade, M., Carothers, A.D., and Hastie, N.D. (2002). Transcriptome analysis of human autosomal trisomy. Hum. Mol. Genet. 11: 3249-3256.
32. Fraser, H.B., Wall, D.P., and Hirsh, A.E. (2003). A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol. Biol. 3: 11.
33. Freeling, M., and Thomas, B.C. (2006). Gene-balanced duplications, like tetraploid, provide predictable drive to increase morphological complexity. Genome Res. 16: 805-814.
34. Goldschmidt, R.B. (1920). Untersuchungen uber inter-sexualitat. Zeits. i. Abst. u. Vererb. 23: 1-199.
35. Grell, E.H. (1962). The dose effect of ma-l+ and ry+ on xanthing dehydrogenease activity in Drosophila melanogaster. Z. Vererbungsl. 93: 371-377.
36. Guo, M., and Birchler, J.A. (1994). Trans-acting dosage effects on the expression of model gene systems in maize aneuploids. Science 266: 1999-2002.
37. Guo, M., Davis, D., and Birchler, J.A. (1996). Dosage effects on gene expression in a maize ploidy series. Genetics 142: 1349-1355.
38. Gupta, V., Parisi, M., Sturgill, D., Nutfall, R., Doctolero, M., Dudko, O.K., Malley, J.D., Eastman, P.S., and Oliver, B. (2006). Global analysis of X-chromosome dosage compensation. J. Biol. 5: 3.
39. Hahn, M.W., Conant, G.C., and Wagner, A. (2004). Molecular evolution in large genetic networks: Does connectivity equal constraint? J. Mol. Evol. 58: 203-211.
40. Jansen, R., Greenbaum, D., and Gerstein, M. (2002). Relating whole-genome expression data with protein-protein interactions. Genome Res. 12: 37-46.
41. Kondrashov, F.A., and Koonin, E.V. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet. 20: 287-290.
42. Lemos, B., Meiklejohn, C.D., and Hartl, D.L. (2004). Regulatory evolution across the protein interaction network. Nat. Genet. 36: 1059-1060.
43. Lee, E.A., Darrah, L.L., and Coe, E.H. (1996). Dosage effects on morphological and quantitative traits in maize aneuploids. Genome 39: 898-908.
44. Maere, S., DeBodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., and Van de Peer, Y. (2005). Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. USA 102: 5454-5459.
45. th Int. Congr. Genetics 1, 213-255.
46. Muller, H.J. (1942). Isolating mechanisms, evolution and temperature. Biol Symp 6: 71-125.
47. Nguyen, D.K., and Disteche, C.M. (2006). Dosage compensation of the active X chromosome in mammals. Nat. Genet. 38: 47-53.
48. O'Brien, S.J., and Gethman, R.C. (1973). Segmental aneuploidy as a probe for structural genes in Drosophila: Mitochondrial membrane enzymes. Genetics 75: 155-167.
49. Ono, T. (1935). Chromosomen und sexualitat von Rumex acetosa. Sci. Rep. Tohoku Univ. (Sendai, Japan). Biology 10: 41-210.
50. Papp, B., Pal, C., and Hurst, L.D. (2003). Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
51. Phillips, J.L., et al. (2001). The consequences of chromosomal aneuploidy on gene expression profiles in a cell line model for prostate carcinogenesis. Cancer Res. 61: 8143-8149.
52. Rabinow, L., Nguyen-Huynh, A.T., and Birchler, J.A. (1991). A transacting regulatory gene that inversely affects the expression of the white, brown and scarlet loci in Drosophila melanogaster. Genetics 129: 463-480.
53. Redon, R., et al. (2006). Global variation in copy nuber in the human genome. Nature 444: 444-454.
54. Saran, N.G., Pletcher, M.T., Natale, J.E., Cheng, Y., and Reeves, R.H. (2003). Global disruption of the cerebellar transcriptome in a Down syndrome mouse model. Hum. Mol. Genet. 12: 2013-2019.
55. Satina, S., Blakeslee, A.F., and Avery, A.G. (1937). Balanced and unbalanced haploids in Datura. J. Hered. 28: 192-202.
56. Schwartz, D. (1971). Genetic control of alcohol dehydrogenase-A competition model for regulation of gene action. Genetics 67: 411-425.
57. Sears, E.R. (1953). Nullisomic analysis in wheat. Am. Nat. 87: 245-252.
58. Sears, E.R. (1954). The aneuploids of common wheat. Missouri Agric. Exp. Sta. Res. Bull. 572.
59. Sharp, A.J., et al. (2005). Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77: 78-88.
60. Simillion, C., Vandepoele, K., Montagu, M.C., Zabeau, M., and Van de Peer, Y. (2002). The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 99: 13627-13632.
61. Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S.G., Cyert, M., Hughes, T.R., Boone, C., and Andrews, B. (2006). Mapping pathways and phenotypes by systemic gene over-expression. Mol. Cell 21: 319-330.
62. Tanksley, S.D. (1993). Mapping polygenes. Annu. Rev. Genet. 27: 205-233.
63. Thomas, B.C., Pedersen, B., and Freeling, M. (2006). Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16: 934-946.
64. Tsafrir, D., et al. (2006). Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Res. 66: 2129-2137.
65. Veitia, R.A. (2002). Exploring the etiology of haploinsufficiency. Bioessays 24: 175-184.
66. Veitia, R.A. (2003). Nonlinear effects in macromolecular assembly and dosage sensitivity. J. Theor. Biol. 220: 19-25.
67. Veitia, R.A. (2004). Gene dosage balance in cellular pathways: Implications for dominance and gene duplicability. Genetics 168: 569-574.
68. Veitia, R.A. (2005). Gene dosage balance: Deletions, duplications and dominance. Trends Genet. 21: 33-35.
69. Yang, J., Lusk, R., and Li, W.H. (2003). Organismal complexity, protein complexity, and gene duplicability. Proc. Natl. Acad. Sci. USA 100: 15661-15665.
70. Wolfe, K.H. (2001). Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet. 2: 333-341.