Regions of human chromosome 2 (2q32-q35) and mouse chromosome 1 show synteny with the pufferfish genome (Fugu rubripes)

Genomics

Volumn 45, Issue 1, 1997, Pages 158-167

  Schofield, J Paul ^a,c   Elgar, Greg ^a   Greystrong, John ^a   Lye, Georgina ^b   Deadman, Rebecca ^b   Micklem, Gos ^b   King, Andrew ^b   Brenner, Sydney ^a   Vaudin, Mark ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARBAMOYL PHOSPHATE SYNTHASE;

ALZHEIMER DISEASE; ANIMAL CELL; ARTICLE; CHROMOSOME ANALYSIS; DNA FLANKING REGION; ENZYME ACTIVITY; EVOLUTION; EXON; GENE EXPRESSION; GENOME; HUMAN; HUMAN CELL; INTRON; MOUSE; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; SYNTENY; TISSUE SPECIFICITY;

EID: 0031259862     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1997.4913     Document Type: Article

References (53)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Anderson, P. M. (1995). Molecular aspects of carbamoyl phosphate synthesis. In "Nitrogen Metabolism and Excretion" (P. J. Walsh and P. A. Wright, Eds.), pp. 33-50, CRC Press, Boca Raton, FL.
3. Asakura, A., Fujisawa-Sehara, A., Komiya, T., Nabeshima, Y., and Nabeshima, Y. (1993). MyoD and myogenin act on the chicken myosin light-chain 1 gene as distinct transcriptional factors. Mol. Cell Biol. 13: 7153-7162.
4. Brenner, S., Elgar, G., Sandford, R., Macrae, A., Venkatesh, B., and Aparicio, S. (1993). Characterization of the pufferfish (fugu) genome as a compact model vertebrate genome. Nature (London) 366: 265-268.
5. Chakraborti, A., and Kozak, C. A. (1992). Microtubule-associated protein genes (Mtap-1, Mtap-2, Mtap-5) map to mouse chromosomes 1, 2, and 13. Mouse Genome 90: 679-681.
6. Chen, K. C., Vannais, D. B., Jones, C., Patterson, D., and Davidson, J. N. (1989). Mapping of the gene encoding the multifunctional protein carrying out the first three steps of pyrimidine biosynthesis to human chromosome 2. Hum. Genet. 82: 40-44.
7. Chen, Y., Hu, H., and Atkinson, B. G. (1994). Characterization and expression of C/EBP-like genes in the liver of Rana catesbeiana tadpoles during spontaneous and thyroid hormone-induced metamorphosis. Dev. Genet. 15: 366-377.
8. Church, G. M., and Gilbert, W. (1984). Genomic sequencing. Proc. Natl. Acad. Sci. USA 81: 1991-1995.
9. Christoffels, V. M., van den Hoff, M. J., Moorman, A. F., and Lamers, W. H. (1995). The far-upstream enhancer of the carbamoyl-phosphate synthetase I gene is responsible for the tissue specificity and hormone inducibility of its expression. J. Biol. Chem. 270: 24932-24940.
10. Cohen-Haguenauer, O., Barton, P. J., Nguyen, V. C., Serero, S., Gross, M. S., Jegou-Foubert, C., de Tand, M. F., Robert, B., Buckingham, M., and Frezal, J. (1988). Assignment of the human fast skeletal muscle myosin alkali light chains gene (MLC1F/MLC3F) to 2q32.1-2qter. Hum. Genet. 78: 65-70.
11. Czosnek, H., Barker, P. E., Ruddle, F. H., and Robert, B. (1985). Chromosomal distribution of genes coding for fast twitch skeletal muscle myosin light chains. Somatic Cell Mol. Genet. 11: 533-540.
12. Donoghue, M., Ernst, H., Wentworth, B., Nadal-Ginard, B., and Rosenthal, N. (1988). A muscle-specific enhancer is located at the 3′ end of the myosin light-chain 1/3 gene locus. Genes Dev. 2: 1779-1790.
13. Doud, S. K., Pan, L. X., Carleton, S., Marmorstein, S., and Siddiqui, M. A. (1995). Adaptational response in transcription factors during development of myocardial hypertrophy. J. Mol. Cell Cardiol. 27: 2359-2372.
14. Gilbert, W., Marchionni, M., and McKnight, G. (1986). On the antiquity of introns. Cell 46: 1271-1275.
15. Goping, I. S., and Shore, G. C. (1994). Interactions between repressor and anti-repressor elements in the carbamyl phosphate synthetase I promoter. J. Biol. Chem. 269: 3891-3896.
16. Haraguchi, Y., Uchino, T., Takiguchi, M., Endo, F., Mori, M., and Matsuda, I. (1991). Cloning and sequence of a cDNA encoding carbamyl phosphate synthetase I: Molecular analysis of hyperammonemia. Gene 107: 335-340.
17. Hartl, F. U., Pfanner, N., Nicholson, D. W., and Neupert, W. (1989). Mitochondrial protein import. Biochim. Biophys. Acta 988: 1-45.
