Sequence organization and functional annotation of human centromeres

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 68, Issue , 2003, Pages 141-149

  Rudd, M K ^a,b   Schueler, M G ^b,c   Willard, H F ^a  

^a DUKE UNIVERSITY   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL CHROMOSOME; CENTROMERE; CHROMOSOME 10; CHROMOSOME 17; CHROMOSOME SEGREGATION; CONFERENCE PAPER; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENETIC ORGANIZATION; GENETIC REGULATION; HETEROCHROMATIN; HUMAN; MITOSIS SPINDLE; PRIORITY JOURNAL; ARTICLE; CELL FUNCTION; HUMAN ARTIFICIAL CHROMOSOME; HUMAN CELL; HUMAN GENOME; X CHROMOSOME;

EID: 3242728393     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2003.68.141     Document Type: Conference Paper

References (78)

1. Alexandrov I., Kazakov A., Tumeneva I., Shepelev V., and Yurov Y. 2001. Alpha-satellite DNA of primates: Old and new families. Chromosoma 110: 253.
2. Ando S., Yang H., Nozaki N., Okazaki T., and Yoda K. 2002. CENP-A, -B, and -C chromatin complex that contains the I-type alpha-satellite array constitutes the prekinetochore in HeLa cells. Mol. Cell. Biol. 22: 2229.
3. Bailey J.A., Yavor A.M., Viggiano L., Misceo D., Horvath J.E., Archidiacono N., Schwartz S., Rocchi M., and Eichler E.E. 2002. Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70: 83.
4. Blower M.D., Sullivan B.A., and Karpen G.H. 2002. Conserved organization of centromeric chromatin in flies and humans. Dev. Cell 2: 319.
5. Brun M., Ruault M., Ventura M., Roizes G., and DeSario A. 2003. Juxtacentromeric region of chromosome 21: A boundary between centromeric heterochromatin and euchromatic chromosome arms. Gene 312: 41.
6. Choo K.H. 2001. Domain organization at the centromere and neocentromere. Dev. Cell 1: 165.
7. Clarke L. 1998. Centromeres: Proteins, protein complexes, and repeated domains at centromeres of simple eukaryotes. Curr. Opin. Genet. Dev. 8: 212.
8. Cleveland D.W., Mao Y., and Sullivan K.F. 2003. Centromeres and kinetochores: From epigenetics to mitotic checkpoint signaling. Cell 112: 407.
9. Collins F.S., Green E.D., Guttmacher A.E., and Guyer M.S. 2003. A vision for the future of genomics research. Nature 422: 835.
10. Copenhaver G.P., Nickel K., Kuromori T., Benito M.I., Kaul S., Lin X., Bevan M., Murphy G., Harris B., Parnell L.D., McCombie W.R., Martienssen R.A., Marra M., and Preuss D. 1999. Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286: 2468.
11. Dong F., Miller J.T., Jackson S.A., Wang G.L., Ronald P.C., and Jiang J. 1998. Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc. Natl. Acad. Sci. 95: 8135.
12. Dunham I., Shimizu N., Roe B.A., Chissoe S., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A., Bagguley C., Bailey J., Barlow K., Bates K.N., Beasley O., Bird C.P., Blakey S., Bridgeman A.M., Buck D., Burgess J., Burrill W.D., and O'Brien K.P., et al. 1999. The DNA sequence of human chromosome 22. Nature 402: 489.
13. Durfy S.J. and Willard H.F. 1989. Patterns of intra- and interarray sequence variation in alpha satellite from the human X chromosome: Evidence for short range homogenization of tandemly repeated DNA sequences. Genomics 5: 810.
14. Ebersole T.A., Ross A., Clark E., McGill N., Schindelhauer D., Cooke H., and Grimes B. 2000. Mammalian artificial chromosome formation from circular alphoid input DNA does not require telomere repeats. Hum. Mol. Genet. 9: 1623.
15. Eichler E.E. and Sankoff D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science 301: 793.
16. Grimes B.R., Rhoades A.A., and Willard H.F. 2002. Alpha-satellite DNA and vector composition influence rates of human artificial chromosome formation. Mol. Ther. 5: 798.
