Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11

Human Molecular Genetics

Volumn 9, Issue 1, 2000, Pages 113-123

  Horvath, Juliann E ^c   Viggiano, Luigi ^a   Loftus, Brendan J ^b   Adams, Mark D ^b   Archidiacono, Nicoletta ^a   Rocchi, Mariano ^b   Eichler, Evan E ^c  

^a Dipto di Anat Patologica e Genet   (Italy)

^b J CRAIG VENTER INSTITUTE   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

SATELLITE DNA;

ARTICLE; CENTROMERE; CHROMOSOME 16P; CHROMOSOME 4Q; CHROMOSOME XQ; DNA SEQUENCE; DNA TRANSPOSITION; EVOLUTION; GENE DUPLICATION; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

PAN TROGLODYTES; PRIMATES;

EID: 0034018260     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/9.1.113     Document Type: Article

References (53)

1. Jackson, M.S., See, C.G., Mulligan, L.M. and Lauffart, B.F. (1996) A 9.75-Mb map across the centromere of human chromosome 10. Genomics, 33, 258-270.
2. Lee, C., Wevrick, R., Fisher, R.B., Ferguson-Smith, M.A. and Lin, C.C. (1997) Human centromeric DNAs. Hum. Genet., 100, 291-304.
3. Willard, H.F. and Waye, J.S. (1987) Chromosome-specific subsets of human alpha satellite DNA: analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat. J. Mol. Evol., 25, 207-214.
4. Alexandrov, I.A., Medvedev, L.I., Mashkova, T.D., Kisselev, L.L., Romanova, L.Y. and Yurov, Y.B. (1993) Definition of a new alpha satellite suprachromosomal family charactcrized by monomeric organization. Nucleic Acids Res., 21, 2209-2215.
5. Willard, H.F. (1991) Evolution of alpha satellite. Curr. Opin. Genet. Dev., 1, 509-514.
6. Jackson, M.S., Rocchi, M., Thompson, G., Hearn, T., Crosier, M., Guy, J., Kirk, D., Mulligan, L., Ricco, A., Piccininni, S. et al. (1999) Sequences flanking the centromere of human chromosome 10 are a complex patchwork of arm-specific sequences, stable duplications, and unstable sequences with homologies to telomeric and other centromeric locations. Hum. Mol. Genet., 8, 205-215.
7. Collins, F.S., Patrinos, A., Jordan, E., Chakravarti, A., Gesteland, R. and Walters, L. (1998) New goals for the U.S. Human genome project: 1998-2003. Science, 282, 682-689.
8. Arnold, N., Stanyon, R., Jauch, A., O'Brien, P. and Wienberg, J. (1996) Identification of complex chromosome rearrangements in the gibbon by fluorescent in situ hybridization (FISH) of a human chromosome 2q specific microlibrary, yeast artificial chromosomes, and reciprocal chromosome painting. Cytogenet. Cell Genet., 74, 80-85.
9. Zachau, H. (1993) The immunoglobulin κ locus - or - what has been learned from looking closely at one-tenth of a percent of the human genome. Gene. 135, 167-173.
10. Eichler, E.E., Lu, F., Shen, Y., Antonacci, R., Jurecic, V., Doggett, N.A., Moyzis, R.K., Baldini, A., Gibbs, R.A. and Nelson, D.L. (1996) Duplication of a gene-rich cluster between 16p1 1.1 and Xq28: a novel pericentromeric-directed mechanism for paralogous genome evolution. Hum. Mol. Genet., 5, 899-912.
11. Eichler, E.E., Budarf, M.L., Rocchi, M., Deaven, L.L., Doggett, N.A., Baldini, A., Nelson, D.L. and Mohrenweiser, H.W. (1997) Interchromosomal duplications of the adrenoleukodystrophy locus: a phenomenon of pericentromeric plasticity. Hum. Mol. Genet., 6, 991-1002.
12. Regnier, V., Meddeb, M., Lecointre, G., Richard, F., Duverger, A., Nguyen, V.C., Dutrillaux, B., Bernheim, A. and Danglot, G. (1997) Emergence and scattering of multiple neurofibromatosis (NF1)-related sequences during hominoid evolution suggest a process of pericentromeric interchromosomal transposition. Hum. Mol. Genet., 6, 9-16.
13. Zimonjic, D., Kelley, M., Rubin, J., Aaronson, S. and Popescu, N. (1997) Fluorescence in situ hybridization analysis of keratinocyte growth factor gene amplification and dispersion in evolution of great apes and humans. Proc. Natl Acad. Sci. USA, 94, 11461-11465.
