請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/31361
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 于宏燦(Hon-Tsen Yu) | |
dc.contributor.author | Meng-Shin Shiao | en |
dc.contributor.author | 蕭孟昕 | zh_TW |
dc.date.accessioned | 2021-06-13T02:45:27Z | - |
dc.date.available | 2006-10-31 | |
dc.date.copyright | 2006-10-31 | |
dc.date.issued | 2006 | |
dc.date.submitted | 2006-10-18 | |
dc.identifier.citation | Chapter I
1. Dobzhansky, T. (1973) Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach. 35: 125-129. 2. Li, W.-H., Gu, Z., Wang, H. & Nakrutenko, A. (2001) Evolutionary analyses of human genome. Nature 409: 847-849. 3. Ohno, S. (1970) Evolution by gene duplication. Berlin, Heidelberg, New York: Springer-Verlag. 4. Long M, Betran, E., Thornton, K. and Wang, W. (2003) The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4: 865-875. 5. Blanc, G., Barakat, A., Guyot, R., Cooke, R. & Delseny, M. (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101. 6. Vision, T. J., Brown, D. G. & Tanksley, S. D. (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117. 7. McLysaght, A., Hokamp, K. & Wolfe, K. H. (2002) Extensive genomic duplication during early chordate evolution. Nat. Genet. 31: 200-204. 8. Friedman, R. & Hughes, A. L. (2001) Pattern and timing of gene duplication in animal genomes. Genome Res. 11: 1842-1847. 9. Hughes, A. L. (1999) Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J of Evol. 48: 565-576. 10. Martin A (2001) Is tetralogy true? Lack of support for the 'One-to-four rule'. Mol. Biol. Evol. 18: 89-93. 11. Bailey, J.A. et al. (2002) Recent segamental duplications in the human genome. Science 297: 1003-1007. 12. Semonte, R. V. & Eichler, E. E. (2002) Segmental duplications and the evolution of the primate genome. Nat. Rev. Genet. 3: 65-72. 13. Prince, V. E. & Pickett, F. B. (2002) Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet. 3: 827-837. 14. Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y.-l., & Postlethwait, J. (1999) Preservation of Duplicate Genes by Complementary, Degenerative Mutations. Genetics 151: 1531-1545. 15. Gilbert, W. (1978) Why genes in pieces? Nature 271: 501. 16. Long, M. & Langley, C. H. (1993) Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Nature 260: 91-95. 17. Patthy, L. (1999) Genome evolution and the evolution of exon-shuffling - a review. Gene 238: 103-114. 18. Sudhof, T. C., Goldstein, J. L., Brown, M. S. & Russel, D.W. (1985) The LDL receptor gene: a mosaic of exons shared with different proteins. Science 228: 815-822. 19. Moran, J. V., DeBerardinis, R. J. & Kazazian, H. H. Jr. (1999) Exon shuffling by L1 retrotransposition. Science 283: 1530-1534. 20. Esnault, C., Maestre, J. & Heidmann, T. (2000) Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24: 363-367. 21. Smit, A. F. (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9: 657-663. 22. Li, W.-H. (2001) Evolutionary analysis of the human genome. Nature 409: 847-849. 23. Makalowske, W., Mitchell, G. A. & Labuda, D. (1994) Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 10: 188-193. 24. Bejerano, G., Lowe, C. B., Ahituv, N., King, B., Siepel, A., Salama, S. R., Rubin, E. M., James Kent W. & Haussler, D. (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441: 87-90. 25. Nekrutenko, A. & Li, W.-H. (2001) Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17: 619-621. 26. Sorek, R., Ast, G. & Graur, D. (2002) Alu-containing exons are alternatively spliced. Genome Res. 12: 1060-1067. 27. Makalowske, W. (2000) Genomic scrap yard: how genomes utilize all the junk. Gene 259: 61-67. 28. Ochman, H., Lawrence, J. G. & Groisman, E. A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304. 29. Koonin, E. V., Makarova, K. S. & Aravind, L. (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Ann. Rev. Microbiol. 55: 709-742. 30. Ochman, H. (2001) Lateral and oblique gene transfer. Curr. Opin. Genet. Dev. 11: 616-619. 