17. Grimes B.R., Schindelhauer D., McGill N.I., Ross A., Ebersole T.A., and Cooke H.J. 2001. Stable gene expression from a mammalian artificial chromosome. EMBO Rep. 2: 910.
18. Guy J., Hearn T., Crosier M., Mudge J., Viggiano L., Koczan D., Thiesen H.J., Bailey J.A., Horvath J.E., Eichler E.E., Earthrowl M.E., Deloukas P., French L., Rogers J., Bentley D., and Jackson M.S. 2003. Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p. Genome Res. 13: 159.
19. Haaf T., Warburton P.E., and Willard H.F. 1992. Integration of human alpha satellite DNA into simian chromosomes: Centromere protein binding and disruption of normal chromosome segregation. Cell 70: 681.
20. 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 microchromosomes. Nat. Genet. 15: 345.
21. Henikoff S. 2002. Near the edge of a chromosome's "black hole". Trends Genet. 18: 165.
22. Henikoff S., Ahmad K., and Malik H.S. 2001. The centromere paradox: Stable inheritance with rapidly evolving DNA. Science 293: 1098.
23. Henning K.A., Novotny E.A., Compton S.T., Guan X.Y., Liu P.P., and Ashlock M.A. 1999. Human artificial chromosomes generated by modification of a yeast artificial chromosome containing both human alpha satellite and single-copy DNA sequences. Proc. Natl. Acad. Sci. 96: 592.
24. Higgins A.W., Schueler M.G., and Willard H.F. 1999. Chromosome engineering: Generation of mono- and dicentric isochromosomes in a somatic cell hybrid system. Chromosoma 108: 256.
25. Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., and Ali J., et al. 2003. The DNA sequence of human chromosome 7. Nature 424: 157.
26. Horvath J.E., Bailey J.A., Locke D.P., and Eichler E.E. 2001. Lessons from the human genome: Transitions between euchromatin and heterochromatin. Hum. Mol. Genet. 10: 2215.
27. Horvath J.E., Viggiano L., Loftus B.J., Adams M.D., Archidiacono N., Rocchi M., and Eichler E.E. 2000. Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11. Hum. Mol. Genet. 9: 113.
28. Ikeno M., Inagaki H., Nagata K., Morita M., Ichinose H., and Okazaki T. 2002. Generation of human artificial chromosomes expressing naturally controlled guanosine triphosphate cyclohydrolase I gene. Genes Cells 7: 1021.
29. 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. Nat. Biotechnol. 16: 431.
30. Inoue K. and Lupski J.R. 2002. Molecular mechanisms for genomic disorders. Annu. Rev. Genomics Hum. Genet. 3: 199.
31. Kniola B., O'Toole E., McIntosh J.R., Mellone B., Allshire R., Mengarelli S., Hultenby K., and Ekwall K. 2001. The domain structure of centromeres is conserved from fission yeast to humans. Mol. Biol. Cell 12: 2767.
32. Kouprina N., Ebersole T., Koriabine M., Pak E., Rogozin I. B., Katoh M., Oshimura M., Ogi K., Peredelchuk M., Solomon G., Brown W., Barrett J. C., and Larionov V. 2003. Cloning of human centromeres by transformation-associated recombination in yeast and generation of functional human artificial chromosomes. Nucleic Acids Res. 31: 922.
33. Lamb J.C. and Birchler J.A. 2003. The role of DNA sequence in centromere formation. Genome Biol. 4: 214.
34. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., and Naylor J., et al. (International Human Genome Sequencing Consortium). 2001. Initial sequencing and analysis of the human genome. Nature 409: 860.
35. Larin Z. and Mejia J.E. 2002. Advances in human artificial chromosome technology. Trends Genet. 18: 313.
36. Laurent A.M., Li M., Sherman S., Roizes G., and Buard J. 2003. Recombination across the centromere of disjoined and nondisjoined chromosome 21. Hum. Mol. Genet. 12: 2229.