14. Ritchie, R.J., Mattei, M.G. and Lalande, M. (1998) A large polymorphic repeat in the pericentromeric region of human chromosome 15q contains three partial gene duplications. Hum. Mol. Genet., 7, 1253-1260.
15. Potier, M., Dutriaux, A., Orti, R., Groet, J., Gibelin, N., Karadima, G., Lutfalla, G., Lynn, A., Van Broeckhoven, C., Chakravarti, A. et al. (1998) Two sequence-ready contigs spanning the two copies of a 200-kb duplication on human 21q: partial sequence and polymorphisms. Genomics, 51, 417-426.
16. Amos-Landgraf, J.M., Ji, Y., Gottlieb, W., Depinet, T., Wandstrat, A.E., Cassidy, S.B., Driscoll, D.J., Rogan, P.K., Schwartz, S. and Nicholls, R.D. (1999) Chromosome breakage in the Prader-Willi and Angelman syndromes involves recombination between large, transcribed repeats at proximal and distal breakpoints. Am. J. Hum. Genet., 65, 370-386.
17. Christian, S.L., Fantes, J.A., Mewbornm S.K., Huang, B. and Ledbetter, D.H. (1999) Large genomic duplicons map to sites of instability in the Prader-Willi/Angelmann syndrome chromosome region (15q11-q13). Hum. Mol. Genet., 8, 1025-1037.
18. Reiter, L.T., Murakami, T., Koeuth, T., Gibbs, R.A. and Lupski, J.R. (1997) The human COX10 gene is disrupted during homologous recombination between the 24 kb proximal and distal CMT1A-REPs. Hum. Mol. Genet., 6, 1595-1603.
19. Greig, G.M., England, S.B., Bedford, H.M. and Willard, H.F. (1989) Chromosome-specific alpha satellite DNA from the centromere of human chromosome 16. Am. J. Hum. Genet., 45, 862-872.
20. Bailey, T. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 28-36.
21. Vissel, B. and Choo, K.H. (1987) Human alpha satellite DNA - consensus sequence and conserved regions. Nucleic Acids Res., 15, 6751-6752.
22. Gaff, C., du Sart, D., Kalitsis, P., Iannello, R., Nagy, A. and Choo, K.H. (1994) A novel nuclear protein binds centromeric alpha satellite DNA. Hum. Mol. Genet., 3, 711-716.
23. Sonnhammer, E. and Durbin, R. (1995) A dot matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene, 167, GC1-GC10.
24. Parsons, J. (1995) Miropeats: graphical DNA sequence comparisons. Comput. Appl. Biosci., 11, 615-619.
25. Warburton, D., Gersen, S., Yu, M., Jackson, C., Handelin, B. and Housman, D. (1990) Monochromosomal rodent-human hybrids from microcell fusion of human lymphoblastoid cells containing an inserted dominant selectable marker. Genomics, 6, 358-366.
26. Neil, D.L., Villasante, A., Fisher, R.B., Vetrie, D., Cox, B. and Tyler-Smith, C. (1990) Structural instability of human tandemly repeated DNA sequences cloned in yeast artificial chromosome vectors. Nucleic Acids Res., 18, 1421-1428.
27. Tyler-Smith, C. and Brown, W.R. (1987) Structure of the major block of alphoid satellite DNA on the human Y chromosome. J. Mol. Biol., 195, 457-470.
28. ISCN (1985) Report of the standing committee on human cytogenetic nomenclature. Birth Defects, 21, 1-117.
29. Li, W. (1997) Molecular Evolution. Sinauer Associates, Sunderland, MA.
30. Goodman, M. (1999) The genomic record of humankind's evolutionary roots. Am. J. Hum. Genet., 64, 31-39.
31. Smith, G.P. (1976) Evolution of repeated DNA sequences by unequal crossover. Science, 191, 528-535.
32. Wevrick, R., Willard, V. and Willard, H. (1992) Structure of DNA near long tandem arrays of alpha satellite DNA at the centromere of human chromosome 7. Genomics, 14, 912-913.
33. Mashkova, T., Oparina, N., Alexandrov, I., Zinovieva, O., Marusina, A., Yurov, Y., Lacroix, M.H. and Kisselev, L. (1998) Unequal cross-over is involved in human alpha satellite DNA rearrangements on a border of the satellite domain. FEBS Lett., 441, 451-457.