31. Pupo, G. M., Lan, R. & Reeves, P.R. (2000) Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl. Acad. Sci. USA 97: 10567-10572. 32. Cho, Y., Qiu, Y.-L., Kuhlman, P. & Palmer, J.D. (1998) Explosive invasion of plant mitochondria by a group I intron. Proc. Natl. Acad. Sci. USA 95: 14244-14249. 33. Bergthorsson, U., Adams, K. L., Thomason, B. & Palmer, J. D. (2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: 197-201. 34. Nurminsky, D. I., Nurminskaya, M. V., De Aguiar, D. & Hartl, D. L. (1998) Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396: 572-575. 35. Wang, W., Yu, H. & Long, M. (2004) Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nat. Genet. 36: 523-527. 36. Enright, A. J., Iliopoulos, I., Kyrpides, N. C. & Ouzounis, C. A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90. 37. Snel, B., Bork, P. & Huynen, M. (2000) Genome evolution - gene fusion versus fission. Trends Genet. 16: 9-11. 38. Wang, W., Zhang, J., Alvarez, C., Llopart, A. & Long, M. (2000) The origin of the jingwei gene and the complex modulat structure of its parental gene, yellow emperor, in Drosophila melanogaster. Mol. Biol. Evol. 17: 1294-1301. 39. Haldane, J. B. S. (1933) The part played by recurrent mutation in evolution. Am. Nat. 67: 5-19. 40. Fisher, R. A. (1935) The sheltering of lethals. Am. Nat. 69: 446-455. 41. Burki, F. & Kaessmann, H. (2004) Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nat. Genet. 36: 1061-1063. 42. Wang, W., Brunet, F. G., Nevo, E. & Long, M. (2002) Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99: 4448-4453. 43. Jones, C. D., Custer, A.W. & Begun, D.J. (2005) Origin and evolution of a chimeric fusion gene in Drosophila subobscura, Drosophila madeirensis, and Drosophila guanche. Genetics 170:207-19 44. Zhang J, Dean, A.M., Brunet, F. & Long, M. (2004) Evolving protein functional diversity in new genes of Drosophila. Proc. Natl. Acad. Sci. USA 101: 16246-16250. Chapter II 1. Long, M., Betran, E., Thornton, K. & Wang, W. (2003) The origin of new genes: Glimpses from the yong and old. Nat Rev Genet 4: 865-875. 2. Force, A, Lynch, M., Pickett, F., Amores, A., Yan, Y., & Postlethwait, J. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545. 3. Lynch, M. & Conery, J. S. (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155. 4. Shiu, S. H., Byrnes, J. K., Pan, R., Zhang, P. & Li, W. H. (2006) Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc. Natl. Acad. Sci. USA 103: 2232-2236. 5. Soares, M. B., Schon, E., Henderson, A., Karathanasis, S. K., Cate, R., Zeitlin, S., Chirgwin, J. & Efstratiadis, A. (1985) RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon. Mol. Cell. Biol. 5: 2090-2103. 6. Wentworth, B. M., Schaefer, I. M., Villa-Komaroff, L. & Chirgwin J. M. (1986) Characterization of the two nonallelic genes encoding mouse preproinsulin. J. Mol. Evol. 23: 305-312. 7. Davies, P., Poirier, C., Deltour, L. & Montagutelli, X. (1994) Genetic reassignment of the Insulin-1 (Ins1) gene to distal mouse chromosome 19. Genomics 21: 665-667. 8. Deltour, L., Montagutelli, X., Guenet, J.-L., Jami, J. & Paldi, A. (1995) Tissue- and developmental stage-specifi imprinting of the mouse proinsulin gene, Ins2. Dev. Biol. 168: 686-688. 9. Deltour, L., Vandamme, J., Jouvenot, Y., Duvillie, B., Kelemen, K., Schaerly, P., Jami, J. & Paldi, A. (2004) Differential expression and imprinting status of Ins1 and Ins2 genes in extraembryonic tissues of laboratory mice. Gene Expr. Patterns 5: 297-300. 10. Kakita, K, Giddings, S. & Permutt, M. A. (1982) Biosynthesis of rat insulins I and II: evidence for differential expression of the two genes. Proc. Natl. Acad. Sci. USA 79: 2803-2807. 11. Chentoufi, A. A. & Polychronakos, C. (2002) Insulin expression levels in the thymus modulate insulin-specific autoreactive T-cell tolerance: the mechanism by which the IDDM2 locus may predispose to diabetes. Diabetes 15: 1383-1390. 