37. Lee C., Critcher R., Zhang J.G., Mills W., and Farr C.J. 2000. Distribution of gamma satellite DNA on the human X and Y chromosomes suggests that it is not required for mitotic centromere function. Chromosoma 109: 381.
38. Lee C., Wevrick R., Fisher R.B., Ferguson-Smith M.A., and Lin C.C. 1997. Human centromeric DNAs. Hum. Genet. 100: 291.
39. Mahtani M.M. and Willard H.F. 1998. Physical and genetic mapping of the human X chromosome centromere: Repression of recombination. Genome Res. 8: 100.
40. Manuelidis L. 1976. Repeating restriction fragments of human DNA. Nucleic Acids Res. 3: 3063.
41. Manuelidis L. and Wu J.C. 1978. Homology between human and simian repeated DNA. Nature 276: 92.
42. Mejia J.E., Willmott A., Levy E., Earnshaw W.C., and Larin Z. 2001. Functional complementation of a genetic deficiency with human artificial chromosomes. Am. J. Hum. Genet. 69: 315.
43. Mills W., Critcher R., Lee C., and Farr C. J. 1999. Generation of an approximately 2.4 Mb human X centromere-based minichromosome by targeted telomere-associated chromosome fragmentation in DT40. Hum. Mol. Genet. 8: 751.
44. Murray A.W. and Szostak J.W. 1983. Construction of artificial chromosomes in yeast. Nature 305: 189.
45. Nagaki K., Song J., Stupar R.M., Parokonny A.S., Yuan Q., Ouyang S., Liu J., Hsiao J., Jones K.M., Dawe R.K., Buell C.R., and Jiang J. 2003. Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163: 759.
46. Nicklas R. B. 1971. Mitosis. Adv. Cell Biol. 2: 225.
47. Ohzeki J., Nakano M., Okada T., and Masumoto H. 2002. CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA. J. Cell Biol. 159: 765.
48. Rieder C.L. and Salmon E.D. 1998. The vertebrate cell kinetochore and its roles during mitosis. Trends Cell Biol. 8: 310.
49. Rozen S., Skaletsky H., Marszalek J.D., Minx P.J., Cordum H.S., Waterston R.H., Wilson R.K., and Page D.C. 2003. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423: 873.
50. Rudd M.K., Mays R.W., Schwartz S., and Willard H.F. 2003. Human artificial chromosomes with alpha satellite-based de novo centromeres show increased frequency of nondisjunction and anaphase lag. Mol. Cell. Biol. 23: 7689.
51. Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S., Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskem D., and Zhang Q., et al. 2003. Human chromosome 7: DNA sequence and biology. Science 300: 767.
52. Schindelhauer D. and Schwarz T. 2002. Evidence for a fast, intrachromosomal conversion mechanism from mapping of nucleotide variants within a homogeneous alpha-satellite DNA array. Genome Res. 12: 1815.
53. Schueler M.G., Higgins A.W., Rudd M.K., Gustashaw K., and Willard H.F. 2001. Genomic and genetic definition of a functional human centromere. Science 294: 109.
54. Skaletsky H., Kuroda-Kawaguchi T., Minx P.J., Cordum H.S., Hillier L., Brown L.G., Repping S., Pyntikova T., Ali J., Bieri T., Chinwalla A., Delehaunty A., Delehaunty K., Du H., Fewell G., Fulton L., Fulton R., Graves T., Hou S.F., Latrielle P., Leonard S., Mardis E., Maupin R., McPherson J., and Miner T., et al. 2003. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825.
55. Smith G.P. 1976. Evolution of repeated DNA sequences by unequal crossover. Science 191: 528.
56. Sonnhammer E.L. and Durbin R. 1995. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: 1.
57. Spence J.M., Critcher R., Ebersole T.A., Valdivia M.M., Earnshaw W.C., Fukagawa T., and Farr C.J. 2002. Co-localization of centromere activity, proteins and topoisomerase II within a subdomain of the major human X alpha-satellite array. EMBO J. 21: 5269.
