Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature

Genome Research

Volumn 13, Issue 5, 2003, Pages 764-772

  Pozzoli, Uberto ^a   Elgar, Greg ^b   Cagliani, Rachele ^a   Riva, Laura ^a   Comi, Giacomo P ^c   Bresolin, Nereo ^a,c   Bardoni, Alessandra ^a   Sironi, Manuela ^a  

^a SCIENTIFIC INSTITUTE   (Italy)

^b MRC UK HGMP Resource Centre   (United Kingdom)

^c UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DYSTROPHIN; GENE PRODUCT; GENOMIC DNA;

ARTICLE; CONTROLLED STUDY; DNA RESPONSIVE ELEMENT; GENE CONTROL; GENE FUNCTION; GENE INSERTION; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CONSERVATION; HUMAN; HYPOTHESIS; INTRON; MAMMAL; MOLECULAR SIZE; MOUSE; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PREDICTION; PRIORITY JOURNAL; PUFFER FISH; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STRUCTURE ANALYSIS; VERTEBRATE; X CHROMOSOME;

AMINO ACID SEQUENCE; ANIMALS; CAENORHABDITIS ELEGANS; CLONING, MOLECULAR; DNA; DNA, HELMINTH; DROSOPHILA MELANOGASTER; DYSTROPHIN; GENES, HELMINTH; GENES, INSECT; GENETIC MARKERS; GIGANTISM; HUMANS; INTERSPERSED REPETITIVE SEQUENCES; INTRONS; MICE; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; TAKIFUGU; TETRAODONTIFORMES;

MAMMALIA; MURINAE; TAKIFUGU; TAKIFUGU RUBRIPES; TETRAODONTIDAE; VERTEBRATA;

EID: 0038781956     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.776503     Document Type: Article

References (58)