12. Nakayama, M., Abiru, N., Moriyama, H., Babaya, N., Liu, E., Miao, D., Yu, L., Wegmann, D. R., Hutton, J. C., Elliott, J. F. & Eisenbarth, G. S. (2005) Prime role for an insulin epitope in the development of type 1 diabetes in NOD mice. Nature 435: 220-223. 13. Moriyama H, Abiru, N., Paronen, J., Sikora, K., Liu, E., Miao, D., Devendra, D., Beilke, J., Gianani, R., Gill, R.G. & Eisenbarth, G.S. (2003) Evidence for a primary islet autoantigen (preproinsulin 1) for insulitis and diabetes in the nonobese diabetic mouse. Proc Natl Acad Sci USA 100: 10376-10381. 14. Jaeckel, E., Lipes, M. A. & von Boehmer, H. (2004) Recessive tolerance to preproinsulin 2 reduces but does not abolish type 1 diabetes. Nat. Immunol. 5: 1028-1190 15. Thebault-Baumont, K., Krief, P., Briand, J. P., Halbout, P., Vallon-Geoffroy, K., Morin, J., Laloux, V., Lehuen, A., Carel, J.C., Jami, J., Muller, S., Boitard, C. (2003) Acceleration of type 1 diabetes mellitus in proinsulin 2-deficient NOD mice. . J. Clin. Invest. 111: 851-857 16. Babaya, N., Nakayama, M., Moriyama, H., Gianani, R., Still, T., Miao, D., Yu, L., Hutton, J.C. & Eisenbarth, G. S. (2006) A new model of insulin-deficient diabetes: male NOD mice with a single copy of Ins1 and no Ins2. Diabetologia 49: 1222-1228. 17. Yang Z & Nielsen, R. (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19: 908-917. 18. Chan, S. J., Episkopou, V., Zeitlin, S., Karathanasis, S.K., MacKrell, A., Steiner, D.F. & Efstratiadis, A. (1984) Guinea pig preproinsulin gene: an evolutionary compromise? Proc Natl Acad Sci USA 81: 5046-5050. 19. O'hUigin C &Li, W.H. (1992) The molecular clock ticks regularly in muroid rodents and hamsters. J Mol Evol 35: 377-384. 20. Nekrutenko, A, Makova, K. D. & Li, W. H. (2002) The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res. 12: 198-202. 21. Steiner, D. F. (2004) The proinsulin C-peptide - a multirole model. Exp. Diabesity Res. 5: 7-14. 22. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595. 23. Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press. 24. Braverman JM, Hudson, R.R., Kaplan, N.L., Langley, C.H., Stephan, W. (1995) The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140: 783-796. 25. Nurminsky DI, Nurminskaya, M.V., Aguilar, D.D. & Hartl, D.L. (1998) Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396: 572-575. 26. Neel, J. (1962) Diabetes mellitus: a 'thrifty' genotype rendered detrimental by 'progress'? Am. J. Hum. Genet. 14: 353-362 27. Vander Molen, J., Frisse, L., Fullerton, S. M., Qian, Y., Del Bosque-Plata, L., Hudson, R. R., Di Rienzo, A. (2005) Population genetics of CAPN10 and GPR35: implications for the evolution of type 2 diabetes variants. Am. J. Hum. Genet. 76: 548-560. 28. Di Rienzo, A. & Hudson, R. R. (2005) An evolutionary framework for common diseases: the ancestral-susceptibility model. Trends Genet. 21: 596-601. 29. Auffray J-C, Vanlerberghe, F. & Britton-Davidian, J. (1990) The house mouse progression in Eurasio: a palaeontological and archaezoological approach. Biol. J. Linn. Soc. Lond. 41: 13-25. 30. Michaux, J., Reyes, A. & Catzeflis, F. (2001) Evolutionary history of the most speciose mammals: Molecular phylogeny of muroid rodents. Mol. Biol. Evol. 18: 2017-2031. 31. Steppan, S. J., Akhverdyan, M. R., Lyapunova, E. A., Fraser, D. G., Vorontsov, N. N., Hoffmann, R. S. & Braun, M. J. (2004) Molecular phylogeny of the marmots (Rodentia: Sciuridae): tests of evolutionary and biogeographic hypotheses. Syst. Biol. 48: 715-734. ChapterIII 1. Charlesworth, B. (1996) The evolution of chromosomal sex determination and dosage compensation. Curr. Biol. 6: 149-162. 2. Vallender, E. J. & Lahn, B. T. (2004) How mammalian sex chromosomes acquired their peculiar gene content. Bioessays 26: 159-169. 3. Rice, W. R. (1984) Sex chromosomes and the evolution of sexual dimorphism. Evolution 38: 735-742. 4. Wang, P. J., McCarrey, J. R., Yang, F. & Page, D.C. (2001) An abundance of X-linked genes expressed in spermatogonia. Nat. Genet. 27: 422-426. 