58. Stankiewicz P. and Lupski J.R. 2002. Molecular-evolutionary mechanisms for genomic disorders. Curr. Opin. Genet. Dev. 12: 312.
59. Sullivan B.A. and Willard H.F. 1998. Stable dicentric X chromsomes with two functional centromeres. Nat. Genet. 20: 227.
60. Sullivan B.A., Blower M.D., and Karpen G.H. 2001. Determining centromere identity: Cyclical stories and forking paths. Nat. Rev. Genet. 2: 584.
61. Sun X., Le H.D., Wahlstrom J.M., and Karpen G.H. 2003. Sequence analysis of a functional Drosophila centromere. Genome Res. 13: 182.
62. Tanaka T.U. 2002. Bi-orienting chromosomes on the mitotic spindle. Curr. Opin. Cell Biol. 14: 365.
63. Trask B.J. 2002. Human cytogenetics: 46 chromosomes, 46 years and counting. Nat. Rev. Genet. 3: 769.
64. Tyler-Smith C., Oakey R.J., Larin Z., Fisher R.B., Crocker M., Affara N.A., Ferguson-Smith M.A., Muenke M., Zuffardi O., Jobling M.A. 1993. Localization of DNA sequences required for human centromere function through an analysis of rearranged Y chromosomes. Nat. Genet. 5: 368.
65. Vafa O. and Sullivan K.F. 1997. Chromatin containing CENP-A and alpha satellite DNA is a major component of the inner kinetochore plate. Curr. Biol. 7: 897.
66. Venter 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., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., and Nelson C., et al. 2001. The sequence of the human genome. Science 291: 1304.
67. Warburton P.E. and Willard H.F. 1990. Genomic analysis of sequence variation in tandemly repeated DNA. Evidence for localized homogenous sequence domains within arrays of alpha-satellite DNA. J. Mol. Biol. 216: 3.
68. -. 1995. Interhomologue sequence variation of alpha satellite DNA from human chromosome 17: Evidence for concerted evolution along haplotypic lineages. J. Mol. Evol. 41: 1006.
69. -. 1996. Evolution of centromeric alpha satellite DNA: Molecular organization within and between human and primate chromosomes. In Human genome evolution (ed. S.T. Jackson and G. Dover), p. 121. BIOS Scientific Publishers, Oxford, United Kingdom.
70. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., Antonarakis S.E., Attwood J., Baertsch R., Bailey J., Barlow K., Beck S., Berry E., Birren B., Bloom T., Bork P., Botcherby M., Bray N., Brent M.R., Brown D.G., and Brown S.D., et al. (Mouse Genome Sequencing Consortium). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520.
71. Waye J.S. and Willard H.F. 1986. Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: Evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome. Mol. Cell. Biol. 6: 3156.
72. Wevrick R. and Willard H.F. 1989. Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: High frequency array-length polymorphism and meiotic stability. Proc. Natl. Acad. Sci. 86: 9394.
73. -. 1991. Physical map of the centromeric region of human chromosome 7: Relationship between two distinct alpha satellite arrays. Nucleic Acids Res. 19: 2295.
74. Wevrick R., Earnshaw W.C., Howard-Peebles P.N., and Willard H.F. 1990. Partial deletion of alpha satellite DNA associated with reduced amounts of the centromere protein CENP-B in a mitotically stable human chromosome rearrangement. Mol. Cell. Biol. 10: 6374.
75. Willard H.F. 1998. Centromeres: The missing link in the development of human artificial chromosomes. Curr. Opin. Genet. Dev. 8: 219.
76. Willard H.F. and Waye J.S. 1987. Hierarchical order in chromosome-specific human alpha satellite DNA. Trends Genet. 3: 192.
77. Willard H.F., Smith K.D., and Sutherland J. 1983. Isolation and characterization of a major tandem repeat family from the human X chromosome. Nucleic Acids Res. 11: 2017.
78. Zhong C.X., Marshall J.B., Topp C., Mroczek R., Kato A., Nagaki K., Birchler J. A., Jiang J., and Dawe R.K. 2002. Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14: 2825.