Evolutionary plasticity of vertebrate Hox genes

Current Genomics

Volumn 5, Issue 6, 2004, Pages 459-472

  Powers, Thomas P ^a,b   Amemiya, Chris T ^a  

^a BENAROYA RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

BAC; Development; Evolution; Genomics; Hox; Vertebrate

Indexed keywords

HOX PROTEIN;

ANTERIOR POSTERIOR AXIS; BACTERIAL ARTIFICIAL CHROMOSOME; BIOINFORMATICS; COMPARATIVE STUDY; DEVELOPMENT; GENE CLUSTER; GENE CONTROL; GENE DUPLICATION; GENE EXPRESSION; GENE FUNCTION; GENE LIBRARY; GENE LOSS; GENE SEQUENCE; GENETIC CONSERVATION; INSECT; METAZOON; MOLECULAR EVOLUTION; NEMATODE; NONHUMAN; PLASTICITY; RESEARCH; REVIEW; SPECIES DIVERSITY; VERTEBRATE;

ANIMALIA; HEXAPODA; METAZOA; NEMATODA; VERTEBRATA;

EID: 4444338618     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389202043349048     Document Type: Review

References (182)

1. Carroll, S.B.; Grenier, J.K. and Weatherbee, S.D. From DNA to diversity: molecular genetics and the evolution of animal design. 2001, Malden: Blackwell Science, 214pg.
2. Raff, R.A. The shape of life: genes, development, and the evolution of animal form. 1996, Chicago: University of Chicago Press. 520pg.
3. Wilkins, A.S. The evolution of developmental pathways. 2002, Sunderland: Sinauer. 603pg.
4. Gilbert, S.F.; Opitz, J.M. and Raff, R.A. Resynthesizing evolutionary and developmental biology. Dev. Biol., 1996, 173(2): 357-372.
5. Raff, R.A. Opinion: Evo-Devo: the evolution of a new discipline. Nature Reviews, 2000, 1: 74-79.
6. Arthur, W. The emerging conceptual framework of evolutionary developmental biology. Nature, 2002, 415(6873): 757-764.
7. Carroll, S.B. Homeotic genes and the evolution of arthropods and chordates. Nature, 1995, 376(6540): 479-485.
8. Peterson, K.J. and Davidson, E.H. Regulatory evolution and the origin of the bilaterians. Proc. Natl. Acad. Sci. USA, 2000, 97(9): 4430-4433.
9. Duboule, D. and Wilkins, A.S. The evolution of 'bricolage'. Trends Genet., 1998, 14(2): 54-59.
10. Davidson, E.H.; Peterson, K.J. and Cameron, R.A. Origin of bilaterian body plans: evolution of developmental regulatory mechanisms. Science, 1995, 270(5240): 1319-1325.
11. Lewis, R. Targeted comparative sequencing illuminates vertebrate evolution. 2002, the Scientist, 16(24).
12. Pennacchio, L.A. and Rubin, E.M. Comparative genomic tools and databases: providing insights into the human genome. J. Clin. Invest., 2003, 111(8): 1099-1106.
13. King, N. Comparative biology and genomics join forces to decipher the diversity of life. Genome. Biol., 2002, 3(8): REPORTS 4023.
14. Thomas, J.W. and Touchman, J.W. Vertebrate genome sequencing: building a backbone for comparative genomics. Trends Genet., 2002, 18(2): 104-108.
15. Reinke, V. and White, K.P. Developmental genomic approaches in model organisms. Annu. Rev. Genomics Hum. Genet., 2002, 3: 153-178.
16. Krumlauf, R. Hox genes in vertebrate development. Cell, 1994, 78(2): 191-201.
17. Botas, J. Control of morphogenesis and differentiation by HOM/Hox genes. Curr. Opin. Cell Biol., 1993, 5(6): 1015-1022.
18. McGinnis, W. and Krumlauf, R. Homeobox genes and axial patterning. Cell, 1992, 68(2): 283-302.
19. Hunter, C.P. and Kenyon, C. Specification of anteroposterior cell fates in Caenorhabditis elegans by Drosophila Hox proteins. Nature, 1995, 377(6546): 229-32.
20. Bachiller, D.; Macias, A.; Duboule, D. and Morata, G. Conservation of a functional hierarchy between mammalian and insect Hox/HOM genes. Embo. J, 1994, 13(8): 1930-1941.
21. Lutz, B.; Lu, H.C.; Eichele, G.; Miller, D. and Kaufman, T.C. Rescue of Drosophila labial null mutant by the chicken ortholog Hoxb-1 demonstrates that the function of Hox genes is phylogenetically conserved. Genes. Dev., 1996, 10(2): 176-184.