5. Khil, P. P., Smirnova, N. A., Romanienko, P. J. & Camerini-Otero, R. D. (2004) The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation. Nat. Genet. 36: 642-646. 6. Richler, C., Soreq, H. and Wahrman, J. (1992) X inactivation in mammalian testis is correlated with inactive X-specific transcription. Nat. Genet. 2: 192-195. 7. Salido, E., Yen, P. H., Mohandas, T. K. & Shapiro, L. J. (1992) Expression of the X-inactivation-associated gene XIST during spermatogenesis. Nat. Genet. 2: 196-199. 8. Wang, P., Page, D. C. & McCarrey, J. R. (2005) Differential expression of sex-linked and autosomal germ-cell-specific genes during spermatogenesis in the mouse. Hum. Mol. Genet. 14: 2911-2918. 9. Lee, J. (2005) Regulation of X-chromosome counting by Tsix and Xite sequences. Science 309: 768-771. 10. Long M, Betran, E., Thornton, K. and Wang, W. (2003) The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4: 865-875. 11. Zhang, J., Dean, A.M., Brunet, F. & Long, M. (2004) Evolving protein functional diversity in new genes of Drosophila. Proc. Natl. Acad. Sci. USA 101: 16246-16250. 12. Rohozinski, J., Lamb, D. J. and Bishop, C. E. (2006) UTP14c is a recently acquired retrogene associated with spermatogenesis and fertility in man. Biol Reprod 74: 644-651. 13. Rohozinski, J. & Bishop, C. E. (2004) The mouse juvenile spermatogonial depletion (jsd) phenotype is due to a mutation in the X-derived retrogene, mUtp14b. Proc. Natl. Acad. Sci. USA 32: 11695-11700. 14. Betran, E., Kevin, T. & Long, M. (2002) Retroposed new genes out of the X in Drosophola. Genome Res. 12: 1854-1859. 15. Dai, H., Yoshimatsu, T. F. and Long, M. (2006) Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes. Gene (accepted) 16. Emerson, J. J., Kaessmann, H., Betran, E., & Long, M. (2004) Extensive gene traffic on the mammalian X chromosome. Science 303: 537-540. 17. Betran, E., Emerson, J. J., Kaessmann, H. & Long, M. (2004) Sex chromosomes and male functions. Where do new genes go? Cell Cycle 3: 837-875. 18. McCarrey, J. R., Berg, W. M., Paragioudakis, S. J., Zhang, P. L., Dilworth, D. D., Arnold, B. L. and Rossi, J. J. (1992) Differential transcription of Pgk genes during spermatogenesis in the mouse. Dev. Biol. 154: 160-168. 19. Marques, A. C., Dupanloup, I., Vinckenbosch, N., Reymond, A. & Kaessmann, H. (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 3: 1-10. 20. Wu, C-I & Xu, E.Y. (2003) Sexual antagonism and X inactivation - the SAXI hypothesis. Trends Genet. 19: 243-247. 21. Charlesworth, B., Coyne, J. A. & Barton, N. H. (1987) The relative rates of evolution of sex chromosomes and autosomes. Am. Nat. 130: 113-146. 22. Betran, E. & Long, M. (2003) Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164: 977-988. 23. Romanienko, P. J. & Camerini-Otero, R.D. (2000) The mouse Spo11 gene is required for meiotic chromosome synapsis. Mol. Cell. 6: 975-987. 24. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595. 25. Depaulis F, & Veuille, M. (1998) Neutrality tests based on the distribution of haplotypes under an infinite-site model. Mol. Biol. Evol. 15: 1788-1790. 26. Rozas, J., Sánchez-DelBarrio, J. C., Messegyer, X. and Rozas, R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497. 27. Hudson, R. R. (1990) Gene genealogies and the coalescent process; Futuyma, D. & Antonovics, J., editor. New York: Oxford University Press. 28. O'hUigin, C. & Li, W. H. (1992) The molecular clock ticks regularly in muroid rodents and hamsters. J. Mol. Evol. 35: 377-384. 29. Ashworth, A., Skene, B., Swift, S. & Lovell-Badge, R. (1990) Zfa is an expressed retroposon derived from an alternative transcript of the Zfx gene. EMBO J. 9: 1529-1534. 30. Luoh, S. W. & Page, D. C. (1994) The structure of the Zfx gene on the mouse X chromosome. Genomics 19: 310-319. 31. Banks, K. G., Johnson, K. A., Lerner, C. P., Mahaffey, C. L., Bronson, R.T. and Simpson, E. M. (2003) Retroposon compensatory mechanism hypothesis not supported: Zfa knockout mice are fertile. Genomics 82: 254-260. 