Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence

Genome Research

Volumn 11, Issue 5, 2001, Pages 833-849

  Nesterova, Tatyana B ^a,b   Slobodyanyuk, Sergey Ya ^a   Elisaphenko, Eugene A ^a   Shevchenko, Alexander I ^a   Johnston, Colette ^b   Pavlova, Marina E ^a   Rogozin, Igor B ^a   Kolesnikov, Nikolay N ^a   Brockdorff, Neil ^b   Zakian, Suren M ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b HAMMERSMITH HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA;

ANIMAL CELL; CONTROLLED STUDY; DNA FLANKING REGION; EVOLUTION; GENE FUNCTION; GENE LOCUS; GENE MAPPING; GENE REARRANGEMENT; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC REGULATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; LETTER; MOLECULAR CLONING; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RODENT; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION; TANDEM REPEAT; VOLE; X CHROMOSOME INACTIVATION;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ANIMALS; ANIMALS, WILD; ARVICOLINAE; BASE SEQUENCE; CELLS, CULTURED; CHROMOSOME MAPPING; CONSERVED SEQUENCE; DNA; EVOLUTION, MOLECULAR; FEMALE; GENES; GENETIC MARKERS; HUMANS; MALE; MICE; MOLECULAR SEQUENCE DATA; RNA, UNTRANSLATED; TANDEM REPEAT SEQUENCES; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; X CHROMOSOME;

EID: 17744388101     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.174901     Document Type: Letter

References (73)

