Sequence analysis of an 80 kb human neocentromere

Human Molecular Genetics

Volumn 8, Issue 2, 1999, Pages 217-227

  Barry, Alyssa E ^a   Howman, Emily V ^a   Cancilla, Michael R ^a   Saffery, Richard ^a   Choo, K H Andy ^a  

^a ROYAL CHILDREN'S HOSPITAL   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); HIGH MOBILITY GROUP PROTEIN;

ARTICLE; BINDING SITE; CENTROMERE; DNA BASE COMPOSITION; DNA SEQUENCE; HUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; TANDEM REPEAT; TRANSPOSON;

EID: 0032942659     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/8.2.217     Document Type: Article

References (78)

1. Brinkley, B.R., Ouspenski, I. and Zinkowski, R.P. (1992) Structure and molecular organization of the centromere/kinetochore complex. Trends Cell. Biol., 2, 14-21.
2. Earnshaw, W.C. and Mackay, A.M. (1994) Role of non-histone proteins in the chromosomal events of mitosis. FASEB J., 8, 947-956.
3. Pluta, A.F., Mackay, A.M., Ainsztein, A.M., Goldberg, I.G. and Earnshaw, W.C. (1995) The centromere: hub of chromosomal activities. Science, 270, 1591-1594.
4. Choo, K.H.A. (1997) The Centromere. Oxford University Press, Oxford.
5. Choo, K.H.A. (1997) Centromere DNA dynamics: latent centromeres and neocentromere formation. Am. J. Hum. Genet., 61, 1225-1233.
6. Muro, Y., Masumoto, H., Yoda, K., Nozaki, N., Ohashi, M. and Okazaki, T. (1992) Centromere protein B assembles human centromeric alpha-satellite DNA at the 17-bp sequence. CENPB-box. J. Cell Biol., 116, 585-596.
7. Pluta, A.F., Saitoh, N., Goldberg, I. and Earnshaw, W.C. (1992) Identification of a subdomain of CENPB that is necessary and sufficient for localization to the human centromere. J. Cell Biol., 116, 1081-1093.
8. Gaff, C., du Sart, D., Kalitsis, P., Iannello, R., Nagy, A. and Choo, K.H.A. (1994) A novel nuclear protein binds centromeric alpha-satellite DNA. Hum. Mol. Genet., 3, 711-716.
9. Romanova, L.Y., Deriagan, G.V., Mashkova, T.D., Tumeneva, I.G., Mushegian, A. R., Kisselev, L.L. and Alexandren, I.A. (1996) Evidence for selection in evolution of alpha-satellite DNA: the central role of CENPB/pJα binding region. J. Mol. Biol., 261, 334-340.
10. Hudson, D.F., Fowler, K.J., Earle, E., Saffery, R., Kalitsis, P., Trowell, H., Hill, J., Wreford, N.G., de Kretser, D.M., Cancilla, M.R., Howman, E., Hii, L., Cutts, S.M., Irvine, D. V. and Choo, K.H.A. (1998) Centromere protein B null mice are mitotically and meiotically normal but have lower body and testis weights. J. Cell Biol., 141, 309-319.
11. Lee, C., Wevrick, R., Fisher, R.B., Ferguson-Smith, M.A. and Lin, C.C. (1997) Human centromeric DNAs. Hum. Genet., 100, 291-304.
12. Wevrick, R., Willard, V.P. and Willard, H.F. (1992) Structure of DNA near long tandem arrays of alpha-satellite DNA at the centromeres of human chromosome 7. Genomics. 14, 912-923.
13. Metzdorf, R., Gottert, E. and Blin, N. (1988) A novel centromeric repetitive DNA from human chromosome 22. Chromosoma, 97, 154-158.
14. Mullenbach, R., Lutz, S., Holzmann, K., Dooley, S. and Blin, N. (1992) A non-alphoid repetitive DNA sequence from human chromosome 21. Hum. Genet., 89, 519-523.
15. Cooper, K.F., Fisher, R.B. and Tyler-Smith, C. (1992) Structure of the pericentric long arm region of the human Y chromosome. J. Mol. Biol., 228, 421-432.
16. Potter, S.S. (1984) Rearranged sequences of a human KpnI element. Proc. Natl Acad. Sci. USA, 81, 1012-1016.
17. Higgins, M.J., Wang, H.S., Shtromas, I., Haliotis, T., Roder, J.C., Holden, J.J. and White, B.N. (1985) Organisation of a repetitive 1.8 kb KpnI sequence localized in the heterochromatin of chromosome 15. Chromosoma, 93, 77-86.