32. Kumar, R. A., Chan, K. L., Wong, A. H., Little, K.Q., Rajcan-Separovic, E., Abrahams, B.S. & Simpson, E.M. (2004) Unexpected embryonic stem (ES) cell mutations represent a concern in gene targeting: lessons from 'fierce' mice. Genesis 38: 51-57. 33. Yonekawa, H., Moriwaki, K., Gotoh, O., Hayashi, J. I., Watanabe, J., Miyashita, N., Petras, M. L. and Tagashira, Y. (1981) Evolutionary relationships among five subspecies of Mus musculus based on restriction enzyme cleavage patterns of mitochondrial DNA. Genetics 98: 801-816. 34. Wang, W., Thornton, K., Emerson, J. J. & Long, M. (2004) Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics 166: 1783-1794. 35. Babaya, N., Nakayama, M., Moriyama, H., Gianani, R., Still, T., Miao, D., Yu, L., Hutton, J.C. & Eisenbarth, G.S. (2006) A new model of insulin-deficient diabetes: male NOD mice with a single copy of Ins1 and no Ins2. Diabetologia 49: 1222-1228. 36. Long, M., Wang, W. & Zhang, J. (1999) Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene 238: 135-141. 37. Vinckenbosch, N., Dupanloup, I. & Kaessmann, H. (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 103: 3220-3225. 38. Lipman, D. (1997) Making (anti)sense of non-coding sequence conservation. Nucleic Acids Res 25: 3580-3583. 39. Li, A. W., Seyoum, G. & Shiu, R. P. and Murphy, P. R. (1996) Expression of the rat BFGF antisense RNA transcript is tissue-specific and developmentally regulated. Mol. Cell Endocrinol. 118: 113-123. 40. Conant, G. C. & Wolfe, K. H. (2006) Functional partitioning of yeast co-expression networks after genome duplication. PLoS Biol. 4: 545-554. 41. Robertson, N. G., Pomponio, R. J., Mutter, G. L. & Morton, C. C. (1991) Testis-specific expression of the human MYCL2 gene. Nucleic Acids Res. 19: 3129-3137. 42. Shashidharan P, Michaelidis, T.M., Robakis, N.K., Kresovali, A., Papamatheakis, J. and Plaitakis, A. (1994) Novel human glutamate dehydrogenase expressed in neural and testicular tissues and encoded by an X-linked intronless gene. J Biol. Chem. 269: 16971-16976. 43. Tanaka H, Kohroki, J., Iguchi, N., Onishi, M. and Nishimune, Y. (2002) Cloning and characterization of a human orthologue of testis-specific succinyl CoA: 3-oxo acid CoA transferase (Scot-t) cDNA. Mol. Hum. Reprod. 8: 16-23. 44. Schmidt E. E. & Schibler, U. (1995) High accumulation of components of the RNA polymerase II transcription machinery in rodent spermatids. Development 121: 2373-2383. 45. Schmidt, E. E. (1996) Transcriptional promiscuity in testes. Curr Biol 6: 768-769. 46. McClintock, J. M., Carlson, R., Mann, D. M. & Prince, V. E. (2001) Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish Hox paralogue group 1 genes. Development 128: 2471-2484. 47. Blanc, G. & Wolfe, K. H. (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 16: 1679-1691. 48. Gu, X., Zhang, Z. & Huang, W. (2005) Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc. Natl. Acad. Sci. U S A 102: 707-712. 49. Wolfe, K. H. & Shields, D. C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713. 50. Blanc, G., Barakat, A., Guyot, R., Cooke, R. & Delseny, M. (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101. 51. Chung, W. Y., Albert, R., Albert, I., Nekrutenko, A. & Makova, K. D. (2005) Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC Bioinformatics 7: 46. 52. Papp, B., Pal, C. & Hurst, L. D. (2003) Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet. 19: 417-422. 53. Castillo-Davis, C. I., Hartl, D. L. and Achaz, G. (2004) cis-Regulatory and protein evolution in orthologous and duplicate genes. Genome Res. 14: 1530-1536. 54. Force, A., Lynch, M., Pickett, F., Amores, A., Yan, Y., & Postlethwait, J. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545. 55. Lynch, M., & Conery, J. S. (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155. 56. Betran, E., Wang, W., Jin, L. & Long, M. (2002) Evolution of the Phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Mol. Biol. Evol. 19: 654-663. 