22. McGinnis, N.; Kuziora, M.A. and McGinnis, W. Human Hox-4.2 and Drosophila deformed encode similar regulatory specificities in Drosophila embryos and larvae. Cell, 1990, 63(5): 969-976.
23. Frasch, M.; Chen, X. and Lufkin, T. Evolutionary-conserved enhancers direct region-specific expression of the murine Hoxa-1 and Hoxa-2 loci in both mice and Drosophila. Development, 1995, 121(4): 957-974.
24. Popperl, H.; Bienz, M.; Studer, M.; Chan, S.K.; Aparicio, S.; Brenner, S.; Mann, R.S. and Krumlauf, R. Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx. Cell, 1995, 81(7): 1031-1042.
25. Awgulewitsch, A. and Jacobs, D. Deformed autoregulatory element from Drosophila functions in a conserved manner in transgenic mice. Nature, 1992, 358(6384): 341-344.
26. Haerry, T.E. and Gehring, W.J.; Intron of the mouse Hoxa-7 gene contains conserved homeodomain binding sites that can function as an enhancer element in Drosophila. Proc. Natl. Acad. Sci. USA, 1996, 93(24): 13884-13889.
27. Lewis, E.B. Homeosis: the first 100 years. Trends Genet., 1994, 10(10): 341-343.
28. Slack, J.M.; Holland, P.W. and Graham, C.F. The zootype and the phylotypic stage. Nature, 1993, 361(6412): 490-492.
29. Ferrier, D.E. and Holland, P.W. Ancient origin of the Hox gene cluster. Nat Rev Genet, 2001, 2(1): 33-38.
30. Schierwater, B. and Desalle, R. Current problems with the zootype and the early evolution of Hox genes. J. Exp. Zool., 2001, 291(2): 169-174.
31. Kourakis, M.J. and Martindale, M.Q. Combined-method phylogenetic analysis of Hox and ParaHox genes of the metazoa. J. Exp. Zool., 2000, 288(2): 175-191.
32. Aboobaker, A.A. and Blaxter, M.L. Hox Gene Loss during Dynamic Evolution of the Nematode Cluster. Curr. Biol., 2003, 13(1): 37-40.
33. Van Auken, K.; Weaver, D.C.; Edgar, L.G. and Wood, W.B. Caenorhabditis elegans embryonic axial patterning requires two recently discovered posterior-group Hox genes. Proc. Natl. Acad. Sci. USA, 2000, 97(9): 4499-4503.
34. Lewis, E.B.; Pfeiffer, B.D.; Mathog, D.R. and Celniker, S.E. Evolution of the homeobox complex in the Diptera. Curr. Biol., 2003, 13(15): R587-R588.
35. Von Allmen, G.; Hogga, I.; Spierer, A.; Karch, F.; Bender, W.; Gyurkovics, H. and Lewis, E. Splits in fruitfly Hox gene complexes. Nature, 1996, 380(6570): 116.
36. Cartwright, P.; Dick, M. and Buss, L.W. HOM/Hox type homeoboxes in the chelicerate Limulus polyphemus. Mol. Phylogenet. Evol., 1993, 2(3): 185-192.
37. Halanych, K.M. and Passamaneck, Y. A brief review of metazoan phylogeny and future prospects in Hox-research. Amer. Zool., 2001, 41: 629-639.
38. Duboule, D. and Dolle, P. The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. Embo. J., 1989, 8(5): 1497-1505.
39. Graham, A.; Papalopulu, N. and Krumlauf, R. The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell, 1989, 57(3): 367-378.
40. Carroll, R.L. Vertebrate paleontology and evolution. 1988, New York: W.H. Freeman and Co. 698pg.
41. Spagnuolo, A.; Ristoratore, F.; Di Gregorio, A.; Aniello, F.; Branno, M. and Di Lauro, R. Unusual number and genomic organization of Hox genes in the tunicate Ciona intestinalis. Gene., 2003, 309(2): 71-79.
42. de Luca di Roseto, G.; Bucciarelli, G. and Bernardi, G. An analysis of the genome of Ciona intestinalis. Gene., 2002, 295(2): 311-316.
43. Ferrier, D.E.K.; Minguillon, C.; Holland, P.W.H. and Garcia-Fernandez, J. The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14. Evolution and Development, 2000, 2(5): 284-293.
44. Garcia-Fernandez, J. and Holland, P.W. Archetypal organization of the amphioxus Hox gene cluster. Nature, 1994, 370(6490): 563-566.
45. McLysaght, A.; Hokamp, K. and Wolfe, K.H. Extensive genomic duplication during early chordate evolution. Nat. Genet., 2002, 31(2): 200-204.