18. Tyler-Smith, C., Oakey, R.J., Larin, Z., Fisher, R.B., Crocker, M., Affara, N.A. et al. (1993) Localization of DNA sequences required for human centromere function through an analysis of rearranged Y chromosomes. Nature Genet., 5, 368-375.
19. Brown, K.E., Barnett, M.A., Burgtorf, C., Shaw, P., Buckle, V.J. and Brown, W.R. (1994) Dissecting the centromere of the human Y chromosome with cloned telomeric DNA. Hum. Mol. Genet., 3, 1227-1237.
20. Farr, C.J., Bayne, R.A.L., Kipling, D., Mills, W., Critcher, R. and Cooke, H.J. (1995) Generation of a human X-derived minichromosome using telomere-associated chromosome fragmentation. EMBO J., 14, 5444-5454.
21. Harrington, J.J., Van Bokkelen, G., Mays, R.W., Gustashaw, K. and Willard, H.F. (1997) Formation of de novo centromeres and construction of first-generation human artificial chromosomes. Nature Genet., 15, 345-355.
22. Ikeno, M., Grimes, B., Okazaki, T., Nakano, M., Saitoh, K., Hoshino, H., McGill, N.I., Cooke, H. and Masumoto, H. (1998) Construction of YAC-based mammalian artificial chromosomes. Nature Biotech., 16, 431-439.
23. Depinet, T.W., Zackowski, J.L., Earnshaw, W.C., Kaffe, S., Sekhon, G.S., Stallard, R., Sullivan, B.A., Vance, G.H., Van Dyke, D.L., Willard, H.F., Zinn, A.B. and Schwartz, S. (1997) Characterization of neocentromeres in marker chromosomes lacking detectable alpha-satellite DNA. Hum. Mol. Genet., 6, 1195-1204.
24. Brown, W. and Tyler-Smith, C. (1995) Centromere activation. Trends Genet., 11, 337-339.
25. Karpen, G.H. and Allshire, R.C. ( 1997) The case for epigenetic effects on centromere identity and function. Trends Genet., 13, 489-496.
26. Choo, K.H.A. (1998) Turning on the centromere. Nature Genet., 18, 3-4.
27. Williams, B.C., Murphy, T.D., Goldberg, M.L. and Karpen, G.H. (1998) Neocentromere activity of structurally acentric minichromosomes in Drosophila. Nature Genet., 18, 30-37.
28. Voullaire, L.E., Slater, H.R., Petrovic, V. and Choo, K.H.A. (1993) A functional marker centromere with no detectable alpha-satellite, satellite III or CENPB protein: activation of a latent centromere? Am. J. Hum. Genet., 52, 1153-1163.
29. du Sart, D., Cancilla, M.R., Earle, E., Mao, J., Saffery, R., Tainton, K.M., Kalitsis, P., Martyn, J., Barry, A.E. and Choo, K.H.A. (1997) A functional neocentromere formed through activation of a latent human centromere and consisting of non-alpha-satellite DNA. Nature Genet., 16, 144-153.
30. Cancilla, M.R., Tainton, K.M., Barry, A.E., Larionov, V., Kouprina, N., Resnick, M., duSart, D. and Choo, K.H.A. (1998) Direct cloning of human 10q25 neocentromere DNA using transformation associated recombination (TAR) in yeast. Genomics, 47, 399-404.
31. Bernardi, G. (1995) The human genome: organization and evolutionary history. Annu. Rev. Genet., 29, 445-476.
32. Choo, K.H., Vissel, B., Nagy, A., Earle, E. and Kalitsis, P. (1991) A survey of the genomic distribution of alpha-satellite DNA on all human chromosomes, and derivation of a new consensus sequence. Nucleic Acids Res., 19, 1179-1182.
33. Kalitsis, P., Earle, E., Vissel, B., Shaffer, L.G. and Choo, K.H.A. (1993) A chromosome 13-specific human satellite 1 DNA subfamily with minor presence on chromosome 21: further studies on Robertsonian translocations. Genomics, 16, 104-112.
34. Meyne, J., Goodwin H.E. and Moyzis, R.K. (1994) Chromosome localization and orientation of the simple sequence repeat of human satellite I DNA. Chromosoma, 103, 99-103.