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. Bailey, J.A., Carrel, L., Chakravarti, A., and Eichler, E.E. 2000. From the cover: Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The Lyon repeat hypothesis. Proc. Natl. Acad. Sci. 97: 6634-6639.
3. Benson, G. 1999. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 27: 573-580.
4. Bird, A.P. 1986. CpG rich islands and the function of DNA methylation. Nature 321: 209-213.
5. Borsani, G., Tonlorenzi, R., Simmler, M.C., Dandolo, L., Arnaud, D., Capra, V., Grompe, M., Pizzuti, A., Muzny, D., Lawrence, C., et al. 1991. Characterization of a murine gene expressed from the inactive X chromosome. Nature 351: 325-329
6. Boyle, A.L., Ballard, S.G., and Ward, D.C. 1990. Differential distribution of long and short interspersed element sequences in the mouse genome: Chromosome karyotyping by fluorescence in situ hybridization. Proc. Natl. Acad. Sci. 87: 7757-7761.
7. Britten, R.J. 1986. Rates of DNA sequence evolution differ between taxonomic groups. Science 231: 1393-1398.
8. Brockdorff, N., Ashworth, A., Kay, G.F., Cooper, P., Smith, S., McCabe, V.M., Norris, D.P., Penny, G.D., Patel, D., and Rastan, S. 1991. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. Nature 351: 329-331.
9. Brockdorff, N., Ashworth, A., Kay, G.F., McCabe, V.M., Norris, D.P., Cooper, P.J., Swift, S., and Rastan, S. 1992. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71: 515-526.
10. Brodsky, L.I., Ivanov, V.V., Kalaydzidis, Y.L., Leontovich, A.M., Nikolaev, V.K., Feranchuk, S.I., Drachev, V.A. 1995. GeneBee-NET: Internet-based server for analyzing biopolymers structure. Biochemistry 60: 923-928.
11. Brown, C.J., Ballabio, A., Rupert, J.L., Lafreniere, R.G., Grompe, M., Tonlorenzi, R., and Willard, H.F. 1991. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349: 38-44.
12. Brown, C.J., Hendrich, B.D., Rupert, J.L., Lafreniere, R.G., Xing, Y., Lawrence, J., and Willard, H.F. 1992. The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71: 527-542.
13. Buzin, C.H., Mann, J.R., and Singer-Sam, J. 1994. Quantitative RT-PCR assays show Xist RNA levels are low in mouse female adult tissue, embryos and embryoid bodies. Development 120: 3529-3536.
14. Campanero, M.R., Armstrong, M.I., and Flemington, E.K. 2000. CpG methylation as a mechanism for the regulation of E2F activity. Proc. Natl. Acad. Sci. 97: 6481-6486.
15. Cattanach, B.M. 1975. Control of chromosome inactivation. Annu. Rev. Genet. 9: 1-18.
16. Cattanach, B.M., Pollard, C.E., and Perez, J.N. 1969. Controlling elements in the mouse X-chromosome. I. Interaction with the X-linked genes. Genet. Res. 14: 223-235.
17. Cattanach, B.M., Perez, J.N., and Pollard, C.E. 1970. Controlling elements in the mouse X-chromosome. II. Location in the linkage map. Genet. Res. 15: 183-195.
18. Catzeflis, F.M., Nevo, E., Ahlquist, J.E., and Sibley, C.G. 1989. Relationships of the chromosomal species in the Eurasian mole rats of the Spalax ehrenbergi group as determined by DNA-DNA hybridization, and an estimate of the spalacid-murid divergence time. J. Mol. Evol. 29: 223-232.
19. Clemson, C.M., McNeil, J.A., Willard, H.F., and Lawrence, J.B. 1996. XIST RNA paints the inactive X chromosome at interphase: Evidence for a novel RNA involved in nuclear/chromosome structure. J. Cell Biol. 132: 259-275.
20. Daniels, R., Zuccotti, M., Kinis, T., Serhal, P., and Monk, M. 1997. XIST expression in human oocytes and preimplantation embryos. Am. J. Hum. Genet. 61: 33-39.
21. Debrand, E., Heard, E., and Avner, P. 1998. Cloning and localization of the murine Xpct gene: Evidence for complex rearrangements during the evolution of the region around the Xist gene. Genomics 48: 296-303.
22. Duthie, S.M., Nesterova, T.B., Formstone, E.J., Keohane, A.M., Turner, B.M., Zakian, S.M., and Brockdorff, N. 1999. Xist RNA exhibits a banded localization on the inactive X chromosome and is excluded from autosomal material in cis. Hum. Mol. Genet. 8: 195-204.
23. Elisaphenko, E.A., Nesterova, T.B., Duthie, S.M., Ruldugina, O.V., Rogozin, I.B., Brockdorff, N., and Zakian, S.M. 1998. Repetitive DNA sequences in the common vole: Cloning, characterization and chromosome localization of two novel complex repeats MS3 and MS4 from the genome of the East European vole Microtus rossiaemeridionalis. Chromosome Res. 6: 351-360.
