Surveying phylogenetic footprints in large gene clusters: Applications to Hox cluster duplications

Molecular Phylogenetics and Evolution

Volumn 31, Issue 2, 2004, Pages 581-604

  Prohaska, Sonja J ^a,b   Fried, Claudia ^a,b   Flamm, Christoph ^b   Wagner, Günter P ^c   Stadler, Peter F ^a,b,d  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b UNIVERSITY OF VIENNA   (Austria)

^c YALE UNIVERSITY   (United States)

^d SANTA FE INSTITUTE   (United States)

Author keywords

Gene duplication; Hox gene clusters; Phylogenetic footprints

Indexed keywords

CHONDRICHTHYES; DANIO RERIO; TAKIFUGU;

EID: 1842679836     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.08.009     Document Type: Article

References (64)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. 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., Postlethwait, J.H., 1998. Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711-1714.
3. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-m., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., Gelpke, M.D.S., Roach, J., Oh, T., Ho, I.Y., Wong, M., Detter, C., Verhoef, F., Predki, P., Tay, A., Lucas, S., Richardson, P., Smith, S.F., Clark, M.S., Edwards, Y.J.K., Dogget, N., Zharkikh, A., Tavtigian, S.V., Pruss, D., Barstead, M., Evans, C., Baden, H., Powell, J., Glusman, G., Rowen, L., Hood, L., H., T.Y., Elgar, G., Hawkins, T., Venkatesh, B., Rokhsar, D., Brenner, S., 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310.
4. Aparicio, S., Hawker, K., Cottage, A., Mikawa, Y., Zuo, L., Venkatesh, B., Chen, E., Krumlauf, R., Brenner, S., 1997. Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat. Genet. 16, 79-83.
5. Arnone, M.I., Davidson, E.H., 1997. The hardwiring of development: organization and function of genomic regulatory systems. Development 124, 1851-1864.
6. Bielawski, J.P., Dunn, K.A., Yang, Z.H., 2000. Rates of nucleotide substitutions and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics 156, 1299-1308.
7. Blanchette, M., Schwikowski, B., Tompa, M., 2002. Algorithms for phylogenetic footprinting. J. Comp. Biol. 9, 211-223.
8. Blanchette, M., Tompa, M., 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739-748.
9. Bron, C., Kerbosch, J., 1973. Algorithm 457: finding all cliques of an undirected graph. CACM 16, 575-577.
10. Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., Batzoglou, S., 2003. LAGAN and multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731.
11. Carroll, S.B., Grenier, J.K., Weatherbee, S.D., 2001. From DNA to Diversity. Blackwell Science, Malden, MA.
12. Carter, A.J., Wagner, G.P., 2002. Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model. Proc. R. Soc. Lond. B Biol. Sci. 269, 953-960.
13. Chiu, C.-h., Amemiya, C., Dewar, K., Kim, C.-B., Ruddle, F.H., Wagner, G.P., 2002. Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc. Natl. Acad. Sci. USA 99, 5492-5497.
14. Chiu, C.-H., Nonaka, D., Xue, L., Amemiya, C.T., Wagner, G.P., 2000. Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transition. Mol. Phylogenet. Evol. 17, 305-316.
15. Davidson, E., 2001. Genomic Regulatory Systems. Academic Press, San Diego.
16. (DOE Joint Genome Institute), 2002. Fugu genome database. version 2.0: http://genome.jgi-psf.org/fugu3/fugu3.home.html, version 3.0: http://genome.jgi-psf.org/fugu6/fugu6.home.html.
17. Duret, L., Bucher, P., 1997. Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol. 7, 399-406.
18. Ebersberger, I., Metzler, D., C. S., Pääbo, S., 2002. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70, 1490-1497.
19. Fickett, J.W., Wasserman, W.W., 2000. Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol. 11, 19-24.
20. Force, A., Amores, A., Postlethwait, J.H., 2002. Hox cluster organization in the jawless vertebrate Petromyzon marinus. J. Exp. Zool. (Mol. Dev. Evol.) 294, 30-46.
21. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.-I., Postlethwait, J., 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545.
22. Fried, C., Prohaska, S.J., Stadler, P.F., 2003. Independent Hox-cluster duplications in lampreys. J. Exp. Zool. Mol. & Dev. Evol., in press.
23. Garcia-Fernández, J., Holland, P.W., 1994. Archetypal organization of the amphioxus hox gene cluster. Nature 370, 563-566.
24. Garey, M.R., Johnson, D.S., 1979. Computers and Intractability. A Guide to the Theory of Nscript℘ Completeness. Freeman, San Francisco.
25. Hahn, M.W., Stajich, J.E., Wray, G.A., 2003. The effects of selection against spurious transcription factor binding sites. Mol. Biol. Evol. 20, 901-906.
26. Hall, B.K., 1992. Evolutionary Developmental Biology. Chapman & Hall, New York.
27. Heinemeyer, T., Wingender, E., Reuter, I., Hermjakob, H., Kel, A.E., Kel, O.V., Ignatieva, E.V., Ananko, E.A., Podkolodnaya, O.A., Kolpakov, F.A., Podkolodny, N.L., Kolchanov, N.A., 1998. Databases on transcriptional regulation: TRANSFAC, TRRD, and COMPEL. Nucleic Acids Res. 26, 364-370.
28. Hertz, G., Stormo, G.D., 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15, 563-577.