46. Gu, X.; Wang, Y. and Gu, J. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat. Genet., 2002, 31(2): 205-209.
47. Escriva, H.; Manzon, L.; Youson, J. and Laudet, V. Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol. Biol. Evol., 2002, 19(9): 1440-1450.
48. Holland, P.W.H. More genes in vertebrates? Genome Evolution, 2003, 75-84.
49. Hughes, A.L. Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J. Mol. Evol., 1999, 48(5): 565-576.
50. Hughes, A.L.; da Silva, J. and Friedman, R. Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome. Res., 2001, 11(5): 771-780.
51. Taylor, J.S. and Brinkmann, H. 2R or not 2R? Trends Genet., 2001, 17(9): 488-489.
52. Lundin, L.; Larhammar, D. and Hallbook, F. Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates. Genome. Evolution., 2003, 53-63.
53. Hughes, A.L. and Friedman, R. 2R or not 2R: Testing hypotheses of genome duplication in early vertebrates. Genome Evolution, 2003, 85-93.
54. Boncinelli, E.; Somma, R.; Acampora, D.; Pannese, M.; D'Esposito, M.; Faiella, A. and Simeone, A. Organization of human homeobox genes. Hum. Reprod, 1988, 3(7): 880-886.
55. Ladjali-Mohammedi, K.; Grapin-Botton, A.; Bonnin, M.A. and Le Douarin, N.M. Distribution of HOX genes in the chicken genome reveals a new segment of conservation between human and chicken. Cytogenet. Cell Genet., 2001, 92(1-2): 157-161.
56. Godsave, S.; Dekker, E.J.; Holling, T.; Pannese, M.; Boncinelli, E. and Durston, A. Expression patterns of Hoxb genes in the Xenopus embryo suggest roles in anteroposterior specification of the hindbrain and in dorsoventral patterning of the mesoderm. Dev. Biol., 1994, 166(2): 465-476.
57. Force, A.; Amores, A. and Postlethwait, J.H. Hox cluster organization in the jawless vertebrate Petromyzon marinus. J. Exp. Zool. Mol. Dev. Evol., 2002, 294: 30-46.
58. Sharman, A.C. and Holland, P.W. Estimation of Hox gene cluster number in lampreys. Int. J. Dev. Biol., 1998, 42(4): 617-620.
59. Irvine, S.Q.; Carr, J.L.; Bailey, W.J.; Kawasaki, K.; Shimizu, N.; Amemiya, C.T. and Ruddle, F.H. Genomic analysis of Hox clusters in the sea lamprey Petromyzon marinus. J. Exp. Zool., 2002, 294(1): 47-62.
60. Kim, C.B.; Amemiya, C.; Bailey, W.; Kawasaki, K.; Mezey, J.; Miller, W.; Minoshima, S,; Shimizu, N.; Wagner, G. and Ruddle, F. Hox cluster genomics in the horn shark, Heterodontus francisci. Proc. Natl. Acad. Sci. USA, 2000, 97(4): 1655-1660,
61. Longhurst, T.J. and Joss, J.M. Homeobox genes in the Australian lungfish, Neoceratodus forsteri. J. Exp. Zool., 285(2): 1999, 140-145.
62. Koh, E.G.; Lam, K.; Christoffels, A.; Erdmann, M.V.; Brenner, S. and Venkatesh, B. Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis. Proc. Natl. Acad. Sci. USA, 2003, 100(3): 1084-1088.
63. Powers, T.P. and Amemiya, C.T. Evidence for a Hox 14 paralog group in vertebrates. Curr. Biol., 2004, 14(5): R183-R184.
64. Nelson, J.S. Fishes of the world. 3rd ed. 1994, New York: John Wiley and Sons. 600pg.
65. Amores, A.; Force, A.; Yan, Y.L.; Joly, L.; Amemiya, C.; Fritz, A.; Ho, R.K.; Langeland, J.; Prince, V.; Wang, Y.L.; Westerfield, M.; Ekker, M. and Postlethwait, J.H. Zebrafish hox clusters and vertebrate genome evolution. Science, 1998, 282(5394); 1711-1714.
66. Malaga-Trillo, E. and Meyer, A. Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Amer. Zool., 2001, 41: 676-686.
67. Amores, A.; Suzuki, T.; Yan, Y.L.; Pomeroy, J.; Singer, A.; Amemiya, C.; and Postlethwait, J.H. Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res., 2004, 14(1): 1-10.
68. Aparicio, S.; Hawker, K.; Cottage, A.; Mikawa, Y.; Zuo, L.; Venkatesh, B.; Chen, E.; Krumlauf, R. and Brenner, S. Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat. Genet., 1997, 16(1): 79-83.
