Fol. Biol. 2004, 50, 1-6
https://doi.org/10.14712/fb2004050010001
Eukaryotic Operon Genes Can Define Highly Conserved Syntenies
References
1. , L., Gilles, A., Shiina, T., Pontarotti, P., Inoko, H. (2002) Evidence of en bloc duplication in vertebrate genomes. Nat. Genet. 31, 100-105.
<https://doi.org/10.1038/ng855>
2. , M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F. et al. (2000) The genome sequence of Drosophila melanogaster. Science 287, 2185-2195.
<https://doi.org/10.1126/science.287.5461.2185>
3. , S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
<https://doi.org/10.1093/nar/25.17.3389>
4. , J., Smith, M., Merakovsky, J., Coulson, M., Hannan, F., Kelly, L. E. (1996) The stoned locus of Drosophila melanogaster produces a dicistronic transcript and encodes two distinct polypeptides. Genetics 143, 1699-1711.
<https://doi.org/10.1093/genetics/143.4.1699>
5. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
<https://doi.org/10.1038/35048692>
6. , T., Evans, D., Link, C. D., Guffanti, A., Lawson, D., Thierry-Mieg, J., Thierry-Mieg, D., Chiu, W. L., Duke, K., Kiraly, M., Kim, S. K. (2002) A global analysis of Caenorhabditis elegans operons. Nature 417, 851-854.
<https://doi.org/10.1038/nature00831>
7. , S., Ashburner, M. (1997) The Adh-related gene of Drosophila melanogaster is expressed as a functional dicistronic messenger RNA: multigenic transcription in higher organisms. EMBO J. 16, 2023-2031.
<https://doi.org/10.1093/emboj/16.8.2023>
8. , S., Zauner, S., Fraunholz, M., Beaton, M., Penny, S., Deng, L. T., Wu, X., Reith, M., Cavalier-Smith, T., Maier, U. G. (2001) The highly reduced genome of an enslaved algal nucleus. Nature 410, 1091-1096.
<https://doi.org/10.1038/35074092>
9. , D., Sankoff, D. (2003) Tests for gene clustering. J. Comput. Biol. 10, 453-482.
<https://doi.org/10.1089/10665270360688129>
10. , D., Zorio, D., MacMorris, M., Winter, C. E., Lea, K., Blumenthal, T. (1997) Operons and SL2 trans-splicing exist in nematodes outside the genus Caenorhabditis. Proc. Natl. Acad. Sci. USA 94, 9751-9756.
<https://doi.org/10.1073/pnas.94.18.9751>
11. , M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S. et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498-511.
<https://doi.org/10.1038/nature01097>
12. , G., Eichinger, L., Szafranski, K., Pachebat, J. A., Bankier, A. T., Dear, P. H., Lehmann, R., Baumgart, C., Parra, G., Abril, J. F. et al. (2002) Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418, 79-85.
<https://doi.org/10.1038/nature00847>
13. , A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M. et al. (1996) Life with 6000 genes. Science 274, 546, 563-567.
<https://doi.org/10.1126/science.274.5287.546>
14. , A., Papalopulu, N., Krumlauf, R. (1989) The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57, 367-378.
<https://doi.org/10.1016/0092-8674(89)90912-4>
15. , T. A., Nicholls, R. D. (2000) Diverse splicing mechanisms fuse the evolutionarily conserved bicistronic MOCS1A and MOCS1B open reading frames. RNA 6, 928-936.
<https://doi.org/10.1017/S1355838200000182>
16. , T. A., Saitoh, S., Nicholls, R. D. (1999) An imprinted, mammalian bicistronic transcript encodes two independent proteins. Proc. Natl. Acad. Sci. USA 96, 5616-5621.
<https://doi.org/10.1073/pnas.96.10.5616>
17. , R. A., Subramanian, G. M., Halpern, A., Sutton, G. G., Charlab, R., Nusskern, D. R., Wincker, P., Clark, A. G., Ribeiro, J. M., Wides, R. et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298, 129-149.
<https://doi.org/10.1126/science.1076181>
18. , S., Ferrer, P., Vincent, A. (1998) Conservation of read-through transcription of the Drosophila serendipity genes during evolution is gratuitous. Mol. Gen. Genet. 259, 484-490.
<https://doi.org/10.1007/s004380050839>
19. , M. D., Duprat, S., Cornillot, E., Metenier, G., Thomarat, F., Prensier, G., Barbe, V., Peyretaillade, E., Brottier, P., Wincker, P. et al. (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414, 450-453.
<https://doi.org/10.1038/35106579>
20. , D. J., van Heyningen, V. (1998) Position effect in human genetic disease. Hum. Mol. Genet. 7, 1611-1618.
<https://doi.org/10.1093/hmg/7.10.1611>
21. , E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921.
