Genomics of the HOX gene cluster

Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology

Volumn 133, Issue 4, 2002, Pages 571-580

  Martinez, Pedro ^a   Amemiya, Chris T ^b  

^a UNIVERSITY OF BERGEN   (Norway)

^b BENAROYA RESEARCH INSTITUTE   (United States)

Author keywords

Bilaterian; Cluster; Evolution; Genomics; Homeobox; HOX; Informatic tools; Mapping; Realisator; Regulation

Indexed keywords

HOX PROTEIN; HOMEODOMAIN PROTEIN;

ARTICLE; EVOLUTION; GENE CLUSTER; GENE LIBRARY; GENE SEQUENCE; GENE STRUCTURE; GENE TARGETING; GENETIC REGULATION; GENOMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; VERTEBRATE; ANIMAL; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION; GENETICS; HOMEOBOX; HUMAN; METABOLISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY; REVIEW;

ANIMALIA; BILATERIA; METAZOA; VERTEBRATA;

ANIMALS; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, HOMEOBOX; GENOMICS; HOMEODOMAIN PROTEINS; HUMANS; MULTIGENE FAMILY; PHYLOGENY;

EID: 0036899957     PISSN: 10964959     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1096-4959(02)00121-5     Document Type: Review

References (87)

1. Acampora D., D'Esposito M., Faiella A., et al. The human HOX gene family. Nucl. Acids Res. 17:(24):1989;10385-10402.
2. Aguinaldo A.M., Turbeville J.M., Linford L.S., et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 387:(6632):1997;489-493.
3. Amemiya C.T., Ota T., Litman G.W. Construction of P1 artificial chromosome (PAC) libraries from lower vertebrates. Birren B., Lai E. Nonmammalian Genomic Analysis: A Practical Guide. 1996;223-256 Academic Press, NY.
4. Amores A., Force A., Yan Y.L., et al. Zebrafish hox clusters and vertebrate genome evolution. Science. 282:(5394):1998;1711-1714.
5. Aparicio S., Hawker K., Cottage A., et al. Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat. Genet. 16:(1):1997;79-83.
6. Arenas-Mena C., Martinez P., Cameron R.A., Davidson E.H. Expression of the Hox gene complex in the indirect development of a sea urchin. Proc. Natl. Acad. Sci. USA. 95:(22):1998;13062-13067.
7. Arenas-Mena C., Cameron A.R., Davidson E.H. Spatial expression of Hox cluster genes in the ontogeny of a sea urchin. Development. 127:(21):2000;4631-4643.
8. Averof M., Akam M. Hox genes and the diversification of insect and crustacean body plans. Nature. 376:(6539):1995;420-423.
9. Bayascas J.R., Castillo E., Munoz-Marmol A.M., Salo E. Planarian Hox genes: novel patterns of expression during regeneration. Development. 124:(1):1997;141-148.
10. Belleville S., Beauchemin M., Tremblay M., Noiseux N., Savard P. Homeobox-containing genes in the newt are organized in clusters similar to other vertebrates. Gene. 114:(2):1992;179-186.
11. Brooke N.M., Garcia-Fernandez J., Holland P.W. The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. Nature. 392:1998;920-922.
12. Cameron R.A., Mahairas G., Rast J.P., et al. A sea urchin genome project: sequence scan, virtual map, and additional resources. Proc. Natl. Acad. Sci. USA. 97:(17):2000;9514-9518.
13. Celniker S.E., Sharma S., Keelan D.J., Lewis E.B. The molecular genetics of the bithorax complex of Drosophila: cis-regulation in the Abdominal-B domain. EMBO J. 13:1990;4277-4286.
14. Chiu C.H., Amemiya C.T., Carr J.L., et al. 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. 210:(2):2000;105-109.
15. Chiu C.H., Amemiya C., Dewar K., Kim C.B., Ruddle F.H., Wagner G. Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc. Natl. Acad. Sci. USA. 99:(8):2002;5492-5497.
16. Copeland N.G., Jenkins N.A., Court D.L. Recombineering: a powerful new tool for mouse functional genomics. Nat. Rev. Genet. 2:(10):2001;769-779.
17. Davidson E.H. Genomic Regulatory Systems: Development and Evolution. 2001;Academic Press, San Diego, CA. 261 pp.