18. Helbing, C. C., and Atkinson, B. G. (1994). 3,5,3′-Triiodothyronine-induced carbamyl-phosphate synthetase gene expression is stabilized in the liver of Rana catesbeiana tadpoles during heat shock. J. Biol. Chem. 269: 11743-11750.
19. Hirayama, Y., Kanoh, S., Nakaya, M., and Watabe, S. (1997). The two essential light chains of carp fast skeletal myosin, LC1 and LC3, are encoded by distinct genes and change their molar ratio following temperature acclimation. J. Exp. Biol. 200: 693-701.
20. Hong, J., Salo, W. L., Lusty, C. J., and Anderson, P. M. (1994). Carbamyl phosphate synthetase III, an evolutionary intermediate in the transition between glutamine-dependent and ammonia-dependent carbamyl phosphate synthetases. J. Mol. Biol. 243: 131-140.
21. Hong, J., Salo, W. J., and Anderson, P. M. (1995). Nucleotide sequence and tissue-specific expression of the multifunctional protein carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase (CAD) mRNA in Squalus acanthias. J. Biol. Chem. 270: 14130-14139.
22. Hong, J., Salo, W. J., Chen, Y., Atkinson, B. G., and Anderson, P. M. (1996). The promoter region of carbamoyl phosphate synthetase III gene of Squalus acanthias. J. Mol. Evol. 43: 602-609.
23. How, G-F., Venkatesh, B., and Brenner, S. (1996). Conserved linkage between the puffer fish (Fugu rubripes) and human genes for platelet-derived growth factor receptor and macrophage colony-stimulating factor receptor. Genome Res. 6: 1185-1191.
24. Huang, X., and Miller, W. (1991). A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 12: 337-357.
25. Iwahana, H., Fujimura, M., Ii, S., Kondo, M., Moritani, M., Takahashi, Y., Yamaoka, T., Yoshimoto, K., and Itakura, M. (1996). Molecular cloning of a human cDNA encoding a trifunctional enzyme of carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase in de novo pyrimidine synthesis. Biochem. Biophys. Res. Commun. 219: 249-255.
26. Kalcheva, N., Albala, J., O'Guin, K., Rubino, H., Garner, C., and Shafit-Zagardo, B. (1995). Genomic structure of human microtubule-associated protein 2 (MAP-2) and characterization of additional MAP-2 isoforms. Proc. Natl. Acad. Sci. USA 92: 10894-10898.
27. Korte, J. J., Salo, W. L., Cabrera, V. M., Wright, P. A., Felskie, A. K., and Anderson, P. M. (1997). Expression of carbamoyl-phosphate synthetase III mRNA during the early stages of development and in muscle of adult rainbow trout (Oncorhynchus mykiss). J. Biol. Chem. 272: 6270-6277.
28. Lagacé, M., Goping, I. S., Muller, C. R., Lazzaro, M., and Shore, G. C. (1992). The carbamoyl phosphate synthetase promoter contains multiple binding sites for C/EBP-related proteins. Gene 118: 231-238.
29. Lewis, S., Wang, D., and Cowan, N. (1988). Microtubule-associated protein MAP2 shares a microtubule binding motif with tau protein. Science 242: 936-939.
30. Marechal, D., Delapierre, D., and Dresse, A. (1988). Cloning and partial sequencing of a new rat brain specific cDNA. Arch. Int. Physiol. Biochim. 96: 231-236.
31. Muller, B., Maeda, K., and Wittinghofer, A. (1990). Sequence of the myosin light chain 1/3 isolated from a rabbit fast skeletal muscle lambda library. Nucleic Acids Res. 18: 6688.
32. Nabeshima, Y., Fujii-Kuriyama, Y., Muramatsu, M., and Ogata, K. (1984). Alternative transcription and two modes of splicing results in two myosin light chains from one gene. Nature 308: 333-338.
33. Neve, R. L., Harris, P., Kurnit, D. M., Kosik, K. S., and Donlon, T. A. (1986). Identification of cDNA clones for the human microtubule-associated protein tau and chromosomal localization of the genes for tau and microtubule-associated protein 2. Brain Res. 1: 271-280.
34. Nyunoya, H., and Lusty, C. J. (1983). The carB gene of Escherichia coli: A duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase. Proc. Natl. Acad. Sci. USA 80: 4629-4633.
35. Nyunoya, H., Broglie, K. E., Widgren, E. E., and Lusty, C. J. (1985). Characterization and derivation of the gene coding for mitochondrial carbamyl phosphate synthetase I of rat. J. Biol. Chem. 260: 9346-9356.
36. Olson, E. (1992). Activation of muscle-specific transcription by myogenic helix-loop-helix proteins. Symp. Soc. Exp. Biol. 46: 331-341.