69. Kurosawa, G.; Yamada, K.; Ishiguro, H. and Hori, H. Hox gene complexity in medaka fish may Be similar to that in pufferfish rather than zebrafish. Biochem. Biophys. Res. Commun., 1999, 260(1): 66-70.
70. Snell, E.A.; Scemama, J.L. and Stellwag, E.J. Genomic organization of the Hoxa4-Hoxa10 region from Morone saxatilis: implications for Hox gene evolution among vertebrates. J. Exp. Zool., 1999, 285(1): 41-49.
71. Prince, V. The Hox Paradox: More complex(es) than imagined. Dev. Biol., 2002, 249(1): 1-15.
72. Naruse, K.; Fukamachi, S.; Mitani, H.; Kondo, M.; Matsuoka, T.; Kondo, S.; Hanamura, N.; Morita, Y.; Hasegawa, K.; Nishigaki, R.; Shimada, A.; Wada, H.; Kusakabe, T.; Suzuki, N.; Kinoshita, M.; Kanamori, A.; Terado, T.; Kimura, H.; Nonaka, M. and Shima, A. A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics, 2000, 154(4): 1773-1784.
73. Van de Peer, Y.; Taylor, J.S. and Meyer, A. Are all fishes ancient polyploids? J. Struct. Funct. Genome, 2003, 3(1-4): 65-73.
74. Wittbrodt, J.; Meyer, A. and Schartl, M. More genes in fish? Bio. Essays, 1998, 20: 511-515.
75. Taylor, J.S.; Van de Peer, Y.; Braasch, I. and Meyer, A. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos. Trans. R. Soc. Lond. B. Biol. Sci., 2001, 356(1414): 1661-1679.
76. Vogel, G. Doubled genes may explain fish diversity. Science, 1998, 281(5380): 1119: 1121.
77. Robinson-Rechavi, M.; Marchand, O.; Escriva, H,; Bardet, P.L.; Zelus, D.; Hughes, S. and Laudet, V. Euteleost fish genomes are characterized by expansion of gene families. Genome Res., 2001, 11(5): 781-788.
78. Taylor, J.S.; Van de Peer, Y. and Meyer, A. Revisiting recent challenges to the ancient fish-specific genome duplication hypothesis. Curr. Biol., 2001, 11(24): R1005-R1008.
79. Robinson-Rechavi, M.; Marchand, O.; Escriva, H. and Laudet, V. An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes. Curr. Biol., 2001, 11(12): R458-R459.
80. Chiu, C.H.; Dewar, K.; Wagner, G.P.; Takahashi, K.; Ruddle, F.; Ledje, C.; Bartsch, P.; Scemama, J.L.; Stellwag, E.; Fried, C.; Prohaska, S.J.; Stadler, P.F, and Amemiya, C.T. Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Res., 2004, 14(1): 11-17.
81. Ledje, C.; Kim, C.B. and Ruddle, F.H. Characterization of Hox genes in the bichir, Polypterus palmas. J. Exp. Zool., 2002, 294(2): 107-111.
82. Pradel, J. and White, R.A. From selectors to realizators. Int. J. Dev. Biol., 1998, 42(3); 417-421.
83. Mannervik, M. Target genes of homeodomain proteins. Bioessays, 1999, 21(4): 267-270.
84. Zhao, Y. and Potter, S.S. Functional specificity of the Hoxa13 homeobox. Development, 2001, 128(16): 3197-3207.
85. Edelman, G.M. and Jones, F.S. Outside and downstream of the homeobox. J. Biol. Chem., 1993, 268(28): 20683-20686.
86. Ford, H.L. Homeobox genes: a link between development, cell cycle, and cancer? Cell Biol. Int., 1998, 22(6): 397-400.
87. Edelman, G.M. and Jones, F.S. Developmental control of N-CAM expression by Hox and Pax gene products. Philos. Trans. R. Soc. Lond. B. Biol. Sci., 1995, 349(1329): 305-312.
88. Pata, I.; Studer, M.; van Doorninck, J.H.; Briscoe, J.; Kuuse, S.; Engel, J.D.; Grosveld, F. and Karis, A. The transcription factor GATA3 is a downstream effector of Hoxb1 specification in rhombomere 4. Development, 1999, 126(23): 5523-5531.
89. Chen, J. and Ruley, H.E. An enhancer element in the EphA2 (Eck) gene sufficient for rhombomere-specific expression is activated by HOXA1 and HOXB1 homeobox proteins. J. Biol. Chem., 1998, 273(38): 24670-24675.
90. Morsi El-Kadi, A.S.; in der Reiden, P.; Durston, A. and Morgan, R. The small GTPase Rap1 is an immediate downstream target for Hoxb4 transcriptional regulation. Mech. Dev., 2002, 113(2): 131-139.