57. Wang, W., Brunet, F. G., Nevo, E. & Long, M. (2002) Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99: 4448-4453. 58. Long, M. & Langley, C. H. (1993) Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Nature 260: 91-95. 59. Moriyama, H., Abiru, N., Paronen, J., Sikora, K., Liu, E., Miao, D., Devendra, D., Beilke, J., Gianani, R., Gill, R.G. & Eisenbarth, G.S. (2003) Evidence for a primary islet autoantigen (preproinsulin 1) for insulitis and diabetes in the nonobese diabetic mouse. Proc. Natl. Acad. Sci. USA 100: 10376-10381. 60. Nakayama, M., Abiru, N., Moriyama, H., Babaya, N., Liu, E., Miao, D., Yu, L., Wegmann, D.R., Hutton, J.C., Elliott, J.F. & Eisenbarth, G.S. (2005) Prime role for an insulin epitope in the development of type 1 diabetes in NOD mice. Nature 435: 220-223. 61. Jaeckel, E., Lipes, M. A. & von Boehmer, H. (2004) Recessive tolerance to preproinsulin 2 reduces but does not abolish type 1 diabetes. Nat. Immunol. 5: 1028-1190 62. Ohno, S. (1970) Evolution by gene duplication. Berlin, Heidelberg, New York: Springer-Verlag. 63. Bradley, J., Baltus, A., Skaletsky, H., Royce-Tolland, M., Dewar, K. & Page, D.C. (2004) An X-to-autosome retrogene is required for spermatogenesis in mice. Nat. Genet. 36: 872-876. 64. Jacobs, S., Schurmann, A., Becker, W., Bockers, T.M., Copeland, N.G., Jenkins, N.A. & Joost, H.G. (1998) The mouse ADP-ribosylation factor-like 4 gene: two separate promoters direct specific transcription in tissues and testicular germ cell. Biochem. J. 335: 259-265. 65. Marino-Ramirez, L., Lewis, K. C., Landsman, D. & Jordan, I. K. (2005) Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenet. Genome. Res. 110: 333-341. 66. Soares MB, Schon, E., Henderson, A., Karathanasis, S.K., Cate, R., Zeitlin, S., Chirgwin, J. & Efstratiadis, A. (1985) RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon. Mol. Cell. Biol. 5: 2090-2103. 67. Wentworth, B M , Schaefer, I. M., Villa-Komaroff, L. & Chirgwin J. M. (1986) Characterization of the two nonallelic genes encoding mouse preproinsulin. J. Mol. Evol. 23: 305-312. 68. Gunkel, N., Yano, T., Markussen, F.H., Olsen, L.C. & Ephrussi, A. (1998) Localization-dependent translation requires a functional interaction between the 5' and 3' ends of oskar mRNA. Genes. Dev. 12: 1652-1664. 69. Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S. and Kellis, M. (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434: 338-345. 70. Lewis, B. P., Burge, C. B. and Bartel, D. P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20. 71. Lagace, M., Xuan, J.Y., Young, S.S., McRoberts, C., Maier, J., Rajcan-Separovic, E. and Korneluk, R.G. (2001) Genomic organization of the X-linked inhibitor of apoptosis and identification of a novel testis-specific transcript. Genomics 77: 181-188. Chpater IV 1. Zemni, R. et al. (2000) A new gene involved in X-linked mental retardation identified by analysis of an X;2 balanced translocation. Nat. Genet. 24: 167-170. 2. Maranduba, C. M., Sa Moreira, E., Muller Orabona, G., Pavanello, R. C., Vianna-Morgante, A. M. & Passos-Bueno, M. R. (2004) Does the P172H mutation at the TM4SF2 gene cause X-linked mental retardation? Am. J. Med. Genet. A 124: 413-415. 3. Gomot, M. et al.. (2002) TM4SF2 gene involvement reconsidered in an XLMR family after neuropsychological assessment. Am. J. Med. Genet. 112: 400-404. 4. Castellvi-Bel, S. & Mila, M. (2001) Genes responsible for nonspecific mental retardation. Mol. Genet. Metab. 72: 104-108. 5. Long, M. & Langley, C. H. (1993) Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Nature 260: 91-95. 6. Betran, E., Wang, W., Jin, L. & Long, M. (2002) Evolution of the Phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Mol. Biol. Evol. 19: 654-663. 7. Aminetzach, Y. T., Macpherson, J. & Petrov, D. A. (2004) Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science 309: 764-767. 