CpG islands in human ZFX and ZFY and mouse Zfx Genes: Sequence similarities and methylation differences

Genomics

Volumn 29, Issue 2, 1995, Pages 353-363

  Luoh, Shiuh Wen ^a   Jegalian, Karin ^a   Lee, Angela ^b   Chen, Ellson Y ^c   Ridley, Anne ^a,d   Page, David C ^a  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b STANFORD UNIVERSITY   (United States)

^c PERKINELMER INC   (United States)

^d LUDWIG INSTITUTE FOR CANCER RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE;

ANIMAL TISSUE; ARTICLE; EXON; FEMALE; GENE; HUMAN; HUMAN CELL; INTRON; MALE; METHYLATION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SOUTHERN BLOTTING; SPECIES DIFFERENCE; TRANSCRIPTION INITIATION; X CHROMOSOME INACTIVATION; Y CHROMOSOME;

ANIMAL; BASE SEQUENCE; COMPARATIVE STUDY; CONSERVED SEQUENCE; CPG ISLANDS; DNA; DNA-BINDING PROTEINS; EVOLUTION; HUMAN; MALE; METHYLATION; MICE; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, P.H.S.; TRANSCRIPTION, GENETIC; X CHROMOSOME; Y CHROMOSOME; ZINC FINGERS;

EID: 0029143820     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1006/geno.1995.9994     Document Type: Article

References (62)