18. Davidson E.H., Rast J.P., Oliveri P., et al. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev. Biol. 246:(1):2002;162-190.
19. de Rosa R., Grenier J.K., Andreeva T., et al. Hox genes in brachiopods and priapulids and protostome evolution. Nature. 399:(6738):1999;772-776.
20. Devenport M.P., Blass C., Eggleston P. Characterization of the Hox gene cluster in the malaria vector mosquito, Anopheles gambiae. Evol. Dev. 2:(6):2000;326-339.
21. Di Gregorio A., Spagnuolo A., Ristoratore F., et al. Cloning of ascidian homeobox genes provides evidence for a primordial chordate cluster. Gene. 156:(2):1995;253-257.
22. Dolle P., Izpisua-Belmonte J.C., Boncinelli E., Duboule D. The Hox-4.8 gene is localized at the 5′ extremity of the Hox-4 complex and is expressed in the most posterior parts of the body during development. Mech. Dev. 36:(1-2):1991;3-13.
23. Dubchak I., Brudno M., Loots G.G., et al. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 10:(9):2000;1304-1306.
24. Duboule D. Vertebrate Hox gene regulation: clustering and/or colinearity? Curr. Opin. Genet. Dev. 8:(5):1998;514-518.
25. Duboule D., Dolle P. The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO J. 8:(5):1989;1497-1505.
26. Ferrier D.E., Akam M. Organization of the Hox gene cluster in the grasshopper, Schistocerca gregaria. Proc. Natl. Acad. Sci. USA. 93:(23):1996;13024-13029.
27. Ferrier D.E., Minguillon C., Holland P.W., Garcia-Fernandez J. The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14. Evol. Dev. 2:(5):2000;284-293.
28. Force A., Amores A., Postlethwait J.H. Hox cluster organization in the jawless vertebrate Petromyzon marinus. J. Exp. Zool. 294:(1):2002;30-46.
29. Galant R., Carroll S.B. Evolution of a transcriptional repression domain in an insect Hox protein. Nature. 415:(6874):2002;910-913.
30. Garcia-Bellido A. Gentic control of wing disc development in Drosophila. Ciba Found. Symp. 29:1975;161-178.
31. Garcia-Fernandez J., Holland P.W. Archetypal organization of the amphioxus Hox gene cluster. Nature. 370:1994;563-566.
32. Gehring W.J., Affolter M., Burglin T. Homeodomain proteins. Ann. Rev. Biochem. 63:1994;487-526.
33. Gould A.P., Brookman J.J., Strutt D.I., White R.A. Targets of homeotic gene control in Drosophila. Nature. 348:(6299):1990;308-312.
34. Gould A., Morrison A., Sproat G., White R.A., Krumlauf R. Positive cross-regulation and enhancer sharing: two mechanisms for specifying overlapping Hox expression patterns. Genes Dev. 11:(7):1997;900-913.
35. Graba Y., Aragnol D., Pradel J. Drosophila Hox complex downstream targets and the function of homeotic genes. Bioessays. 19:(5):1997;379-388.
36. Grandien K., Sommer R.J. Functional comparison of the nematode Hox gene lin-39 in C. elegans and P. pacificus reveals evolutionary conservation of protein function despite divergence of primary sequences. Genes Dev. 15:(16):2001;2161-2172.
37. Holland P.W., Garcia-Fernandez J. Hox genes and chordate evolution. Dev. Biol. 173:(2):1996;382-395.
38. Holland L.Z., Schubert M., Kozmik Z., 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. Dev. 1:(3):1999;153-165.
39. Ioannou P., Amemiya C.T., Garnes J., et al. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nat. Genet. 6:1994;84-89.
40. Irvine S.Q., Martindale M.Q. Expression patterns of anterior Hox genes in the polychaete Chaetopterus: correlation with morphological boundaries. Dev. Biol. 217:(2):2000;333-351.
41. Irvine S.Q., Carr J.L., Bailey W.J., et al. Genomic analysis of Hox clusters in the sea lamprey Petromyzon marinus. J. Exp. Zool. 294:(1):2002;47-62.
42. Jaffe L., Ryoo H.D., Mann R.S. A role for phosphorylation by casein kinase II in modulating Antennapedia activity in Drosophila. Genes Dev. 11:(10):1997;1327-1340.