29. Holland, P.W.H., Garcia-Fernández, J., Williams, N.A., Sidow, A., 1994. Gene duplication and the origins of vertebrate development. Development (Suppl.), 125-133.
30. Hughes, J.D., Estep, P.W., Tavazoie, S., Church, G.M., 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296, 1205-1214.
31. Irvine, S.Q., Carr, J.L., Bailey, W.J., Kawasaki, K., Shimizu, N., Amemiya, C.T., Ruddle, F.H., 2002. Genomic analysis of Hox clusters in the sea lamprey, Petromyzon marinus. J. Exp. Zool. (Mol. Dev. Evol.) 294, 47-62.
32. Kappen, C., Schughart, K., Ruddle, F.H., 1989. Two steps in the evolution of antennapedia-class vertebrate homeobox genes. Proc. Natl. Acad. Sci. USA 86, 5459-5463.
33. Leung, J.Y., McKenzie, F.E., Uglialoro, A.M., Flores-Villanueva, P.O., Sorkin, B.C., Yunis, E.J., Hartl, D.L., Goldfeld, A.E., 2000. Identification of phylogenetic footprints in primate tumor necrosis factor-α promoters. Proc. Natl. Acad. Sci. USA 97, 6614-6618.
34. Loots, G., Ovcharenko, I., Pachter, L., Dubchak, I.E.R., 2002. rVISTA for comparative sequence-based discovery of functional transcription factor binding sites. Genome. Res. 12, 832-839.
35. Ludwig, M.Z., 2002. Functional evolution of noncoding DNA. Curr. Opin. Genet. Dev. 12, 634-639.
36. Ludwig, M.Z., Bergman, C., Patel, N.H., Kreitman, M., 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403, 564-567.
37. Málaga-Trillo, E., Meyer, A., 2001. Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Am. Zool. 41, 676-686.
38. Manen, J., Savolainen, V., Simon, P., 1994. The atpB and rbcL promoters in plastid DNAs of a wide dicot range. J. Mol. Evol. 38, 577-582.
39. McClintock, J.M., Kheirbek, M.A., Prince, V.E., 2002. Knockdown of duplicated zebrafish hoxb1 genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention. Development 129, 2339-2354.
40. McCue, L., Thompson, W., Carmack, C., Ryan, M., Liu, J., Derbyshire, V., Lawrence, C., 2001. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29, 774-782.
41. McGinnis, W., Krumlauf, R., 1992. Homeobox genes and axial patterning. Cell 68, 283-302.
42. Morgenstern, B., 1999. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211-218.
43. Müller, F., Blader, P., Strähle, U., 2002. Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements. Bioessays 24, 564-572.
44. Peer, Y.V.d., Taylor, J.S., I. B., Meyer, A., 2001. The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J. Mol. Evol. 53, 436-446.
45. Prince, V.E., 2002. The hox paradox: more complex(es) than imagined. Dev. Biol. 249, 1-15.
46. Prohaska, S.J., Fried, C., Amemiya, C.T., Ruddle, F.H., Wagner, G.P., Stadler, P.F., 2003. The shark HoxN cluster is homologous to the human HoxD cluster. J. Mol. Evol. (in press).
47. Prohaska, S.J., Fried, C., Stadler, P.F., 2003b. Analysis of phylogenetic footprint patterns in large gene clusters. In: N.N. (Ed.), German Conference on Biocomputing 2003 (in press). Preprints of the Leipzig Bioinformatics Initiative BIOINF-03-017 (in press).
48. Raff, R., 1996. The Shape of Life. Chicago University Press, Chicago, IL.
49. Roth, F.P., Hughes, J.D., Estep, P.W., Church, G.M., 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16, 939-945.
50. Ruddle, F.H., Bentley, K.L., Murtha, M.T., Risch, N., 1994. Gene loss and gain in the evolution of the vertebrates. Development (Suppl.), 155-161.
51. (Sanger Institute), 2002. The Danio rerio sequencing project. http://www.sanger.ac.uk/Projects/D_rerio/.
52. Santini, S., Boore, J.L., Meyer, A., 2003. Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res. 13, 1111-1122.
53. Schubert, F.R., Nieselt-Struwe, K., Gruss, P., 1993. The antennapedia-type homeobox genes have evolved from three precursors separated early in metazoan evolution. Proc. Natl. Acad. Sci. USA 90, 143-147.
54. Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., Miller, W., 2000. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res. 4, 577-586.
55. Sinha, S., Tompa, M., 2002. Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 30, 5549-5560.
56. Smit, A.F.A., 1999. Interspersed repeats and other mementos of transposable elements in the mammalian genomes. Curr. Opin. Genet. Dev. 9, 657-663.
57. Stern, D.L., 2000. Evolutionary developmental biology and the problem of variation. Evolution 54, 1079-1091.
58. Sumiyama, K., Kim, C., Ruddle, F.H., 2001. An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships. Genomics 71, 260-262.
59. Tagle, D.A., Koop, B.F., Goodman, M., Slightom, J.L., Hess, D.L., Jones, R.T., 1988. Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203, 439-455.
60. Tautz, D., 2000. Evolution of transcriptional regulation. Curr. Opin. Genet. Dev. 10, 575-579.
61. Thompson, J.D., Higgs, D.G., Gibson, T.J., 1994. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
62. Wagner, A., 1999. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 15, 776-784.
63. Workman, C.T., Stormo, G.D., 2000. ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. In: Pacific Symposium on Biocomputing, pp. 467-478.
64. Yi, S., Ellsworth, D.L., Li, W.H., 2002. Slow molecular clocks in old world monkeys, apes and humans. Mol. Biol. Evol. 19, 2191-2198.