35. Tagarro, I., Wiegant, J., Raap, A.K., Gonzalez-Aguilera, J.J. and Fernandez-Peralta, A.M. (1994) Assignment of human satellite 1 DNA as revealed by fluorescent in situ hybridization with oligonucleotides. Hum. Genet., 93, 125-128.
36. Prosser, J. Frommer, M., Paul, C. and Vincent, P.C. (1986) Sequence relationships of three human satellite DNAs. J. Mol. Biol., 187, 145-155.
37. Grady, D., Ratliff, R., Robinson, D., McCanlies, E., Meyne, J. and Moyzis, R.K. (1992) Highly conserved repetitive DNA sequences are present at human centromeres. Proc. Natl Acad. Sci. USA, 89, 1695-1699.
38. Frommer, M., Prosser, J., Tkachuk, D., Reisner, A.M. and Vincent, P.C. (1982) Simple repeated sequences in human satellite DNA. Nucleic Acids Res., 10, 547-563.
39. Kipling, D., Mitchell, A., Masumoto, H., Wilson, H., Nicol, L. and Cooke, H. (1995) CENPB binds a novel centromeric sequence in the Asian mouse Mus caroli. Mol. Cell. Biol., 15, 4009-4020.
40. Solomon, M., Strauss, F. and Varshavsky, A. (1986) A mammalian high mobility group protein recognizes any stretch of six A-T base pairs in duplex DNA. Proc. Natl Acad. Sci. USA, 83, 1276-1280.
41. Spitzner, J.R. and Muller, M.T. (1988) A consensus sequence for cleavage by vertebrate DNA topoisomerase II. Nucleic Acids Res., 16, 5533-5556.
42. Jeffreys, A.J., Wilson, V. and Thein, S.L. (1985) Hypervariable 'minisatellite' regions in human DNA. Nature, 314, 67-73.
43. Nakamura, Y., Leppert, M., O' Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoto, E., Hoff, M., Kumlin, E. and White, R. (1987) Variable number of tandem repeat (VNTR) markers for human gene mapping. Science, 235, 1616-1622.
44. Smit, A.F.A. (1996) The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev., 6, 743-748.
45. Smit, A.F.A. and Green, P. Repeat Masker (http://ftp.genome.washington. edu/RM/Repeat Masker.html ).
46. Calabretta, B., Robberson, D.L., Barrera-Saldana, H.A., Lambrou, T.P. and Saunders, G.F. (1982) Genome instability in a region of human DNA enriched in Alu repeat sequences. Nature, 296, 219-225.
47. Korenberg, J.R. and Rykowski, M.C. (1988) Human genome organization: Alu, LINEs and the molecular structure of metaphase chromosome bands. Cell, 53, 391-400.
48. Sullivan, K.F., Hechenberger, M. and Masri, K. (1994) Human CENPA contains a histone H3 related histone fold domain that is required for targeting to the human centromere. J. Cell Biol., 127, 581-592.
49. Wilson, R., Anscough, R., Baynes, C. Berks, M. Bonfield, J., Burton, J., Connell, M., Copsey, T., Cooper, J. et al. (1994) 2.2 Mb of contiguous nucleotide sequence from chromosome III of C.elegans. Nature, 368, 32-38.
50. Stoler, S., Keth, K.C., Cumick, K.E. and Fitzgerald-Hayes, M. (1995) A mutation in CSE4, an essential gene encoding a novel chromatin-associated protein in yeast, causes chromosome nondisjunction and cell-cycle arrest at mitosis. Genes Dev., 9, 573-586.
51. Palmer, D.K. and Margolis, R.L. (1985) Kinetochore components recognized by human autoantibodies are present on mononucleosomes. Mol. Cell. Biol., 5, 173-186.
52. Palmer, D.K., O'Day, K., Wener, M.H., Andrews, B.S. and Margolis, R.L. (1987) A 17-kD centromere protein (CENPA) copurifies with nucleosome core particles and with histones. J. Cell Biol., 104, 805-815.
53. Johns, E.W. (1982) The HMG Chromosomal Proteins. Academic Press, New York.
54. Grosschedl, R., Giese, K. and Pagel, J. (1994) HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. Trends Genet., 10, 94-100.
55. Levinger, L. and Varshavsky, A. (1982) Protein D1 preferentially binds (A+T)-rich satellite DNA. Proc. Natl Acad. Sci. USA, 79, 7152-7156.