91. Mann, R.S. and Affolter, M. Hox proteins meet more partners. Curr. Opin. Genet. Dev., 1998, 8(4): 423-429.
92. Mann, R.S. The specificity of homeotic gene function. BioEssays, 1995, 17(10): 855-863.
93. Chariot, A.; Gielen, J.; Merville, M.P. and Bours, V. The homeodomain-containing proteins: an update on their interacting partners. Biochem. Pharmacol., 1999, 58(12): 1851-1857.
94. Akam, M. Hox genes, homeosis and the evolution of segment identity: no need for hopeless monsters. Int. J. Dev. Biol., 1998, 42(3): 445-451.
95. Castelli-Gair, J. Implications of the spatial and temporal regulation of Hox genes on development and evolution. Int. J. Dev. Biol., 1998, 42(3): 437-444.
96. Weatherbee, S.D.; Halder, G.; Kim, J.; Hudson, A. and Carroll, S. Ultrabithorax regulates genes at several levels of the wing-patterning hierarchy to shape the development of the Drosophila haltere. Genes. Dev., 1998, 12(10): 1474-1482.
97. Hughes, C.L. and Kaufman, T.C. Hox genes and the evolution of the arthropod body plan. Evol. Dev., 2002, 4(6): 459-499.
98. Muller, J.; Gaunt, S. and Lawrence, P.A. Function of the Polycomb protein is conserved in mice and flies. Development, 1995, 121(9): 2847-2852.
99. Simon, J.A. and Tamkun, J.W. Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes. Curr. Opin. Genet. Dev., 2002, 12(2): 210-218.
100. Manley, N.R. and Capecchi, M.R. Hox group 3 paralogous genes act synergistically in the formation of somitic and neural crest-derived structures. Dev. Biol., 1997, 192(2): 274-288.
101. Pitera, J.E.; Smith, V.V.; Thorogood, P. and Milla, P.J. Coordinated expression of 3′ hox genes during murine embryonal gut development: an enteric Hox code. Gastroenterology, 1999, 117(6): 1339-1351.
102. de Santa Barbara, P. and Roberts, D.J. Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development, 2002, 129(3): 551-561.
103. Duboule, D. Vertebrate hox gene regulation: clustering and/or colinearity? Curr. Opin. Genet. Dev., 1998, 8(5): 514-518.
104. Spitz, F.; Gonzalez, F. and Duboule, D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell, 2003, 113(3): 405-417.
105. Di Rocco, G.; Gavalas, A.; Popperl, H.; Krumlauf, R.; Mavilio, F. and Zappavigna, V. The recruitment of SOX/OCT complexes and the differential activity of HOXA1 and HOXB1 modulate the Hoxb1 auto-regulatory enhancer function. J. Biol. Chem., 2001, 276(23): 20506-20515.
106. Gilthorpe, J.; Vandromme, M.; Brend, T.; Gutman, A.; Summerbell, D.; Totty, N. and Rigby, P.W. Spatially specific expression of Hoxb4 is dependent on the ubiquitous transcription factor NFY. Development, 2002, 129(16): 3887-3899.
107. Oxtoby, E. and Jowett, T. Cloning of the zebrafish krox-20 gene (krx-20) and its expression during hindbrain development. Nucleic Acids Res., 1993, 21(5): 1087-1095.
108. Moens, C.B.; Cordes, S.P.; Giorgianni, M.W.; Barsh, G.S. and Kimmel, C.B. Equivalence in the genetic control of hindbrain segmentation in fish and mouse. Development, 1998, 125(3): 381-391.
109. Nonchev, S.; Vesque, C.; Maconochie, M.; Seitanidou, T.; Ariza-McNaughton, L.; Frain, M.; Marshall, H.; Sham, M.H.; Krumlauf, R. and Charnay, P. Segmental expression of Hoxa-2 in the hindbrain is directly regulated by Krox-20. Development, 1996, 122(2): 543-554.
110. Lufkin, T. Transcriptional control of Hox genes in the vertebrate nervous system. Curr. Opin. Genet. Dev., 1996, 6(5): 575-580.
111. Shimeld, S.M. Retinoic acid, HOX genes and the anterior-posterior axis in chordates. BioEssays, 1996, 18(8): 613-616.
112. Schilling, T.F. and Knight, R.D. Origins of anteroposterior patterning and Hox gene regulation during chordate evolution. Phil. Trans. R. Soc. Lond B., 2001, 356: 1599-1613.
113. Be-Vialar, S.; Itasaki, N. and Krumlauf, R. Initiating Hox gene expression: in the early chick neural tube differential sensitivity to FGF and RA signaling subdivides the HoxB genes in two distinct groups. Development, 2002, 129(22): 5103-5115.