37. Periasamy, M., Strehler, E. E., Garfinkel, L. I., Gubits, R. M., Ruiz-Opazo, N., and Nadal-Ginard, B. (1984). Fast skeletal muscle myosin light chains 1 and 3 are produced from a single gene by a combined process of differential RNA transcription and splicing. J. Biol. Chem. 259: 13595-13604.
38. Proudfoot, N.J., and Brownlee, G. G. (1976). 3′ non-coding region sequences in eukaryotic messenger RNA. Nature 263: 211-214.
39. Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T. (1995). MatInd and MatInspector - New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 23: 4878-4884.
40. Robert, B., Daubas, P., Akimenko, M. A., Cohen, A., Garner, I., Guenet, J. L., and Buckingham, M. (1984). A single locus in the mouse encodes both myosin light chains 1 and 3, a second locus corresponds to a related pseudogene. Cell 39: 129-140.
41. Sambrook, J., Fritsch, E. E., and Maniatis, T. (1989). "Molecular Cloning: A Laboratory Manual," 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
42. Schofield, J. P. (1993). Molecular studies on an ancient gene encoding for carbamoyl-phosphate synthetase. Clin. Sci. 84: 119-128.
43. Simmer, J. P., Kelly, R. E., Rinker, A. G., Scully, J. L., and Evans, D. R. (1990). Mammalian carbamyl phosphate synthetase (CPS): DNA sequence and evolution of the CPS domain of the Syrian hamster multifunctional protein CAD. J. Biol. Chem. 265: 10395-10402.
44. Strehler, E. E., Periasamy, M., Strehler-Page, M. A., and Nadal-Ginard, B. (1985). Myosin light-chain 1 and 3 gene has two structurally distinct and differentially regulated promoters evolving at different rates. Mol. Cell Biol. 5: 3168-3182.
45. Summar, M. L., Dasouki, M. J., Schofield, J. P., Krishnamani, M. R., Vnencak-Jones, C., Tuchman, M., Mao, J., and Phillips, J. A. (1995). Physical and linkage mapping of human carbamyl phosphate synthetase I (CPS1) and reassignment from 2p to 2q35. Cytogenet. Cell Genet. 71: 266-267.
46. Theze, N., Hardy, S., Wilson, R., Allo, M. R., Mohun, T., and Thiebaud, P. (1995). The MLC 1f/3f gene is an early marker of somitic muscle differentiation in Xenopus laevis embryo. Dev. Biol. 171: 352-362.
47. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
48. Trower, M. K., Orton, S. M., Purvis, I. J., Sanseau, P., Riley, J., Christodoulou, C., Burt, D., See, C. G., Elgar, G., Sherrington, R., Rogaev, E. I., St. George-Hyslop, P., Brenner, S., and Dykes, C. W. (1996). Conservation of synteny between the genome of the pufferfish (Fugu rubripes) and the region on human chromosome 14 (14q24.3) associated with familial Alzheimer disease (AD3 locus). Proc. Natl. Acad. Sci. USA 93: 1366-1369.
49. Van den Hoff, M. J., van de Zande, L. P., Dingemanse, M. A., Das, A. T., Labruyere, W., Moorman, A. F., Charles, R., and Lamers, W. H. (1995). Isolation and characterization of the rat gene for carbamoylphosphate synthetase I. Eur. J. Biochem. 228: 351-361.
50. Venkatesh, B., Tay, B. H., Elgar, G., and Brenner, S. (1996). Isolation, characterisation and evolution of nine pufferfish (Fugu rubripes) actin genes. J. Mol. Biol. 259: 655-665.
51. Wilson, R., Ainscough, R., Andersson, K., Baynes, C., Berks, M., Bonfield, J., Burton, J., Connell, M., Copsey, T., Cooper, J., Coulson, A., Craxton, M., Dear, S., Du, Z., Durbin, R., Favello, A., Fraser, A., Fulton, L., Gardner, A., Green, P., Hawkins, T., Hillier, L., Jier, M., Johnston, L., Jones, M., Kershaw, J., Kirsten, J., Laisster, N., Latreille, P., Lighning, J., Lloyd, C., Mortimore, B., O'Callaghan, M., Parsons, J., Percy, C., Rifken, L., Roopra, A., Saunders, D., Shwonkeen, R., Sims, M., Smaldon, N., Smith, A., Smith, M., Sonnhammer, E., Staden, R., Sulston, J., Thierry-Meig, J., Thomas, K., Vaudin, M., Vaughan, K., Waterston, R., Watson, A., Weinstock, L., Wilkinson-Sproat, J., and Wohldman, P. (1994). 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature 368: 32-38.
52. Woese, C. R., Kandler, O., and Wheelis, M. L. (1990). Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87: 4576-4579.
53. Wright, P.A., Felskie, A., and Anderson, P. M. (1995). Induction of ornithine-urea cycle enzymes and nitrogen metabolism and excretion in rainbow trout (Oncorhynchus mykiss) during early life stages. J. Exp. Biol. 198: 127-135.