1. Ahn, A.H. and Kunkel, L.M. 1993. The structural and functional diversity of dystrophin. Nat. Genet. 3: 283-291.
2. Aparicio, S., Morrison, A. Gould, A. Gilthorpe, J., Chaudhuri, C. Rigby, P., Krumlauf, R., and Brenner, S. 1995. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl. Acad. Sci. 92: 1684-1688.
3. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A. et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
4. Austin, R.C., Howard, P.L., D'Souza, V.N., Klamut, H.J., and Ray, P.N. 1995. Cloning and characterization of alternatively spliced isoforms of Dp71. Hum. Mol. Genet. 4: 1475-1483.
5. Barton, L.M., Göttgens, B., Gering, M., Gilbert, J.G.R, Grafham, D., Rogers, J., Bentley, D., Patient R., and Green, A.R. 2001. Regulation of the stem cell leukemia (SCL) gene: A tale of two fishes. Proc. Natl. Acad. Sci. 98: 6747-6752.
6. Batzoglou, S., Pachter, L., Mesirov, J.P., Berger, B., and Lander, E.S. 2000. Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Res. 10: 950-958.
7. Baxendale, S., Abdulla, S., Elgar, G., Buck, D., Berks, M., Micklem, G., Durbin, R., Bates, G., Brenner, S., and Beck, S. 1995. Comparative sequence analysis of the human and pufferfish Huntington's disease genes. Nat. Genet. 10: 67-76.
8. Bell, M.V., Cowper, A.E., Lefranc, M.P., Bell, J.I., and Screaton, G.R. 1998. Influence of intron length on alternative splicing of CD44. Mol. Cell. Biol. 18: 5930-41.
9. Bessou, C., Giugia, J.B., Franks, C.J., Holden-Dye, L., and Segalat, L. 1998. Mutations in the Caenorhabditis elegans dystrophin-like gene dys-1 lead to hyperactivity and suggest a link with cholinergic transmission. Neurogenetics. 2: 61-72.
10. Betts, M.J., Guigo, R., Agarwal, P., and Russell, R.B. 2001. Exon structure conservation despite low sequence similarity: A relic of dramatic events in evolution? EMBO J. 20: 5354-5360.
11. Bies, R.D., Phelps, S.F., Cortez, M.D., Roberts, R., Caskey, C.T., and Chamberlain, J.S. 1992. Human and murine dystrophin mRNA transcripts are differentially expressed during skeletal muscle, heart, and brain development. Nucleic Acids Res. 20: 1725-1731.
12. Blake, D.J., Schofield, J.N., Zuellig, R.A., Gorecki, D.C., Phelps, S.R., Barnard, E.A., Edwards, Y.H., and Davies, K.E. 1995. G-utrophin, the autosomal homologue of dystrophin Dp116, is expressed in sensory ganglia and brain. Proc Natl. Acad. Sci. 92: 3697-3701.
13. Bolanos-Jimenez F., Bordais, A., Behra, M., Strahle, U., Mornet, D., Sahel, J., and Rendon, A. 2001. Molecular cloning and characterization of dystrophin and Dp71, two products of the Duchenne Muscular Dystrophy gene, in zebrafish. Gene 274: 217-226.
14. Byers, T.J., Lidov, H.G.W., and L. M. Kunkel, 1993. An alternative dystrophin transcript specific to peripheral nerve. Nat. Genet. 4: 77-81.
15. Chiaromonte, F., Yang, S., Elnitski, L., Yap, V.B., Miller, W., and Hardison, R.C. 2001. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proc. Natl. Acad. Sci. 98: 14503-14508.
16. den Dunnen, J.T., Grootscholten, P.M., Bakker, E., Blonden, L.A., Ginjaar, H.B., Wapenaar, M.C., van Paassen, H.M., van Broeckhoven, C., Pearson, P.L., and van Ommen, G.J. 1989. Topography of the Duchenne muscular dystrophy (DMD) gene: FIGE and cDNA analysis of 194 cases reveals 115 deletions and 13 duplications. Am. J. Hum. Genet. 45: 835-847.
17. Deutsch, M. and Long, M. 1999. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27: 3219-3228.
18. D'Souza, V.N., Thi Man, N., Morris, G.E., Karges, W., Pillers, D.A.M. and Ray, P.N. 1995. A novel dystrophin isoform is required for normal retinal electrophysiology. Hum. Mol. Genet. 4: 837-842.
19. Dubchak, I., Brudno, M., Loots, G.G., Pachter, L., Mayor, C., Rubin, E.M., and Frazer, K.A. 2000. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 10: 1304-1306.
20. Elgar, G., Rattray, F., Greystrong, J., and Brenner, S. 1995. Genomic structure and nucleotide sequence of the p55 gene of the puffer fish Fugu rubripes. Genomics. 27: 442-446.
21. Elgar, G., Sandford, R., Aparicio, S., Macrae, A., Venkatesh, B., and Brenner, S. 1996. Small is beautiful: Comparative genomics with the pufferfish (Fugu rubripes). Trends Genet. 12: 145-150.
22. Feener, C.A., Koenig, M., and Kunkel, L.M. 1989. Alternative splicing of human dystrophin mRNA generates isoforms at the carboxy terminus. Nature 338: 509-511.
23. Gellner, K. and Brenner S. 1999. Analysis of 148 kb of genomic DNA around the wnt1 locus of Fugu rubripes. Genome Res. 9: 251-258.
24. Gorecki, D.C., Monaco, A.P., Derry, J.M.J., Walker, A.P., Barnard, E.A., and Barnard, P.J. 1992. Expression of four alternative dystrophin transcripts in brain regions regulated by different promoters. Hum. Mol. Genet. 1: 505-510.
25. Gottgens, B., Barton, L.M., Gilbert, J.G., Bench, A.J., Sanchez, M.J., Bahn, S., Mistry, S., Grafham, D., McMurray, A., Vaudin, M. et al. 2000. Analysis of vertebrate SCL loci identifies conserved enhancers. Nat. Biotechnol. 18: 181-186.
26. Greener, M.J. and Roberts, R.G. 2000. Conservation of components of the dystrophin complex in Drosophila. FEBS Lett. 482: 13-18.
27. Greener, M.J., Sewry, C.A., Muntoni, F., and Roberts, R.G. 2002. The 3-untranslated region of the dystrophin gene - Conservation and consequences of loss. Eur. J. Hum. Genet. 7: 413-420.
28. Hardison, R.C., Oeltjen, J., and Miller, W. 1997. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res. 7: 959-966.