1. Adler, D. A., Bressler, S. L., Chapman, V. M., Page, D. C., and Dis-teche, C. M. (1991). Inactivation of the Zfx gene on the mouse X chromosome. Proc. Natl. Acad. Sci. USA 88: 4592-4595.
2. Affara, N. A., Lau, Y. F., Briggs, H., Davey, P., Jones, M. H., Khwaja, O., Mitchell, M., and Sargent, C. (1994). Report of the first international workshop on Y chromosome mapping. Cytogenet. Cell Genet. 67: 359-402.
3. Agulnik, A. I., Mitchell, M. J., Mattei, M.-G., Borsani, G., Avner, P. A., Lerner, J. L., and Bishop, C. E. (1994). A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human. Hum. Mol. Genet. 3: 879-884.
4. Aissani, B., and Bernardi, G. (1991). Cp G islands: Features and distribution in the genomes of vertebrates. Gene 106: 173-183.
5. Antequera, F., and Bird, A. (1993). Number of Cp G islands and genes in human and mouse. Proc. Natl. Acad. Sci. USA 90: 11995-11999.
6. Ashworth, A., Swift, S., and Affara, N. (1989). Sequence of c DNA for murine Zfy-1, a candidate for Tdy. Nucleic Acids Res. 17: 2864.
7. Ashworth, A., Rastan, S., Lovell-Badge, R., and Kay, G. (1991). X-chromosome inactivation may explain the difference in viability of XO humans and mice. Nature 351: 406-408.
8. Bird, A. P. (1986). Cp G-rich islands and the function of DNA methyla-tion. Nature 321: 209-213.
9. Blagowidow, N., Page, D. C., Huff, D., and Mennuti, M. T. (1989). Ullrich-Turner syndrome in an XY female fetus with deletion of the sex-deermining portion of the Y chromosome. Am. J. Med. Genet. 34: 159-162.
10. Brown, C. J., and Willard, H. F. (1990). Localization of a gene that escapes inactivation to the X chromosome proximal short arm: Implications for X inactivation. Am. J. Hum. Genet. 46: 273-279.
11. Burgoyne, P. S. (1989). Mammalian sex determination: Thumbs down for zinc finger? Nature 342: 860-862.
12. Cantrell, M. A., Bicknell, J. N., Pagon, R. A., Page, D. C., Walker, D. C., Saal, H. M., Zinn, A. B., and Disteche, C. M. (1989). Molecular analysis of 46, XY females and regional assignment of a new Y-chromosome-specific probe. Hum. Genet. 83: 88-92.
13. Chen, E. Y., Kuang, W.-J., and Lee, A. L. (1991). Overview of manual and automated DNA sequencing by the dideoxy chain termination method. Methods 3: 3-19.
14. Ellison, J. W., Ramos, C., Yen, P. H., and Shapiro, L. J. (1992). Structure and expression of the human pseudoautosomal gene XE7. Hum. Mol. Genet. 1: 691-696.
15. Erickson, R. P., Zwingman, T., and Ao, A. (1993). Gene expression, X-inactivation, and methylation during spermatogenesis: The case of Zfa, Zfx, and Zfy in mice. Mol. Reprod. Dev. 35: 114-120.
16. Feinberg, A. P., and Vogelstein, B. (1984). A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Addendum. Anal. Biochem. 137: 266-267.
17. Fisher, E. M. C, Beer-Romero, P., Brown, L. G., Ridley, A., Mc Neil, J. A., Lawrence, J. B., Willard, H. F., Bieber, F. R., and Page, D. C. (1990). Homologous ribosomal protein genes on the human X and Y chromosomes: Escape from X inactivation and possible implications for Turner syndrome. Cell 63: 1205-1218.
18. Goodfellow, P., Pym, B., Mohandas, T., and Shapiro, L. J. (1984). The cell surface antigen locus, MIC2X, escapes X-inactivation. Am. J. Hum. Genet. 36: 777-782.
19. Hayashida, H., Kuma, K., and Miyata, T. (1992). Interchromosomal gene conversion as a possible mechanism for explaining divergence patterns of ZFY-related genes. J. Mol. Evol. 35: 181-183.
20. Henikoff, S. (1984). Unindirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene 28: 351-359.
21. Kay, G. F., Ashworth, A., Penny, G. D., Dunlop, M., Swift, S., Brock-dorff, N., and Rastan, S. (1991). A candidate spermatogenesis gene on the mouse Y chromosome is homologous to ubiquitin-activating enzyme E1. Nature 354: 486-489.
22. Koopman, P., Gubbay, J., Collignon, J., and Lovell-Badge, R. (1989). Zfy gene expression patterns are not compatible with a primary role in mouse sex determination. Nature 342: 940-942.
23. Koopman, P., Ashworth, A., and Lovell-Badge, R. (1991). The ZFY gene family in humans and mice. Trends Genet. 7: 132-136.
24. Larsen, F., Gundersen, G., Lopez, R., and Prydz, H. (1992). Cp G islands as gene markers in the human genome. Genomics 13: 1095-1107.
25. Lau, Y. F., and Chan, K. M. (1989). The putative testis-determining factor and related genes are expressed as discrete-sized transcripts in adult gonadal and somatic tissues. Am. J. Hum. Genet. 45: 942-952.
26. Luoh, S. W., and Page, D. C. (1994). The structure of the Zfx gene on the mouse X chromosome. Genomics 19: 310-319.
27. Lyon, M. F. (1993). Epigenetic inheritance in mammals. Trends Genet. 9: 123-128.
28. Maizel, J. V., Jr., and Lenk, R. P. (1981). Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc. Natl. Acad. Sci. USA 78: 7665-7669.
29. Mardon, G., Mosher, R., Disteche, C. M., Nishioka, Y., Mc Laren, A., and Page, D. C. (1989). Duplication, deletion, and polymorphism in the sex-determining region of the mouse Y chromosome. Science 243: 78-80.
30. Mardon, G., and Page, D. C. (1989). The sex-determining region of the mouse Y chromosome encodes a protein with a highly acidic domain and 13 zinc fingers. Cell 56: 765-770.
31. Mardon, G., Luoh, S. W., Simpson, E. M., Gill, G., Brown, L. G., and Page, D. C. (1990). Mouse Zfx protein is similar to Zfy-2: Each contains an acidic activating domain and 13 zinc fingers. Mol. Cell. Biol. 10: 681-688.
32. Migeon, B. R., Shapiro, L. J., Norum, R. A., Mohandas, T., Axelman, J., and Dabora, R. L. (1982). Differential expression of steroid sulphatase locus on active and inactive human X chromosome. Nature 299: 838-840.
33. Mitchell, M., Simon, D., Affara, N., Ferguson-Smith, M., Avner, P., and Bishop, C. (1989). Localization of murine X and autosomal sequences homologous to the human Y located testis-determining region. Genetics 121: 803-809.