8. Betran, E., Kevin, T. & Long, M. (2002) Retroposed new genes out of the X in Drosophola. Genome Res. 12: 1854-1859. 9. Emerson, J. J., Kaessmann, H., Betran, E., & Long, M. (2004) Extensive gene traffic on the mammalian X chromosome. Science 303: 537-540. 10. Dai, H., Yoshimatsu, T. F. & Long, M (2006) Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes. Gene (accepted) 11. Khil, P. P., Smirnova, N. A., Romanienko, P. J. & Camerini-Otero, R. D. (2004) The mouse X chromosome is enriched for sex-bias genes not subject to selection by meiotic sex chromosome inactivation. Nat. Genet. 36: 642-646. 12. Guo, J. H., Huang, Q., Studholme, D. J., Wu, C. Q. & Zhao, Z. (2005) Transcriptomic analyses support the similarity of gene expression between brain and testis in human as well as mouse. Cytogenet. Cell Genet. 111: 107-109. 13. Liao, B. Y. & Zhang, J. (2006) Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol. Biol. Evol. 23: 530-540. 14. Sun, S., Ting, C.-T. & Wu, C.-I. (2004) The normal function of a speciation gene, Odysseus, and its hybrid sterility effect. Science 305: 81-83. 15. Wilda, M. et al. (2000) Do the constraints of human speciation cause expression of the same set of genes in brain, testis, and placenta? Cytogenet. Cell Genet. 91: 300-302. 16. Gu, J. & Gu, X. (2003) Induced gene expression in human brain after the split from chimpanzee. Trends Genet. 19: 63-65. 17. Saetre, P. et al. (2004) From wild wolf to domestic dog: gene expression changes in the brain. Brain Res. Mol. Brain Res. 126: 198-206. 18. Ting, C.-T., Tsaur, S.-C., Wu, M.-L. & Wu, C.-I. (1998) A Rapidly Evolving Homeobox at the Site of a Hybrid Sterility Gene. Science 282: 1501 - 1504. 19. Zechner, U., Wilda, M., Kehrer-Sawatzki, H., Vogel, W., Fundele, R., Hameister, H. (2001) A high density of X-linked genes for general cognitive ability: a run-away process shaping human evolution? Trends Genet. 17: 697-701. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/31361 | - |
dc.description.abstract | 本研究主要分為兩大部分。第一部分我們以老鼠體內兩份胰島素基因為模式,探討重複基因及其母基因如何共同演化。第二部分探討X染色體關聯反轉錄基因(X-related retrogenes)的演化。
在先前的研究中發現,不同於其他哺乳類動物,小家鼠(Mus musculus)及溝鼠(Rattus norvegicus)基因體中有兩份胰島素基因。胰島素重複基因(Ins1)經由不完全反轉錄胰島素母基因(Ins2)而產生,因此重複基因只有一個內含子(intron)。這兩份胰島素基因除了基因結構不同外,他們擁有高度相似的蛋白質轉錄序列,並在胰島素調控路徑中扮演相似的角色。此外,兩份胰島素基因被認為具有不同的表現功能: 只表現胰島素重複基因會加速糖尿病的症狀,而過量表現胰島素母基因卻能抑制糖尿病的進程。結合本研究及本實驗室先前的結果,我們發現胰島素重複基因只存在於鼠亞科動物(Murinae)的基因體。並且經由Ka/Ks檢驗結果顯示,兩份胰島素基因在我們檢測的鼠亞科動物基因體中都是有功能的。此外,我們還發現小家鼠體內的兩份胰島素基因都顯著受到正向選汰的影響。換句話說,擁有兩份基因對小家鼠個體有必然的優勢。因此,我們提出一個小家鼠胰島素基因演化的假說。大約在10,000年前,小家鼠的祖先仍未開始依賴人類生存的生活模式。因此,擁有重複基因的個體因為能有效儲存醣類而佔有優勢。當小家鼠能從人類的穀倉獲得充足的糧食之後,胰島素母基因能防止糖尿病的發生。然而,小家鼠仍然是人類趕盡殺絕的對象,使得牠們的食物來源並沒有辦法獲得百分之百保證。因此,我們在現今的小家鼠野外族群中,仍然可以發現正向選汰同時作用於兩份胰島素基因的證據。 在第二部分的研究中,我們探討與X染色體相關的反轉錄基因的演化。由我們先前的研究中發現,反轉錄基因在基因體中並不是隨機分布。果蠅及哺乳動物的基因體中,在X染色體與體染色體之間跳躍的反轉錄基因,顯著多於在體染色體之間跳躍的基因。一般相信,造成反轉錄基因不隨機分布的原因,是由於雄性的X染色體會在精子發生(spermatogenesis)的晚期被去活化(inactivated),使得X染色體上的基因無法正常表達。因此,X染色體上的基因會傾向於獲得在體染色體上的替補。根據檢測結果,我們判斷正向選汰主導了反轉錄基因的不隨機分布。然而,目前的研究僅止於基因體層次的分析,並無針對單一反轉錄基因及其母基因做深入的探討。因此在第二部分的研究中,我們廣泛的搜索小家鼠整個基因體內年輕的反轉錄新基因,進而研究這些反轉錄基因與其母基因之間功能的分化,以及選汰對基因體保有兩份序列相似基因的機制。我們的研究發現,不同於母基因,反轉錄新基因不只是雄性專一,而且都在精子發生的晚期表達。這個結果證實了我們的假說:反轉錄新基因成為X染色體上母基因的替補。更進一步分析小家鼠族群的族群序列,發現正向選汰扮演重要的角色。因此,我們推論,X關聯基因在體染色體擁有一份序列相似的基因,並且演化出新的雄性功能有利於生物體的演化。除此之外,幾乎所有的反轉錄基因都從相鄰的基因體序列獲得新的非轉錄區域(untranslated regions, UTRs)。顯示非轉錄區域在新基因獲得新功能上扮演重要的角色。 | zh_TW |
dc.description.abstract | The mechanisms of how duplicate genes are retained in genomes remain an important question. Retrogenes are those intronless duplicate genes originated from reverse transcriptions of mRNA and integrated into genomic locations which are different from parental genes. More and more retrogenes are identified as being responsible for novel functions in mammals, particularly those involving in male fertilities. In my dissertation, I used insulin genes in rodent as a model for studying evolution of mammalian retrogenes and also identified several X chromosome related novel retrogenes in the mouse genome.