114. Katsuyama, Y.; Wada, S.; Yasugi, S. and Saiga, H. Expression of the labial group Hox gene HrHox-1 and its alteration induced by retinoic acid in development of the ascidian Halocynthia roretzi. Development, 1995, 121(10): 3197-3205.
115. Holland, L.Z. and Holland, N.D. Expression of AmphiHox-1 and AmphiPax-1 in amphioxus embryos treated with retinoic acid: insights into evolution and patterning of the chordate nerve cord and pharynx. Development, 1996, 122(6): 1829-1838.
116. Dubrulle, J.; McGrew, M.J. and Pourquie, O. FGF signaling controls somite boundary position and regulates segmentation clock control of spatiotemporal Hox gene activation. Cell, 2001, 106(2): 219-232.
117. Gould, A.; Morrison, A.; Sproat, G.; White, R.A. and Krumlauf, R. Positive cross-regulation and enhancer sharing: two mechanisms for specifying overlapping Hox expression patterns. Genes. Dev., 1997, 11(7): 900-913.
118. Mann, R.S. Why are hox genes clustered? BioEssays, 1997, 19(8): 661-664.
119. Stokes, M.D. and Holland, N.D. The lancelet. Amer. Sci., 1998, Nov-Dec, 552-560.
120. Holland, L.Z. and Holland, N.D. Evolution of neural crest and placodes: amphioxus as a model for the ancestral vertebrate? J. Anat., 2001, 199(Pt 1-2): 85-98.
121. Shimeld, S.M. The evolution of dorsoventral pattern formation in the chordate neural tube. Amer. Zool., 1999, 39: 641-649.
122. Holland, L.Z.; Kene, M.; Williams, N.A. and Holland, N.D. Sequence and embryonic expression of the amphioxus engrailed gene (AmphiEn): the metameric pattern of transcription resembles that of its segment-polarity homolog in Drosophila. Development, 1997, 124(9): 1723-1732.
123. Kozmik, Z.; Holland, N.D.; Kalousova, A.; Paces, J.; Schubert, M. and Holland, L.Z. Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. Development, 1999, 126(6): 1295-1304.
124. Holland, L.Z.; Schubert, M.; Kozmik, Z. and Holland, N.D. AmphiPax3/7, an amphioxus paired box gene: insights into chordate myogenesis, neurogenesis, and the possible evolutionary precursor of definitive vertebrate neural crest. Evol. Devel., 1999, 1(3): 153-165.
125. Jackman, W.R. and Kimmel, C.B. Coincident iterated gene expression in the amphioxus neural tube. Evol. Dev., 2002, 4(5): 366-374.
126. Wada, H.; Garcia-Fernandez, J. and Holland, P.W. Colinear and segmental expression of amphioxus Hox genes. Dev. Biol., 1999, 213(1): 131-141.
127. Manzanares, M.; Wada, H.; Itasaki. N.; Trainor, P.A.; Krumlauf, R. and Holland, P.W. Conservation and elaboration of Hox gene regulation during evolution of the vertebrate head. Nature, 2000, 408(6814): 854-857.
128. Greer, J.M.; Puetz, J.; Thomas, K.R. and Capecchi, M.R. Maintenance of functional equivalence during paralogous Hox gene evolution [see comments]. 2000, Nature, 403(6770): 661-665.
129. Ohno, S. Evolution by Gene Duplication. 1970, Berlin: Springer Verlag.
130. Bruce, A.E.; Oates, A.C.; Prince, V.E. and Ho, R.K. Additional hox Clusters in the zebrafish: divergent expression patterns belie equivalent activities of duplicate hoxB5 genes. Dev. Evol., 2001, 3(3): 127-144.
131. Lynch, M. and Force, A. The probability of duplicate gene preservation by subfunctionalization. Genetics, 2000, 154(1): 459-473.
132. Force, A.; Lynch, M.; Pickett, F.B.; Amores, A.; Yan, Y.L. and Postlethwait, J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 1999, 151(4): 1531-1545.
133. Jozefowicz, C.; McClintock, J. and Prince, V. The fates of zebrafish Hox gene duplicates. Genome Evolution, 2003, 185-194.
134. McClintock, J.M.; Carlson, R.; Mann, D.M. and Prince, V.E. Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish Hox paralog group 1 genes, Development, 2001, 128(13): 2471-2484.
135. McClintock,J.M.; Kheirbek, M.A. and Prince, V.E. Knockdown of duplicated zebrafish hoxb1 genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention. Development, 2002, 129(10): 2339-2354.
136. Burke, A.C.; Nelson, C.E.; Morgan, B.A. and Tabin, C. Hox genes and the evolution of vertebrate axial morphology. Development, 1995, 121(2): 333-346.