34. Mizusawa, S., Nishimura, S., and Seela, F. (1986). Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of d GTP. Nucleic Acids Res. 14: 1319-1324.
35. Nagamine, C. M., Chan, K. M., Kozak, C. A., and Lau, Y. F. (1989). Chromosome mapping and expression of a putative testis-determining gene in mouse. Science 243: 80-83.
36. Nagamine, C. M., Chan, K., Hake, L. E., and Lau, Y. F. (1990). The two candidate testis-determining Y genes (Zfy-1 and Zfy-2) are differentially expressed in fetal and adult mouse tissues. Genes Dev. 4: 63-74.
37. Page, D. C., Mosher, R., Simpson, E. M., Fisher, E. M. C, Mardon, G., Pollack, J., Mc Gillivray, B., de la Chapelle, A., and Brown, L. G. (1987). The sex-determining region of the human Y chromosome encodes a finger protein. Cell 51: 1091-1104.
38. Page, D. C., Fisher, E. M., Mc Gillivray, B., and Brown, L. G. (1990). Additional deletion in sex-determining region of human Y chromosome resolves paradox of X, t(Y;22) female. Nature 346: 279-281.
39. Palmer, M. S., Sinclair, A. H., Berta, P., Ellis, N. A., Goodfellow, P. N., Abbas, N. E., and Fellous, M. (1989). Genetic evidence that ZFY is not the testis-determining factor. Nature 342: 937-939.
40. Palmer, M. S., Berta, P., Sinclair, A. H., Pym, B., and Goodfellow, P. N. (1990). Comparison of human ZFY and ZFX transcripts. Proc. Natl. Acad. Sci. USA 87: 1681-1685.
41. Pfeifer, G. P., Tanguay, R. L., Steigerwald, S. D., and Riggs, A. D. (1990). In vivo footprint and methylation analysis by PCR-aided genomic sequencing: Comparison of active and inactive X chromosomal DNA at the Cp G island and promoter of human PGK-1. Genes Dev. 4: 1277-1287.
42. Pritchard, C. A., Goodfellow, P. J., and Goodfellow, P. N. (1987). Mapping the limits of the human pseudoautosomal region and a candidate sequence for the male-determining gene. Nature 328: 273-275.
43. Race, R. R., and Sanger, R. (1975). ''Blood Groups in Man," Blackwell Scientific, London.
44. Sanger, F., Nicklen, S., and Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74: 5463-5467.
45. Schiebel, K., Weiss, B., Wohrle, D., and Rappold, G. (1993). A human pseudoautosomal gene, ADP/ATP translocase, escapes X-inactiva-tion whereas a homologue on Xq is subject to X-inactivation. Nature Genet. 3: 82-87.
46. Schneider-Gadicke, A., Beer-Romero, P., Brown, L. G., Mardon, G., Luoh, S. W., and Page, D. C. (1989a). Putative transcription activator with alternative isoforms encoded by human ZFX gene. Nature 342: 708-711.
47. Schneider-Gadicke, A., Beer-Romero, P., Brown, L. G., Nussbaum, R., and Page, D. C. (1989b). ZFX has a gene structure similar to ZFY, the putative human sex determinant, and escapes X inactivation. Cell 57: 1247-1258.
48. Shapiro, L. J., Mohandas, T., Weiss, R., and Romeo, G. (1979). Noninactivation of an X-chromosome locus in man. Science 204: 1224-1226.
49. Shimmin, L. C., Chang, B. H., and Li, W. H. (1993). Male-driven evolution of DNA sequences. Nature 362: 745-747.
50. Simpson, E. M., and Page, D. C. (1991). An interstitial deletion in mouse Y chromosomal DNA created a transcribed Zfyfusion gene. Genomics 11: 601-608.
51. Singer-Sam, J., and Riggs, A. D. (1993). X chromosome inactivation and DNA methylation. In ''DNA Methylation: Molecular Biology and Biological Significance" (J. P. Jost and H. P. Saluz, Eds.), Vol. 64, pp. 358-384, Birkhauser Verlag, Basel.
52. Sirota, L., Zlotogora, Y., Shabtai, F., Halbrecht, I., and Elian, E. (1981). 49, XYYYY: A case report. Clin. Genet. 19: 87-93.
53. Slim, R., Levilliers, J., Ludecke, H. J., Claussen, U., Nguyen, V. C., Gough, N. M., Horsthemke, B., and Petit, C. (1993). A human pseudoautosomal gene encodes the ANT3 ADP/ATP translocase and escapes X-inactivation. Genomics 16: 26-33.
54. Southern, E. M. (1975). Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98: 503-517.
55. Su, H., and Lau, Y. F. (1992). Demonstration of a stage-specific expression of the ZFY protein in fetal mouse testis using anti-peptide antibodies. Mol. Reprod. Dev. 33: 252-258.
56. Tribioli, C., Tamanini, F., Patrosso, C., Milanesi, L., Villa, A., Pergoli-zzi, R., Maestrini, E., Rivella, S., Bione, S., Mancini, M., et al. (1992). Methylation and sequence analysis around Eag I sites: Identification of 28 new Cp G islands in Xq24-Xq28. Nucleic Acids Res. 20: 727-733.
57. Wolf, S. F., Jolly, D. J., Lunnen, K. D., Friedman, T., and Migeon, B. R. (1984). Methylation of the hypoxanthine phosphoribosyl-transferase locus on the human X chromosome: Implications for X-chromosome inactivation. Proc. Natl. Acad. Sci. USA 81: 2806-2810.
58. Zacksenhaus, E., Gill, R. M., Phillips, R. A., and Gallie, B. L. (1993). Molecular cloning and characterization of the mouse RB1 promoter. Oncogene 8: 2343-2351.
59. Zambrowicz, B. P., Zimmerman, J. W., Harendza, C. J., Findley, S. D., Simpson, E. M., Page, D. C., Brinster, R. L., and Palmiter, R. D. (1994a). Expression of a Zfy-1/lac Ztransgene in the somatic cells of the embryonic gonad and germ cells of the adult testis. Development 120: 1549-1559.
60. Zambrowicz, B. P., Findley, S. D., Simpson, E. M., Page, D. C., and Palmiter, R. D. (1994b). Characterization of the murine Zfy1 and Zfy2 promoters. Genomics 24: 406-408.
61. Zinn, A. R., Bressler, S. L., Beer-Romero, P., Adler, D. A., Chapman, V. M., Page, D. C., and Disteche, C. M. (1991). Inactivation of the Rps4 gene on the mouse X chromosome. Genomics 11: 1097-1101.
62. Zwingman, T., Erickson, R. P., Boyer, T., and Ao, A. (1993). Transcription of the sex-determining region genes Sry and Zfy in the mouse preimplantation embryo. Proc. Natl. Acad. Sci. USA 90: 814-817.