56. Disney, J., Johnson, K., Magnuson, N., Sylvester, S. and Reeves, R. (1989) High mobility group protein HMGI localizes to G/Q- and C-hands of human and mouse chromosomes. J. Cell Biol., 109, 1975-1982.
57. Straus, F. and Varshavsky, A. (1984) A protein binds to satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome. Cell, 37, 889-901.
58. Earnshaw, W.C. and Heck, M. (1985) Localization of topoisomerase II in mitotic chromosomes. J. Cell Biol., 100, 1716-1725.
59. Earnshaw, W.C., Halligan, B., Cooke, C.A., Heck, M. and Liu, L. (1985) Topoisomerase II is a structural component of mitotic chromosome scaffolds. J. Cell Biol., 100, 1706-1715.
60. Gasser, S. and Laemmli, U. (1986) The organization of chromatin loops: characterization of a scaffold attachment site. EMBO J., 5, 511-518.
61. Roca, J. (1995) The mechanisms of DNA topoisomerases. Trends Biochem. Sci., 20, 156-160.
62. Berger, J., Gamblin, S., Harrison, S. and Wang, J. (1996) Structure and mechanism of DNA topoisomerase II. Nature, 379, 225-232.
63. Rattner, J.B., Hendzel, M.J., Sommer Furbee, C., Muller, M.T. and Bazett-Jones, D.P. (1996) Topoisomerase IIα is associated with the mammalian centromere in a cell cycle- and species-specific manner and is required for proper centromere/kinetochore structure. J. Cell Biol., 134, 1097-1107.
64. Sumner, A. (1996) The distribution of topoisomerase II on mammalian chromosomes. Chromosome Res., 4, 4-5.
65. Strissel, P.L., Espinosa, R. III, Rowley, J.D. and Swift, H. (1996) Scaffold attatchment regions in centromere-associated DNA. Chromosoma, 105, 122-133.
66. Rattner, J.B. (1991) The structure of the mammalian centromere. BioEssays, 13, 51-56.
67. Schulman, I. and Bloom, K.S. (1991) Centromeres: an integrated protein:DNA complex required for chromosome movement. Annu. Rev. Cell Biol., 7, 311-336.
68. Alfenito, M.R. and Birchler, J.A. (1993) Molecular characterization of a maize B chromosome centric sequence. Genetics, 135, 589-597.
69. Clarke, L., Baum, M., Marschall, I.G., Ngan, V.K. and Steiner, N.C. (1993) Structure and function of Schizosaccharomyces pombe centromeres. Cold Spring Harbor Symp. Quant. Biol., 58, 687-695.
70. Tyler-Smith, C. and Willard, H.F. (1993) Mammalian chromosome structure. Curr. Opin. Genet. Dev., 3, 390-397.
71. Brown, K.E., Barnett, M.A., Burgtorf, C., Shaw, P., Buckle, V.J. and Brown, W.R. (1994) Dissecting the centromere of the human Y chromosome with cloned telomeric DNA. Hum. Mol. Genet., 3, 1227-1237.
72. Sun, X., Wahlstrom, J. and Karpen, G. (1997) Molecular structure of a functional Drosophila centromere. Cell, 91, 1007-1019.
73. Behrens, F., Claussen, U., Iyer, L.M., Green, E.D., Horsthemke, B., Williamson, R., Huxley, C. and Coutelle, D. (1997) Isolation of DNA from the centromere of human chromosome 7 by microdissection. Chromosome Res., 5, 215-220.
74. Greig, G.M. and Willard, H.F. (1992) Beta-satellite DNA: characterization and localization of two subfamilies from the distal and proximal short arms of the human acrocentric chromosomes. Genomics, 12, 573-580.
75. Moyzis, R.K., Tomey, D.C., Meyne, J., Buckingham, J.M., Wu, J.-R., Burks, C., Sirotkin, K.M. and Goad, W.B. (1989) The distribution of interspersed repetitive DNA sequences in the human genome. Genomics, 4, 273-289.
76. Zhang, J. and Madden, T.L. (1997) PowerBLAST: a new network BLAST application for interactive and automated sequences analysis and annotation. Genome Res., 7, 649-656.
77. Australian National Genome Information Service (ANGIS) (http://mell. angis.org.au/).
78. Genetics Computer Group (1994) Program Manual for the Wisconsin Package, Version 8.