CAGGG repeats and the pericentromeric duplication of the hominoid genome

Genome Research

Volumn 9, Issue 11, 1999, Pages 1048-1058

  Eichler, Evan E ^a   Archidiacono, Nicoletta ^b   Rocchi, Mariano ^b  

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

^b Instituto di Genetica   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; GUANINE;

ARTICLE; CENTROMERE; CHROMOSOME; CONTROLLED STUDY; EVOLUTION; EXON; GENE DUPLICATION; HUMAN; INTRON; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PRIMATE; PRIORITY JOURNAL;

ANIMALS; BASE SEQUENCE; CENTROMERE; CHROMOSOMES, HUMAN, PAIR 1; CHROMOSOMES, HUMAN, PAIR 10; CHROMOSOMES, HUMAN, PAIR 14; CHROMOSOMES, HUMAN, PAIR 15; CHROMOSOMES, HUMAN, PAIR 16; CHROMOSOMES, HUMAN, PAIR 2; CHROMOSOMES, HUMAN, PAIR 22; CHROMOSOMES, HUMAN, PAIR 9; EVOLUTION, MOLECULAR; GENE DUPLICATION; HOMINIDAE; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; X CHROMOSOME;

CERCOPITHECOIDEA; HOMINOIDEA; MAMMALIA; MYA; PRIMATES;

EID: 0032750691     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.9.11.1048     Document Type: Article

References (40)