24. Hedges, S.B., Parker, P.H., Sibley, C.G., and Kumar, S. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381: 226-229.
25. Hendrich, B.D., Brown, C.J., and Willard, H.F. 1993. Evolutionary conservation of possible functional domains of the human and murine XIST genes. Hum. Mol. Genet. 2: 663-672.
26. Hendrich, B.D., Plenge, R.M., and Willard, H.F. 1997. Identification and characterization of the human XIST gene promoter: Implications for models of X chromosome inactivation. Nucleic Acids Res. 25: 2661-2671.
27. Herzing, L.B., Romer, J.T., Horn, J.M., and Ashworth, A. 1997. Xist has properties of the X-chromosome inactivation centre. Nature 386: 272-275.
28. Higgins, D.G. and Sharp, P.M. 1988. CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene 73: 237-244.
29. Hong, Y.-K., Ontiveros, S.D., Chen, C., and Strauss, W.M. 1999. A new structure for the murine Xist gene and its relationship to chromosome choice/counting during X-chromosome inactivation. Proc. Natl. Acad. Sci. 96: 6829-6834.
30. Hong, Y.K., Ontiveros, S.D., and Strauss, W.M. 2000. A revision of the human XIST gene organization and structural comparison with mouse Xist. Mamm. Genome 11: 220-224.
31. Huang, X. and Miller W. 1991. A Time-Efficient, Linear-Space Local Similarity Algorithm. Adv. Appl. Math. 12: 373-381
32. Jaeger, J.J., Tong, H., Buffetaut, E., and Inrgavat R. 1985. The first fossil rodent from the Miocene of nothern Thailand and their bearing on the problems of the origin of the Muridae. Rev. Paleobiol. 4: 1-7.
33. Johnston, P.G. and Cattanach, B.M. 1981. Controlling elements in the mouse. IV. Evidence of non-random X-inactivation. Genet. Res. 37: 151-160.
34. Johnston, C.M., Nesterova, T.B., Formstone, E.J., Newall, A.E.T., Duthie, S.M., Sheardown, S.A., and Brockdorff, N. 1998. Developmentally regulated Xist promoter switch mediates initiation of X inactivation. Cell 94: 809-817.
35. Jurka, J. 2000. Repbase update: A database and an electronic journal of repetitive elements. Trends Genet. 16: 418-420.
36. Kay, G.F., Penny, G.D., Patel, D., Ashworth, A., Brockdorff, N. and Rastan, S. 1993. Expression of Xist during mouse development suggests a role in the initiation of X chromosome inactivation. Cell 72: 171-182.
37. Lee, J.T., Strauss, W.M., Dausman, J.A., and Jaenisch, R. 1996. A 450 kb transgene displays properties of the mammalian X-inactivation center. Cell 86: 83-94.
38. Lee, J.T. and Jaenisch, R. 1997. Long-range cis effects of ectopic X-inactivation centres on a mouse autosome. Nature 386: 275-279.
39. Lee, J.T., Davidow, L.S., and Warshawsky, D. 1999. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat. Genet. 21: 400-404.
40. Li, W.H., Gouy, M., Sharp, P.M., O'huigin, C., and Yang, Y.W. 1990. Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks. Proc. Natl. Acad. Sci. 87: 6703-6707.
41. Lindsay, E.H. 1978. Eucricetodon asiaticus (Matthew and Granger), an Oligocene rodent (Cricetidae) from Mongolia. J. Paleontol. 52: 590-595.
42. Lyon, M.F. 1961. Gene action in the X chromosome of the mouse (Mus musculus L.). Nature 190: 372-373.
43. _. 1998. X-Chromosome inactivation: A repeat hypothesis. Cytogenet. Cell Genet. 80: 133-137.
44. Makalowski, W. and Boguski, M. S. 1998. Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. 95: 9407-9412.
45. Mallon, A.M., Platzer, M., Bate, R., Gloeckner, G., Botcherby, M.R., Nordsiek, G., Strivens, M.A., Kioschis, P., Dangel, A., Cunningham, D., et al. 2000. Comparative genome sequence analysis of the Bpa/Str region in mouse and man. Genome Res. 10: 758-775.
46. Marahrens, Y., Panning, B., Dausman, J., Strauss, W., and Jaenisch, R. 1997. Xist-deficient mice are defective in dosage compensation but not spermatogenesis. Genes & Dev. 11: 156-166.
47. Matera, A.G., Hellmann, U., and Schmid, C.W. 1990. A transpositionally and transcriptionally competent Alu subfamily. Mol. Cell. Biol. 10: 5424-5432.
48. Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
49. Mayorov, V.I., Adkison, L.R., Vorobyeva, N.V., Khrapov, E.A., Kholodhov, N.G., Rogozin, I.B., Nesterova, T.B., Protopopov, A.I., Sablina, O.V., Graphodatsky, A.S., et al. 1996. Organization and chromosomal localization of a B1-like containing repeat of Microtus subarvalis. Mamm. Genome 7: 593-597.