34. Haaf, T. and Willard, H. (1997) Chromosome-specific alpha-satellite DNA from the centromere of chimpanzee chromosome 4. Chromosoma, 106, 226-232.
35. Archidiacono, N., Antonacci, R., Marzella, R., Finelli, P., Lonoce, A. and Rocchi, M. (1995) Comparative mapping of human alphoid sequences in great apes using fluorescence in situ hybridization. Genomics, 25, 477-484.
36. Romanova, L.Y., Deriagin, G.V., Mashkova, T.D., Tumeneva, I.G., Mushegian, A.R., Kisselev, L.L. and Alexandrov, I.A. (1996) Evidence for selection in evolution of alpha satellite DNA: the central role of CENP-B/pJ alpha binding region. J. Mol. Biol., 261, 334-340.
37. Borden, P., Jaenichen, R. and Zachau, H. (1990) Structural features of transposed human Vκ genes and implications for the mechanism of their transpositions. Nucleic Acids Res., 18, 2101-2107.
38. Eichler, E.E., Archidiacono, N. and Rocchi, M. (1999) CAGGG repeals and the pericentromeric duplication of the hominoid genome. Genome Res., 9, 1048-1058.
39. Zimmer, F., Hameister, H., Schek, H. and Zachau, H. (1990) Transposition of human immunoglobulin V kappa genes within the same chromo-some and the mechanism of their amplification. EMBO J., 9, 1535-1542.
40. Warburton, P. and Willard, H. (1996) Evolution of centromeric alpha satellite DNA: molecular organization within and between human and primate chromosomes. In Jackson, M., Strachan, T. and Dover, G. (eds), Human Genome Evolution. BIOS Scientific, Guildford, UK, pp. 121-145.
41. Durfy, S.J. and Willard, H.F. (1990) Concerted evolution of primate alpha satellite DNA. Evidence for an ancestral sequence shared by gorilla and human X chromosome alpha satellite. J. Mol. Biol., 216, 555-566.
42. Baldini, A., Smith, D.I., Rocchi, M., Miller, O.J. and Miller, D.A. (1989) A human alphoid DNA clone from the EcoRI dimeric family: genomic and internal organization and chromosomal assignment. Genomics, 5, 822-828.
43. Hulsebos, T., Schonk, D., van Dalen, I., Coerwinkel-Driessen, M., Schepens, J., Ropers, H.H. and Wieringa, B. (1988) Isolation and characterization of alphoid DNA sequences specific for the pericentric regions of chromosomes 4, 5, 9, and 19. Cytogenet. Cell Genet., 47, 144-148.
44. Gravholt, C.H., Friedrich, U., Caprani, M. and Jorgensen, A.L. (1992) Breakpoints in Robertsonian translocations are localized to satellite III DNA by fluorescence in situ hybridization. Genomics, 14, 924-930.
45. Choo, K.H. (1990) Role of acrocentric cen-pter satellite DNA in Robertsonian translocation and chromosomal non-disjunction. Mol. Biol. Med., 7, 437-439.
46. Loftus, B., Kim, U., Sneddon, V., Kalush, F., Brandon, R., Fuhrmann, J., Mason, T., Crosby, M., Barnstead, M., Cronin, L. et al. (1999) Genome duplications and other features in 12 Mbp of DNA sequence from human chromosome 16p and 16q. Genomics, 60, 295-308.
47. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
48. Lichter, P., Tang, C.J., Call, K., Hermanson, G., Evans, G.A., Housman, D. and Ward, D.C. (1990) High-resolution mapping of human chromosome II by in situ hybridization with cosmid clones. Science, 247, 64-69.
49. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
50. Swofford, D.L. and Begle, D.P. (1993) PAUP: Phylogenetic Analysis Using Parsimony. Illinois Natural History Survey, Champaign, IL.
51. Kumar, S., Tamura, K. and Nei, M. (1993) MEGA: Molecular Evolutionary Genetic Analysis, version 1.0. Pennsylvania State University, University Park, PA.
52. Miyata, T. and Yasunaga, T. (1981) Rapidly evolving mouse alpha-globin-related pseudo gene and its evolutionary history. Proc. Natl Acad. Sci. USA, 78, 450-453.
53. Miyamoto, M., Slightom, J. and Goodman, M. (1987) Phylogenetic relations of humans and apes from DNA sequences in the psi eta-globin region. Science, 238, 369-373.