29. Higgins, D., Thompson, J., Gibson, T., Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: 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.
30. Koenig, M., Monaco A.P., and Kunkel, L.M. 1988. The complete sequence of dystrophin predicts a rod-shaped cytoskeletal protein. Cell 53: 219-228.
31. Lander E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
32. Lederfein, D., Levy, Z., Augier, N., Mornet, D., and Morris, G. 1992. A 71-kd protein is a major product of the Duchenne muscular dystrophy gene in brain and other nonmuscle tissues. Proc. Natl. Acad. Sci. 89: 5346-5350.
33. Lidov, H.G.W., Selig, S., and Kunkel, L.M. 1995. Dp140: A novel 140-kDA CNS transcript from the dystrophin locus. Hum. Mol. Genet. 4: 329-335.
34. Loots, G.G., Locksley, R.M., Blankespoor, C.M., Wang, Z.E., Miller, W., Rubin, E.M., and Frazer, K.A. 2000. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288: 136-140.
35. Love, D.R., Hill, D.F., Dickson, G., Spurr, N.K., Byth, B.C., Marsden, R.F., Walsh, F.S., Edwards, Y.H., and Davies, K.E. 1989. An autosomal transcript in skeletal muscle with homology to dystrophin. Nature 339: 55-58.
36. Macrae, A.D. and Brenner, S. 1995. Analysis of the dopamine receptor family in the compact genome of the puffer fish Fugu rubripes. Genomics 23: 436-446.
37. Maheshwar, M.M., Sandford, R., Nellist, M., Cheadle, J.P., Sgotto, B., Vaudin, M., and Sampson, J.R. 1996. Comparative analysis and genomic structure of the tuberous sclerosis 2 (TSC2) gene in human and pufferfish. Hum. Mol. Genet. 5: 562.
38. Mason, P.J., Stevens, D.J., Luzzatto, L., Brenner, S., and Aparicio, S. 1995. Genomic structure and sequence of the Fugu rubripes glucose-6-phosphate dehydrogenase gene (G6PD). Genomics 26: 587-591.
39. Mattick, J.S. 1994. Introns: Evolution and function. Curr. Opin. Genet. Dev. 4: 823-831.
40. Mattick, J.S. 2001. Noncoding RNAs: The architects of eukaryotic complexity. EMBO Rep. 2: 986-991.
41. McNaughton, J.C., Cockburn, D.J., Hughes, G., Jones, W.A., Laing, N.G., Ray, P.N., Stockwell, P.A., and Petersen, G.B. 1998. Is gene deletion in eukaryotes sequence-dependent? A study of nine deletion junctions and nineteen other deletion breakpoints in intron 7 of the human dystrophin gene. Gene 222: 41-51.
42. Neuman, S., Kahan, A., Volk, T., Yaffe, D., and Nudel, U. 2001. The dystrophin/utrophin homologues in Drosophila and in sea urchin. Gene 263: 17-29.
43. Nobile, C., Marchi, J., Nigro, V., Roberts, R.G., and Danieli, G.A. 1997. Exon-intron organization of the human dystrophin gene. Genomics 45: 421-424.
44. Nudel, U., Zuk, D., Einat, P., Zeelon, E., Levy, Z., Neuman, S., and Yaffe, D. 1989. Duchenne muscular dystrophy gene product is not identical in muscle and brain. Nature 337: 76-78.
45. Pearce, M., Blake, D.J., Tinsley, J.M., Byth, B.C., Campbell, L., Monaco, A.P., and Davies, K.E. 1993. The utrophin and dystrophin genes share similarities in genomic structure. Hum. Mol. Genet. 2: 1765-1772.
46. Popperl, H., Bienz, M., Studer, M., Chan, S.K., Aparicio, S., Brenner, S., Mann, R.S., and Krumlauf, R. 1995. Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx. Cell 81: 1031-1042.
47. Powers, D.A. 1991. Evolutionary genetics of fish. Adv. Genet. 29: 119-228.
48. Pozzoli, U., Sironi, M., Cagliani, R., Comi, G.P., Bardoni, A., and Bresolin, N. 2002. Comparative analysis of the human dystrophin and utrophin gene structures. Genetics 160: 793-798.
49. Roberts, R.G. and Bobrow, M. 1998. Dystrophins in vertebrates and invertebrates. Hum. Mol. Genet. 7: 589-595.
50. Sathasivam, K., Baxendale, S., Mangiarini, L., Bertaux, F., Hetherington, C., Kanazawa, I., Lehrach, H., and Bates, G.P. 1997. Aberrant processing of the Fugu HD (FrHD) mRNA in mouse cells and in transgenic mice. Hum. Mol. Genet. 6: 2141-2149.
51. Senapathy, P., Shapiro, M.B., and Harris, N.L. 1990. Splice junctions, branch point sites, and exons: Sequence statistics, identification, and applications to genome project. Methods Enzymol. 183: 252-278.
52. Sironi, M., Cagliani, R., Pozzoli, U., Bardoni, A., Comi, G.P., Giorda, R., and Bresolin, N. 2002. The dystrophin gene is alternatively spliced throughout its coding sequence. FEBS Lett. 517: 163-166.
53. Sironi, M., Pozzoli, U., Cagliani, R., Giorda, R., Comi, G.P., Bardoni, A., Menozzi, G., and Bresolin, N. 2003. Relevance of sequence and structure elements for deletion events in the dystrophin gene major hot-spot. Hum. Genet. 112: 272-288.
54. Surono, A., Takeshima, Y., Wibawa, T., Premono, Z.A., and Matsuo, M. 1997. Six novel transcripts that remove a huge intron ranging from 250 to 800 kb are produced by alternative splicing of the 5′ region of the dystrophin gene in human skeletal muscle. Biochem. Biophys. Res. Commun. 239: 895-899.
55. Tinsley, J.M., Blake D.J., Roche, A., Fairbrother, U., and Riss, J. 1992. Primary structure of dystrophin-related protein. Nature 360: 591-593.
56. Venkatesh, B., Ning, Y., and Brenner, S. 1999. Late changes in spliceosomal introns define clades in vertebrate evolution. Proc. Natl. Acad. Sci. 96: 10267-10271.
57. Wang, J., Pansky, A., Venuti, J.M., Yaffe, D., and Nudel, U. 1998. A sea urchin gene encoding dystrophin-related proteins. Hum. Mol. Genet. 7: 581-588.
58. Wilson, J., Putt, W., Jimenez, C., and Edwards, Y.H. 1999. Up71 and Up140, two novel transcripts of utrophin that are homologues of short forms of dystrophin. Hum. Mol. Genet. 8: 1271-1278.