43. Jagla K., Stanceva I., Dretzen G., Bellard F., Bellard M. A distinct class of homeodomain proteins is encoded by two sequentially expressed Drosophila genes from the 93D/E cluster. Nucl. Acids Res. 22:1994;1202-1207.
44. Kim C.B., Amemiya C., Bailey W., et al. Hox cluster genomics in the horn shark, Heterodontus francisci. Proc. Natl. Acad. Sci. USA. 97:(4):2000;1655-1660.
45. Kmita-Cunisse M., Loosli F., Bierne J., Gehring W.J. Homeobox genes in the ribbonworm Lineus sanguineus: evolutionary implications. Proc. Natl. Acad. Sci. USA. 95:(6):1998;3030-3035.
46. Kornfeld K., Saint R.B., Beachy P.A., Harte P.J., Peattie D.A., Hogness D.S. Structure and expression of a family of Ultrabithorax mRNAs generated by alternative splicing and polyadenylation in Drosophila. Genes Dev. 3:(2):1989;243-258.
47. Laughon A., Howell W., Scott M.P. The interaction of proteins encoded by Drosophila homeotic and segmentation genes with specific DNA sequences. Development. 104 Suppl. 1988;75-83.
48. Leemans R., Loop T., Egger B., et al. Identification of candidate downstream genes for the homeodomain transcription factor Labial in Drosophila through oligonucleotide-array transcript imaging. Genome Biol. 2(5):2001;RESEARCH0015.
49. Lewis E. A gene complex controlling segmentation in Drosophila. Nature. 276:1978;565-570.
50. Lewis D.L., DeCamillis M., Bennett R.L. Distinct roles of the homeotic genes Ubx and abd-A in beetle embryonic abdominal appendage development. Proc. Natl. Acad. Sci. USA. 97:(9):2000;4504-4509.
51. Livesey F.J., Furukawa T., Steffen M.A., Church G.M., Cepko C.L. Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr. Biol. 10:(6):2000;301-310.
52. Locascio A., Aniello F., Amoroso A., Manzanares M., Krumlauf R., Branno M. Patterning the ascidian nervous system: structure, expression and transgenic analysis of the CiHox3 gene. Development. 126:(21):1999;4737-4748.
53. Long S., Byrne M. Evolution of the echinoderm Hox gene cluster. Evol. Dev. 3:(5):2001;302-311.
54. Malaga-Trillo E., Meyer A. Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Am. Zool. 41:2001;676-686.
55. Mann R.S., Chan S.K. Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins. Trends Genet. 12:(7):1996;258-262.
56. Manzanares M., Wada H., Itasaki N., Trainor P.A., Krumlauf R., Holland P.W. Conservation and elaboration of Hox gene regulation during evolution of the vertebrate head. Nature. 408:(6814):2000;854-857.
57. Margulies E.H., Kardia S.L., Innis J.W. A comparative molecular analysis of developing mouse forelimbs and hindlimbs using serial analysis of gene expression (SAGE). Genome Res. 11:(10):2001;1686-1698.
58. Martinez P., Rast J.P., Arenas-Mena C., Davidson E.H. Organization of an echinoderm Hox gene cluster. Proc. Natl. Acad. Sci. USA. 96:(4):1999;1469-1474.
59. Mastick G.S., McKay R., Oligino T., Donovan K., Lopez A.J. Identification of target genes regulated by homeotic proteins in Drosophila melanogaster through genetic selection of Ultrabithorax protein-binding sites in yeast. Genetics. 139:(1):1995;349-363.
60. Mayor C., Brudno M., Schwartz J.R., et al. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 16:(11):2000;1046-1047.
61. McClintock J.M., Carlson R., Mann D.M., Prince V.E. Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish paralogue group 1 genes. Development. 128:2001;2471-2484.
62. Meyer A., Schartl M. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr. Opin. Cell Biol. 11:(6):1999;699-704.
63. Misof B.Y., Wagner G.P. Evidence for four Hox clusters in the killifish Fundulus heteroclitus (teleostei). Mol. Phylogenet. Evol. 5:(2):1996;309-322.
64. Moroni M.C., Vigano M.A., Mavilio F. Regulation of the human HOXD4 gene by retinoids. Mech. Dev. 44:(2-3):1993;139-154.
65. Naruse K., Fukamachi S., Mitani H., et al. A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics. 154:(4):2000;1773-1784.