50. Mazurok, N.A., Rubtsov, N.B., Nesterova, T.B., and Zakian, S.M. 1994. High resolution G-banding of chromosomes in Microtus kirgisorum (Muridae, Rodentia). Cytogenet. Cell Genet. 67: 208-210.
51. Mazurok, N.A., Nesterova, T.B., and Zakian, S.M. 1995. High-resolution G-banding of chromosomes in Microtus subarvalis (Rodentia, Arvicolidae). Hereditas 123: 47-52.
52. Mazurok, N.A., Isaenko, A.A., Nesterova, T.B., and Zakian, S.M. 1996. High-resolution G-banding of chromosones in the common vole Microtus arvalis (Rodentia, Arvicolidae). Hereditas 124: 229-232.
53. Mazurok, N.A., Rubtsova, N.V., Isaenko, A.A., Pavlova, M.E., Slobodyanyuk, S.Ya., Nesterova, T.B., and Zakian, S.M. 2001. Comparative chromosome and mitochondrial DNA analyses and phylogenetic relationships within common voles (Microtus, Arvicolidae). Chromosome Res. 9: 107-120.
54. Medstrand, P., Landry, J.-R., and Mager, D.L. 2001. Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans. J. Biol. Chem. 276: 1896-1903.
55. Nesterova, T.B., Mazurok, N.A., Matveeva, N.M., Shilov, A.G., Yantsen, E.I., Ginsburg, E.K., Goss, S.J., and Zakian, S.M. 1994. Demonstration of the X-linkage and order to the genes GLA, G6PD, HPRT, and PGK in two vole species of the genus Microtus Cytogenet. Cell Genet. 65: 250-255.
56. Nesterova, T.B., Duthie, S.M., Mazurok, N.A., Isaenko, A.A., Rubtsova, N.V., Zakian, S.M., and Brockdorff, N. 1998. Comparative mapping of X chromosomes in vole species of the genus Microtus. Chromosome Res. 6: 41-48.
57. Novacek, M.J. 1992. Mammalian phylogeny: Shaking the tree. Nature 356: 121-125
58. Oeltjen, J.C., Malley, T.M., Muzny, D.M., Miller, W., Gibbs, R.A., and Belmont, J.W. 1997. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res. 7: 315-329.
59. Panning, B., Dausman, J., and Jaenisch, R. 1997. X chromosome inactivation is mediated by Xist RNA stabilization. Cell 90: 907-916.
60. Pearson, W.R. and Lipman, D.J. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. 85: 2444-2448.
61. Penny, G.D., Kay, G.F., Sheardown, S.A., Rastan, S., and Brockdorff, N. 1996. Requirement for Xist in X chromosome inactivation. Nature 379: 131-137.
62. Rastan, S. and Brown, S.D. 1990. The search for the mouse X-chromosome inactivation centre. Genet. Res. 56: 99-106.
63. Ray, P.F., Winston, R.M., and Handyside, A.H. 1997. XIST expression from the maternal X chromosome in human male preimplantation embryos at the blastocyst stage. Hum. Mol. Genet. 6: 1323-1327.
64. Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
65. Sassaman, D.M., Dombroski, B.A., Moran, J.V., Kimberland, M.L., Naas, T.P., DeBerardinis, R.J., Gabriel, A., Swergold, G.D., and Kazazian, H.H. 1997. Many human L1 elements are capable of retrotransposition. Nature Genet. 16: 37-43.
66. Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., and Miller, W. 2000. PipMaker: A Web Server for Aligning Two Genomic DNA Sequences. Genome Res. 10: 577-586.
67. Sheardown, S.A., Duthie, S.M., Johnston, C.M., Newall, A.E., Formstone, E.J., Arkell, R.M., Nesterova, T.B., Alghisi, G.C., Rastan, S., and Brockdorff, N. 1997a. Stabilization of Xist RNA mediates initiation of X chromosome inactivation. Cell 91: 99-107.
68. Sheardown, S.A., Newall, A.E., Norris, D.P., Rastan, S., and Brockdorff, N. 1997b. Regulatory elements in the minimal promoter region of the mouse Xist gene. Gene 203: 159-168.
69. Simmler, M.C., Cattanach, B.M., Rasberry, C., Rougeulle, C., and Avner, P. 1993. Mapping the murine Xce locus with (CA)n repeats. Mamm. Genome 4: 523-530.
70. Simmler, M.C., Cunningham, D.B., Clerc, P., Vermat, T., Caudron, B., Cruaud, C., Pawlak, A., Szpirer, C., Weissenbach, J., Claverie, J.M., et al. 1996. A 94 kb genomic sequence 3′ to the murine Xist gene reveals an AT rich region containing a new testis specific gene Tsx. Hum. Mol. Genet. 5: 1713-1726.
71. o promoter. Proc. Natl. Acad. Sci. 96: 14424-14429.
72. Zakian, S.M., Kulbakina, N.A., Meyer, M.N., Semenova, L.A., Bochkarev, M.N., Radjabli, S.I., and Serov, O.L. 1987. Non-random inactivation of the X-chromosome in interspecific hybrid voles. Genet. Res. 50: 23-27.
73. Zakian, S.M., Nesterova, T.B., Cheryaukene, O.V., and Bochkarev, M.N. 1991. Heterochromatin as a factor affecting X-inactivation in interspecific female vole hybrids (Microtidae, Rodentia). Genet. Res. 58: 105-110.