137. Gilbert, S.F. Developmental biology. 5th ed. 1997, Sunderland: Sinauer Associates. 918pg.
138. Cohn, M.J. and Tickle, C. Developmental basis of limblessness and axial patterning in snakes. Nature, 1999, 399(6735): 474-479.
139. Gaunt, S.J. Evolutionary shifts of vertebrate structures and Hox expression up and down the axial series of segments: a consideration of possible mechanisms. Int. J. Dev. Biol., 2000, 44(1): 109-117.
140. Shashikant, C.S.; Bieberich, C.J.; Belting, H.G.; Wang, J.C.; Borbely, M.A. and Ruddle, F.H. Regulation of Hoxc-8 during mouse embryonic development: identification and characterization of critical elements involved in early neural tube expression. Development, 1995, 121(12): 4339-4347.
141. Bradshaw, M.S.; Shashikant, C.S.; Belting, H.G.; Bollekens, J.A. and Ruddle, F.H. A long-range regulatory element of Hoxc8 identified by using the pClasper vector. Proc. Natl. Acad. Sci. USA, 1996, 93(6): 2426-2430.
142. Belting, H.G.; Shashikant, C.S. and Ruddle, F.H. Modification of expression and cis-regulation of Hoxc8 in the evolution of diverged axial morphology. Proc. Natl. Acad. Sci. USA, 1998, 95(5): 2355-2360.
143. Juan, A.H. and Ruddle, F.H. Enhancer timing of Hox gene expression: deletion of the endogenous Hoxc8 early enhancer. Development, 2003, 130(20): 4823-4834.
144. Shashikant, C.S.; Kim, C.B.; Borbely, M.A.; Wang, W.C. and Ruddle, F.H. Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element. Proc. Natl. Acad. Sci. USA, 1998, 95(26): 15446-15451.
145. Carr, J.L.; Shashikant, C.S.; Bailey, W.J. and Ruddle, F.H. Molecular evolution of Hox gene regulation: cloning and transgenic analysis of the lamprey HoxQ8 gene, J. Exp. Zool., 1998, 280(1): 73-85.
146. Holder, M.T.; Erdmann, M.V.; Wilcox, T.P.; Caldwell, R.L. and Hillis, D.M. Two living species of coelacanths? Proc. Natl. Acad. Sci. USA, 1999, 96(22): 12616-12620.
147. Weinberg, S. A fish caught in time: the search for the coelacanth. 2000, New York: Harper Collins. 220pg.
148. Clack, J.A. Gaining Ground: the origin and evolution of tetrapods. 2002, Bloomington: Indiana University Press. 369pg.
149. Wagner, G.P. and Chiu, C.H. The tetrapod limb: a hypothesis on its origin. J. Exp. Zool., 2001, 291(3): 226-240.
150. Sordino, P.; van der Hoeven, F. and Duboule, D. Hox gene expression in teleost fins and the origin of vertebrate digits. Nature, 1995, 375(6533): 678-681.
151. van der Hoeven, F.; Sordino, P.; Fraudeu, N.; Izpisua-Belmonte, J.C. and Duboule, D. Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HOXD complex. Mech. Dev., 1996, 54(1): 9-21.
152. Sordino, P.; Duboule, D. and Kondo, T. Zebrafish Hoxa and Evx-2 genes: cloning, developmental expression and implications for the functional evolution of posterior Hox genes. Mech. Dev., 1996, 59(2): 165-175.
153. Kmita, M.; Kondo, T. and Duboule, D. Targeted inversion of a polar silencer within the HoxD complex re-allocates domains of enhancer sharing. Nat. Genet., 2000, 26(4): 451-454.
154. Newman, S.A. Sticky fingers: Hox genes and cell adhesion in vertebrate limb development. Bioessays, 1996, 18(3): 171-174.
155. Minelli, A. Limbs and tail as evolutionarily diverging duplicates of the main body axis. Evolution and Development, 2000, 2(3): 157-165.
156. Capdevila, J. and Belmonte, J.C.I. Perspectives on teh evolutionary origin of tetrapod limbs. J. Exp. Zool. (Mol. Dev. Evol.), 2000, 288: 287-303.
157. Coates, M.I. and Colin, M.J. Fins, limbs, and tails: outgrowths and axial patterning in vertebrate evolution. BioEssays, 1998, 20: 371-381.
158. Martinez-Arias and A.Stewart, A. Molecular Principles of Animal Development. 2002, New York: Oxford Univeristy Press. 410pg.
159. Geraudie, J. and Borday Birraux, V. Posterior hoxa genes expression during zebrafish bony fin ray development and regeneration suggests their involvement in scleroblast differentiation. Dev. Genes. Evol., 2003, 213(4): 182-186.