1. Amann, J., M. Valentine, V.J. Kidd, and J.M. Lahti. 1996. Localization of chil-related helicase genes to human chromosome regions 12p11 and 12p13: Similarity between parts of these genes and conserved human telomeric-associated DNA. Genomics 32: 260-265.
2. Borden, P., R. Jaenichen, and H. Zachau. 1990 Structural features of transposed human Vk genes and implications for the mechanism of their transpositions. Nucleic Acids Res. 18: 2101-2107.
3. Brand-Arpon, V., S. Rouquier, H. Massa, P.J. de Jong, C. Ferraz, P.A. Ioannou, J.G. Demaille, B.J. Trask, and D. Giorgi. 1999. A genomic region encompassing a cluster of olfactory receptor genes and a myosin light chain kinase (MYLK) gene is duplicated on human chromosome regions 3q13-q21 and 3p13. Genomics 56: 98-110.
4. Charlesworth, B., P. Sniegowski, and W. Stephan. 1994. The evolutionary dynamics of repetitive DNA in eukaryotcs. Nature 371: 215-220.
5. Chute, I., Y. Le, T. Ashley, and M.J. Dobson. 1997. The telomere-associated DNA from human chromosome 20p contains a pseudotelomere structure and shares sequences with the subtelomeric regions of 4q and 18p. Genomics 46: 51-60.
6. Dempsey, L.A., H. Sun, L.A. Hanakahi, and N. Maizels. 1999. G4 DNA binding by LR1 and its subunits, nucleolin and hnRNP D, A role for G-G pairing in immunoglobulin switch recombination. J. Biol. Chem. 274: 1066-1071.
7. Dover, G. 1982. Molecular drive: A cohesive mode of species evolution. Nature 299: 111-117.
8. Dunnick, W., G. Hertz, L. Scappino, and C. Gritzmacher. 1993. DNA sequences at immunoglobulin switch region recombination sites. Nucleic Acids Res. 21: 364-372.
9. Eichler, E.E. 1998. Masquerading repeats: Paralogous pitfalls of the Human genome. Genome Res. 8: 758-762.
10. Eichler, E.E., F. Lu, Y. Shen, R. Antonacci, V. Jurecic, N.A. Doggett, R.K. Moyzis, A. Baldini, R.A. Gibbs, and D.L. Nelson. 1996. Duplication of a gene-rich cluster between 16p11.1 and Xq28: A novel pericentromeric-directed mechanism for paralogous genome evolution. Hum. Mol. Genet. 5: 899-912.
11. Eichler, E.E., M.L. Budarf, M. Rocchi, L.L. Deaven, N.A. Doggett, A. Baldini, D.L. Nelson, and H.W. Mohrenweiser. 1997. Interchromosomal duplications of the adrenoleukodystrophy locus: A phenomenon of pericentromeric plasticity. Hum. Mol. Genet. 6: 991-1002.
12. Frantz, J.D. and W. Gilbert. 1995. A novel yeast gene product, G4p1, with a specific affinity for quadruplex nucleic acids. J. Biol. Chem. 270: 20692-20697.
13. Grewal, P.K., M. van Geel, R.R. Frants, P. de Jong, and J.E. Hewitt. 1999. Recent amplification of the human FRG1 gene during primate evolution. Gene 227: 79-88.
14. Iyer, G., R. Krahe, L. Goodwin, N. Doggett, M. Siciliano, V. Funanage, and R. Proujansky. 1996. Identification of a testis-expressed creatine transporter gene at 16p11.2 and confirmation of the X-linked locus to Xq28. Genomics 34: 143-146.
15. Jackson, M.S., M. Rocchi, G. Thompson, T. Hearn, M. Crosier, J. Guy, D. Kirk, L. Mulligan, A. Ricco, S. Piccininni 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.
16. 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.
17. Li, W. 1997. Molecular evolution. Sinauer Associates, Sunderland, MA.
18. Lichter, P., C.J. Tang, K. Call, G. Hermanson, G.A. Evans, D. Housman, and D.C. Ward. 1990. High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247: 64-69.
19. Liu, Z., A. Lee, and W. Gilbert. 1995. Gene disruption of a G4-DNA-dependent nuclease in yeast leads to cellular senescence and telomere shortening. Proc. Natl. Acad. Sci. 92: 6002-6006.
20. Lundin, L. 1993. Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16: 1-19.
21. Mills, F.C., J.S. Brooker, and R.D. Camerini-Otero. 1990. Sequences of human immunoglobulin switch regions: Implications for recombination and transcription. Nucleic Acids Res. 18: 7305-7316.
22. Miyamoto, M., J. Slightom, and M. Goodman. 1987. Phylogenetic relations of humans and apes from DNA sequences in the psi eta-globin region. Science 238: 369-373.
23. Miyata, T. and T. Yasunaga. 1981. Rapidly evolving mouse alpha-globin-related pseudo gene and its evolutionary history. Proc. Natl. Acad. Sci. 78: 450-453.
24. Ohno, S. 1970. Evolution by gene duplication. Springer Verlag, Berlin/Heidelberg/New York, Germany/NY.
25. _. 1993. Patterns in genome evolution. Curr. Opin. Genet. Dev. 3: 911-914.
26. Parsons, J. 1995. Miropeats: Graphical DNA sequence comparisons. Comput. Appl. Biosci. 11: 615-619.
27. Regnier, V., M. Meddeb, G. Lecointre, F. Richard, A. Duverger, V.C. Nguyen, B. Dutrillaux, A. Bernheim, and G. Danglot. 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.
28. Ritchie, R.J., M.G. Mattei, and M. Lalande. 1998. A large polymorphic repeat in the pericentromeric region of human chromosome 15q contains three partial gene duplications. Hum. Mol. Genet. 7: 1253-1260.
29. Sandoval, N., D. Bauer, V. Brenner, J. Coy, B. Drescher, P. Kioschis, B. Korn, G. Nyakatura, A. Poustka, K. Reichwald et al. 1996. The genomic organization of a human creatine transporter (CRTR) gene located in Xq28. Genomics 35: 383-385.
30. Sen, D. and W. Gilbert. 1988. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications in meiosis. Nature 334: 364-366.
31. Smith, G.P. 1976. Evolution of repeated DNA sequences by unequal crossover. Science 191: 528-535.
32. Snapper, C.M., K.B. Marcu and P. Zelazowski. 1997. The immunoglobulin class switch: Beyond "accessibility." Immunity 6: 217-223.
33. Takahata, N. and Y. Satta. 1997. Evolution of the primate lineage leading to modern humans: Phylogenetic and demographic inferences from DNA sequences. Proc. Natl. Acad. Sci. 94: 4811-4815.
34. Thompson, J.D., D.G. Higgins, and T.J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
35. Trask, B., C. Friedman, A. Martin-Gallardo, L. Rowen, C. Akinbami, J. Blankenship, C. Collins, D. Giorgi, S. Iadonato, F. Johnson et al. 1998. Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes. Hum. Mol. Genet. 7: 13-26.
36. Trask, B.J., H. Massa, V. Brand-Arpon, K. Chan, C. Friedman, O.T. Nguyen, E.E. Eichler, G. van den Engh, S. Rouquier, H. Shizuya et al. 1998b. Large multi-chromosomal duplications encompass many members of the olfactory receptor gene family in the human genome. Hum. Mol. Genet. 7: 2007-2020.
37. Williamson, J.R. 1994. G-quartet structures in telomeric DNA. Annu. Rev. Biophys. Biomol. Struct. 23: 703-730.
38. Wolfe, K. and D. Shields. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
39. Wong, Z., N. Royle, and A. Jeffreys. 1990. A novel human DNA polymorphism resulting from transfer of DNA from chromosome 6 to chromosome 16. Genomics 7: 222-234.
40. Zimonjic, D., M. Kelley, J. Rubin, S. Aaronson, and N. Popescu. 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. 94: 11461-11465.