22. , S. J. (1991) Expression of growth/differentiation factor 1 in the nervous system: conservation of a bicistronic structure. Proc. Natl. Acad. Sci. USA 88, 4250-4254.
<https://doi.org/10.1073/pnas.88.10.4250>
23. , H., Jang, J. K., Graham, J., Nycz, K., McKim, K. S. (2000) Two genes required for meiotic recombination in Drosophila are expressed from a dicistronic message. Genetics 154, 1735-1746.
<https://doi.org/10.1093/genetics/154.4.1735>
24. , R., Cohn, R., Kedes, L., Mohun, T. (1983) Expression and organization of histone genes. Annu. Rev. Genet. 17, 239-277.
<https://doi.org/10.1146/annurev.ge.17.120183.001323>
25. McLysaght, A., Seoighe, C., Wolfe, K. H. (2000) High frequency of inversions during eukaryote gene order evolution. In: Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, eds. Sankoff, D., Nadeau, J. H., pp. 47-58, Kluwer Academic Publisher, Dordrecht.
26. , J. H., Sankoff, D. (1998) Counting on comparative maps. Trends Genet. 14, 495-501.
<https://doi.org/10.1016/S0168-9525(98)01607-2>
27. , M. J., Coulier, F., Birnbaum, D., Pontarotti, P. (1998) Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol. Biol. Evol. 15, 1145-1159.
<https://doi.org/10.1093/oxfordjournals.molbev.a026022>
28. , S. L., Holland, P. W. (2000) Evidence for 14 homeobox gene clusters in human genome ancestry. Curr. Biol. 10, 1059-1062.
<https://doi.org/10.1016/S0960-9822(00)00676-X>
29. , C., Leveugle, M., Birnbaum, D., Coulier, F. (2001) Homeobox gene clusters and the human paralogy map. FEBS Lett. 491, 237-242.
<https://doi.org/10.1016/S0014-5793(01)02187-1>
30. , J., Dorche, C., Stallmeyer, B., Mendel, R. R., Cohen, N., Zabot, M. T. (1999) Human molybdopterin synthase gene: genomic structure and mutations in molybdenum cofactor deficiency type B. Am. J. Hum. Genet. 64, 706-711.
<https://doi.org/10.1086/302296>
31. , R. A., Miksch, J. L., Xie, X. L., Cornish, J. A., Galewsky, S. (1990) Expression of the Drosophila gonadal gene: alternative promoters control the germ-line expression of monocistronic and bicistronic gene transcripts. Development 108, 613-622.
<https://doi.org/10.1242/dev.108.4.613>
32. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018.
<https://doi.org/10.1126/science.282.5396.2012>
33. Trachtulec, Z., Forejt, J. (2000) Syntenies of unrelated genes conserved in mammals and nonvertebrates (a review). In: Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, eds. Sankoff, D., Nadeau, J. H., pp. 357-366. Kluwer Academic Publishers, Dordrecht.
34. , Z., Forejt, J. (2001) Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast. Mamm. Genome 12, 227-231.
<https://doi.org/10.1007/s003350010259>
35. , Z., Hamvas, R. M., Forejt, J., Lehrach, H. R., Vincek, V., Klein, J. (1997) Linkage of TATA-binding protein and proteasome subunit C5 genes in mice and humans reveals synteny conserved between mammals and invertebrates. Genomics 44, 1-7.
<https://doi.org/10.1006/geno.1997.4839>
36. , J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A. et al. (2001) The sequence of the human genome. Science 291, 1304-1351.
<https://doi.org/10.1126/science.1058040>
37. , C., Bork, P. (2002) Teamed up for transcription. Nature 417, 797-798.
<https://doi.org/10.1038/417797a>
38. , L., Schuler, D., Brimacombe, R. (1988) Protein binding sites on Escherichia coli 16S ribosomal RNA; RNA regions that are protected by proteins S7, S9 and S19, and by proteins S8, S15 and S17. Nucleic Acids Res. 16, 1233-1250.
<https://doi.org/10.1093/nar/16.4.1233>
39. , V., Gwilliam, R., Rajandream, M. A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S. et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415, 871-880.
<https://doi.org/10.1038/nature724>
40. , D., Cremer, T., Saffrich, R., Fischer, R., Trendelenburg, M. F., Ansorge, W., Stelzer, E. H. (1998) Structure and dynamics of human interphase chromosome territories in vivo. Hum. Genet. 102, 241-251.
<https://doi.org/10.1007/s004390050686>
41. , D. A., Cheng, N. N., Blumenthal, T., Spieth, J. (1994) Operons as a common form of chromosomal organization in C. elegans. Nature 372, 270-272.
<https://doi.org/10.1038/372270a0>