In Chapter 2, we show the first case of the retention of a retrogene by co-adaptive evolution with its parental copy in the mouse genome. Unlike human, preproinsulins previously were identified as a two-gene system with a duplicate retrogene in mouse and rat. Preproinsulin 1 (Ins1) was found to be retroposed from the partial processed mRNA of preproinsulin 2 (Ins2). Here we further demonstrate that Ins1 only exists within the subfamily Murinae, indicating its specificity to the rodent species, and both Ins2 and Ins1 are under strong functional constraints in these species. Interestingly, by examining spectra of nucleotide polymorphisms, we detect positive selection acting on both Ins2 and Ins1 gene regions in the mouse natural population. The analyses of gene flanking regions and substitutions further indicate that the positive Darwinian selection is unique to the gene surrounding regions. The existence of Ins1 was posited to accelerate diabetes in non obese diabetic mice in the previous literatures. Our studies demonstrate the first case of the fixation and adaptation of a retrogene in association with a harmful phenotype, Type 1 Diabetes. Moreover, several amino acid sites were also identified as evolving under positive Darwinian selection in both insulin coding regions. In conclusion, our data suggests a rapid adaptive divergence in the mouse insulin two-gene system and cast the new insight into the mechanisms that retain new gene duplicates in the genomes. In Chapter 3, we integrated genome-wide investigations and expression analyses to elucidate the evolution of X-related retrogene pairs in rodents. Directional movements of male-related retrogenes have been identified in mammals and flies. Several selection-based mechanisms have been proposed. Testing these selection-based hypotheses requires examinations of evolutionary genetics and expression-related biological properties of these new retrogenes. We demonstrate that all the X-derived autosomal retrogenes evolved a more restricted male function: they are expressed exclusively or predominantly in the testis, particularly, during the late stages of spermatogenesis. In contrast, parental genes are expressed in various tissues and all the spermatogenetic stages. We further observed that positive selection is only targeting on X-derived autosomal retrogenes with new male functions, suggesting that retrogenes may have evolved new testis functions complementary to the parental genes without male specific functions. In the two cases we observed in this study, not only retrogenes but also parental counterparts evolve adaptively, indicating a tendency of increasing in diversity selectively by gene duplication. Furthermore, most retrogenes we identified to have recruited novel sequences as the untranslated regions (UTRs), suggesting evolution of new regulatory elements in these UTRs. | en |
dc.description.provenance | Made available in DSpace on 2021-06-13T02:45:27Z (GMT). No. of bitstreams: 1 ntu-95-F89225003-1.pdf: 903393 bytes, checksum: 5d3fc34debb4fce65d3b3a32838b17d9 (MD5) Previous issue date: 2006 | en |
dc.description.tableofcontents | 致謝................................................................................................................................I
中文摘要.....................................................................................................................III ABSTRACT.................................................................................................................V LIST OF TABLES.....................................................................................................IV LIST OF FIGURES.....................................................................................................X LIST OF APPENDIXES...........................................................................................XI CHAPTER I GENERAL INTRODUCTION............................................................................................1 General Introduction…………………………………………………………………….1 Mechanisms of new gene initiation...................................................................................5 Gene duplication..........................................................................................................................5 Exon shuffling..............................................................................................................................6 Retroposition................................................................................................................................7 Mobile elements...........................................................................................................................8 Horizontal transfer......................................................................................................................9 Gene fission and fusion..............................................................................................................10 Mixture of duplication mechanisms..........................................................................................10 Evolution forces that drive changes in new genes.........................................................10 The role of retroposition in the genomes........................................................................12 Structure of Thesis……………………………………………………………………...13 References.........................................................................................................................15 CHAPTER II THE CO-ADAPTIVE EVOLUTION OF INSULIN TWO-GENE SYSTEM IN MOUSE.........20 Introduction......................................................................................................................21 Materials and methods.....................................................................................................23 Result and discussions......................................................................................................26 Origination of duplicate retrogene, Ins1...................................................................................26 Functionality of Ins2 and Ins1 in Rodent Species.....................................................................27 Co-adaptive Evolution of Insulin Two-gene System.................................................................28 Scenario of Evolution of Insulin Two-gene System..................................................................30 Conclusion.........................................................................................................................32 References.........................................................................................................................33 CHAPTER III EVOLUTION OF X-RELATED RETROGENES IN MOUSE..............................................47 Introduction......................................................................................................................48 Evolution of sex chromosomes in mammals..............................................................................48 Evolution of X-related retrogenes.............................................................................................50 Materials and methods.....................................................................................................53 Selection of retrogene candidates..............................................................................................53 Ka/Ks ratios estimation of young retrogenes in rodent.............................................................54 Expression analyses...................................................................................................................56 DNA sequence analyses.............................................................................................................56 Gene structure identification.....................................................................................................57 Results................................................................................................................................58 X-related young retrogenes evolved more restricted male functions........................................58 Selection is targeting on gene pairs with novel male functions.................................................60 Retrogenes acquire untranslated regions (UTRs) de novo....................................................... 63 Discussions.........................................................................................................................65 Selection-based mechanisms in driving genes out of X.............................................................65 Restricted male expression pattern of X-derived autosomal retrogenes...................................66 Co-adaptive evolution of gene pairs with novel male functions................................................67 The de novo acquisition of UTRs may play an important role in functional novelties.............69 Conclusions.......................................................................................................................71 References.........................................................................................................................72 CHAPTER IV PROSPECTS..................................................................................................................88 | |
dc.language.iso | zh-TW | |
dc.title | 小家鼠基因體內反轉錄基因的演化 | zh_TW |
dc.title | Evolution of Retrogenes in the Mouse Genome | en |
dc.type | Thesis | |
dc.date.schoolyear | 95-1 | |
dc.description.degree | 博士 | |
dc.contributor.coadvisor | 龍漫遠(Manyuan Long) | |
dc.contributor.oralexamcommittee | 張慧羽,丁肇棣,曹順成 | |
dc.subject.keyword | 小家鼠,反轉錄基因,演化, | zh_TW |
dc.subject.keyword | mouse,retrogenes,evolution, | en |
dc.relation.page | 123 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2006-10-18 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 動物學研究研究所 | zh_TW |
顯示於系所單位: | 動物學研究所 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-95-1.pdf 目前未授權公開取用 | 882.22 kB | Adobe PDF |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。