66. Ohno S. Evolution by Gene Duplication. 1970;Springer-Verlag, Berlin.
67. Peterson K.J., Irvine S.Q., Cameron R.A., Davidson E.H. Quantitative assessment of Hox complex expression in the indirect development of the polychaete annelid Chaetopterus sp. Proc. Natl. Acad. Sci. USA. 97:(9):2000;4487-4492.
68. Powers T.P., Hogan J., Ke Z., et al. Characterization of the Hox cluster from the mosquito Anopheles gambiae (Diptera: Culicidae). Evol. Dev. 2:(6):2000;311-325.
69. Rast J.P., Amore G., Calestani C., Livi C.B., Ransick A., Davidson E.H. Recovery of developmentally defined gene sets from high-density cDNA macroarrays. Dev. Biol. 228:(2):2000;270-286.
70. Ruvkun G., Hobert O. The taxonomy of developmental control in Caenorhabditis elegans. Science. 282:(5396):1998;2033-2041.
71. Saleh M., Rambaldi I., Yang X.J., Featherstone M.S. Cell signaling switches HOX-PBX complexes from repressors to activators of transcription mediated by histone deacetylases and histone acetyltransferases. Mol. Cell Biol. 20:(22):2000;8623-8633.
72. Schwartz S., Zhang Z., Frazer K.A., et al. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res. 10:(4):2000;577-586.
73. Semenza G.L. Transciption factors and human disease. Oxford Monographs on Medical Genetics, no. 37. 1998;Oxford University Press, New York, NY. 368 pp.
74. Shizuya H., Birren B., Kim U.J., et al. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. USA. 89:(18):1992;8794-8797.
75. Sordino P., van der Hoeven F., Duboule D. Hox gene expression in teleost fins and the origin of vertebrate digits. Nature. 375:(6533):1995;678-681.
76. Spitz F., Gonzalez F., Peichel C., Vogt T.F., Duboule D., Zakany J. Large scale transgenic and cluster deletion analysis of the HoxD complex separate an ancestral regulatory module from evolutionary innovations. Genes Dev. 15:(17):2001;2209-2214.
77. Stuart J.J., Brown S.J., Beeman R.W., Denell R.E. A deficiency of the homeotic complex of the beetle Tribolium. Nature. 350:(6313):1991;72-74.
78. Sumiyama K., Irvine S.Q., Stock D.W., et al. Genomic structure and functional control of the Dlx3-7 bigene cluster. Proc. Natl. Acad. Sci. USA. 99:(2):2002;780-785.
79. Taylor J.S., Peer Y.V.D., Braasch I., Meyer A. Comparative genomics provides evidence for an ancient genome duplication event in fish. Phil. Trans. R. Soc. Lond. B. 356:2001;1661-1679.
80. Tkatchenko A.V., Visconti R.P., Shang L., et al. Overexpression of Hoxc13 in differentiating keratinocytes results in downregulation of a novel hair keratin gene cluster and alopecia. Development. 128:(9):2001;1547-1558.
81. Ueno K., Hui C.C., Fukuta M., Suzuki Y. Molecular analysis of the deletion mutants in the E homeotic complex of the silkworm Bombyx mori. Development. 114:(3):1992;555-563.
82. Vachon G., Cohen B., Pfeifle C., McGuffin M.E., Botas J., Cohen S.M. Homeotic genes of the Bithorax complex repress limb development in the abdomen of the Drosophila embryo through the target gene Distal-less. Cell. 71:(3):1992;437-450.
83. van der Hoeven F., Zakany J., Duboule D. Gene transpositions in the HoxD complex reveal a hierarchy of regulatory controls. Cell. 85:(7):1996;1025-1035.
84. Weatherbee S.D., Halder G., Kim J., Hudson A., Carroll S. Ultrabithorax regulates genes at several levels of the wing-patterning hierarchy to shape the development of the Drosophila haltere. Genes Dev. 12:(10):1998;1474-1482.
85. Von Allmen G., Hogga I., Spierer A., et al. Splits in fruitfly Hox gene complexes. Nature. 380:(6570):1996;116.
86. Yanze N., Spring J., Schmidli C., Schmid V. Conservation of Hox/ParaHox-related genes in the early development of a cnidarian. Dev. Biol. 236:(1):2001;89-98.
87. Zhao Y., Potter S.S. Functional specificity of the Hoxa13 homeobox. Development. 128:(16):2001;3197-3207.