160. Coates, M.I.; Jeffery, J.E. and Rut, M. Fins to limbs: what the fossils say. Evol. Dev., 2002, 4(5): 390-401.
161. Knezevic, V.; De Santo, R.; Schughart, K.; Huffstadt, U.; Chiang, C.; Mahon, K.A. and Mackem, S. Hoxd-12 differentially affects preaxial and postaxial chondrogenic branches in the limb and regulates Sonic hedgehog in a positive feedback loop. Development, 1997, 124(22): 4523-4536.
162. Stadler, H.S.; Higgins, K.M. and Capecchi, M.R. Loss of Eph-receptor expression correlates with loss of cell adhesion and chondrogenic capacity in Hoxa13 mutant limbs. Development, 2001, 128(21): 4177-4188.
163. Chiu, C.; Nonaka, D.; Xue, L.; Amemiya, C.T. and Wagner, G.P. Evolution of Hoxa-11 in Lineages Phylogenetically Positioned along the Fin-Limb Transition. Mol. Phylogenet. Evol., 2000, 17(2): 305-316.
164. Spitz, F.; Gonzalez, F.; Peichel, C.; Vogt, T.F.; Duboule, D. and Zakany, J. Large scale transgenic and cluster deletion analysis of the HoxD complex separate an ancestral regulatory module from evolutionary innovations. Genes. Dev., 2001, 15(17): 2209-2214.
165. Martinez, P. and Amemiya, C.T. Genomics of the HOX gene cluster. Comp. Biochem. Physiol. B. Biochem. Mol. Biol., 2002, 133(4): 571-580.
166. Chiu, C.H.; Amemiya, C.; Dewar, K.; Kim, C.B.; Ruddle, F.H. and Wagner, G.P. Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc. Natl. Acad. Sci. USA, 2002, 99(8): 5492-5497.
167. Santini, S.; Boore, J.L. and Meyer, A. Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res., 2003, 13(6A), 1111-1122.
168. Schwartz, S.; Zhang, Z.; Frazer, K.A.; Smit, A.; Riemer, C.; Bouck, J.; Gibbs, R.; Hardison, R. and Miller, W. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res., 2000, 10(4): 577-586.
169. Mayor, C.; Brudno, M.; Schwartz, J.R.; Poliakov, A.; Rubin, E.M.; Frazer, K.A.; Pachter, L.S. and Dubchak, I. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 2000, 16(11): 1046-1047.
170. Loots, G.G.; Ovcharenko, I.; Pachter, L.; Dubchak, I. and Rubin, E.M. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res., 2002, 12(5): 832-839.
171. Hardison, R.C. Conserved noncoding sequences are reliable guides to regulatory elements. Trends. Genet., 2000, 16(9): 369-372.
172. Blanchette, M. and Tompa, M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res., 2002, 12(5): 739-748.
173. Pennacchio, L.A. and Rubin, E.M. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet., 2001, 2(2): 100-109.
174. Chiu, C.H.; Amemiya, C.T.; Carr, J.L.; Bhargava, J.; Hwang, J.K.; Shashikant, C.S.; Ruddle, F.H. and Wagner, G.P. A recombinogenic targeting method to modify large-inserts for cis-regulatory analysis in transgenic mice: construction and expression of a 100-kb, zebrafish Hoxa-11b-lacZ reporter gene. Dev. Genes. Evol., 2000, 210(2): 105-109.
175. Yu, D.; Ellis, H.M.; Lee, E.C.; Jenkins, N.A.; Copeland, N.G. and Court, D.L. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA, 2000, 97(11): 5978-5983.
176. Copeland, N.G.; Jenkins, N.A. and Court, D.L. Recombineering: a powerful new tool for mouse functional genomics. Nat. Rev. Genet., 2001, 2(10): 769-779.
177. Lee, E.C.; Yu, D.; Martinez de Velasco, J.; Tessarollo, L.; Swing, D.A.; Court, D.L.; Jenkins, N.A. and Copeland, N.G. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics, 2001, 73(1): 56-65.
178. Jessen, J.R.; Willett, C.E. and Lin, S. Artificial chromosome transgenesis reveals long-distance negative regulation of rag1 in zebrafish. Nat. Genet., 1999, 23(1): 15-16.
179. He, L.; and Hannon, G. J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet., 2004, 5(7): 522-531.
180. Chen, C. Z.; Li, L.; Lodish, H. F.; Bartel, D. P. MicroRNAs modulate hematopoietic lineage differentiation. Science, 2004, 303(5654): 83-86.
181. Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116(2): 281-297.
182. Yekta, S.; Shih, I. H.; and Bartel D. P. MicroRNA-directed cleavage of HOXB8 mRNA. Science, 2004, 304(5670): 594-596.