Genomic structure and evolution of the ancestral chromosome fusion site in 2q13-2q14.1 and paralogous regions on other human chromosomes

Genome Research

Volumn 12, Issue 11, 2002, Pages 1651-1662

  Fan, Yuxin ^a   Linardopoulou, Elena ^a   Friedman, Cynthia ^a   Williams, Eleanor ^a   Trask, Barbara J ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TELOMERASE;

ANIMAL CELL; ARTICLE; CENTROMERE; CHROMOSOME 22Q; CHROMOSOME 2Q; CHROMOSOME 9P; CHROMOSOME 9Q; CHROMOSOME REARRANGEMENT; CHROMOSOME STRUCTURE; CONTROLLED STUDY; FEMALE; GENE DUPLICATION; GENE SEQUENCE; GENE STRUCTURE; HUMAN; HUMAN CELL; HUMAN CHROMOSOME; HUMAN GENOME; MALE; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PRIMATE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

ANIMALS; BASE COMPOSITION; BASE PAIRING; CHROMOSOMES, HUMAN, PAIR 2; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENOME, HUMAN; GORILLA GORILLA; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INTERSPERSED REPETITIVE SEQUENCES; MALE; PAN TROGLODYTES; POLYMERASE CHAIN REACTION; PONGO PYGMAEUS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSLOCATION, GENETIC; TWO-HYBRID SYSTEM TECHNIQUES;

ANIMALIA; PRIMATES;

EID: 0036851314     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.337602     Document Type: Article

References (45)

1. Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J., and Eichler, E.E. 2001. Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res. 11: 1005-1017.
2. 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: 83-100.
3. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Rapp, B.A., and Wheeler, D.L. 2002. GenBank. Nucleic Acids Res. 30: 17-20.
4. Bernardi, G. 1995. The human genome: Organization and evolutionary history. Annu. Rev. Genet. 29: 445-476.
5. Bertoni, L., Attolini, C., Tessera, L., Mucciolo, E., and Giulotto, E. 1994. Telomeric and nontelomeric (TTAGGG)n sequences in gene amplification and chromosome stability. Genomics 24: 53-62.
6. Boutouil, M., Fetni, R., Qu, J., Dallaire, L., Richer, C.L., and Lemieux, N. 1996. Fragile site and interstitial telomere repeat sequences at the fusion point of a de novo (Y;13) translocation. Hum. Genet. 98: 323-327.
7. Brand-Arpon, V., Rouquier, S., Massa, H., de Jong, P.J., Ferraz, C., Ioannou, P.A., Demaille, J.G., Trask, B.J., and Giorgi, D. 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.
8. Carroll, M.L., Roy-Engel, A.M., Nguyen, S.V., Salem, A.H., Vogel, E., Vincent, B., Myers, J., Ahmad, Z., Nguyen, L., Sammarco, M., et al. 2001. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J. Mol. Biol. 311: 17-40.
9. Chen, F.C. and Li, W.H. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68: 444-456.
10. Ciccodicola, A., D'Esposito, M., Esposito, T., Gianfrancesco, F., Migliaccio, C., Miano, M.G., Matarazzo, M.R., Vacca, M., Franze, A., Cuccurese, M., et al. 2000. Differentially regulated and evolved genes in the fully sequenced Xq/Yq pseudoautosomal region. Hum. Mol. Genet. 9: 395-401.
11. Desmaze, C., Alberti, C., Martins, L., Pottier, G., Sprung, C.N., Murnane, J.P., and Sabatier, L. 1999. The influence of interstitial telomeric sequences on chromosome instability in human cells. Cytogenet. Cell Genet. 86: 288-295.
12. 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.
13. Fan, Y., Newman, T., Linardopoulou, E., and Trask, B.J. 2002. Gene Content and Function of the Ancestral Chromosome Fusion Site in Human Chromosome 2q13-2q14.1 and Paralogous Regions. Genome Res. (this issue).
14. Glusman, G. and Lancet, D. 2000. GESTALT: A workbench for automatic integration and visualization of large-scale genomic sequence analyses. Bioinformatics 16: 482-483.
15. Hoglund, M., Mitelman, F., and Mandahl, N. 1995. A human 12p-derived cosmid hybridizing to subsets of human and chimpanzee telomeres. Cytogenet. Cell Genet. 70: 88-91.
16. Ijdo, J., Baldini, A., Ward, D.C., Reeders, S.T., and Wells, R.A. 1991. Origin of human chromosome 2: An ancestral telomere-telomere fusion. Proc. Natl. Acad. Sci. 88: 9051-9055.
17. Ijdo, J.W., Baldini, A., Wells, R.A., Ward, D.C., and Reeders, S.T. 1992. FRA2B is distinct from inverted telomere repeat arrays at 2q13. Genomics 12: 833-835.
18. Jauch, A., Wienberg, J., Stanyon, R., Arnold, N., Tofanelli, S., Ishida, T., and Cremer, T. 1992. Reconstruction of genomic rearrangements in great apes and gibbons by chromosome painting. Proc. Natl. Acad. Sci. 89: 8611-8615.
19. Jukes, T.H. and Cantor, C.R. 1969. Evolution of protein molecules. In Mammalian protein metabolism (eds. H.N. Munro and J.B. Allison), pp. 21-123. Academic Press, New York.
20. Kasai, F., Takahashi, E., Koyama, K., Terao, K., Suto, Y., Tokunaga, K., Nakamura, Y., and Hirai, M. 2000. Comparative FISH mapping of the ancestral fusion point of human chromosome 2. Chromosome Res. 8: 727-735.
21. Lese, C.M., Fantes, J.A., Riethman, H.C., and Ledbetter, D.H. 1999. Characterization of physical gap sizes at human telomeres. Genome Res. 9: 888-894.
22. Lukusa, T., Devriendt, K., Holvoet, M., and Fryns, J.P. 2000. Dicentric chromosome 9 due to tandem duplication of the 9p11-q13 region: Unusual chromosome 9 variant. Am. J. Med. Genet. 91: 192-197.
23. Mah, N., Stoehr, H., Schulz, H.L., White, K., and Weber, B.H. 2001. Identification of a novel retina-specific gene located in a subtelomeric region with polymorphic distribution among multiple human chromosomes. Biochim. Biophys. Acta 1522: 167-174.
24. Martin, C.L., Wong, A., Gross, A., Chung, J., Fantes, J.A., and Ledbetter, D.H. 2002. The evolutionary origin of human subtelomeric homologies-Or where the ends begin. Am. J. Hum. Genet. 70: 972-984.
25. Martin-Gallardo, A., Lamerdin, J., Sopapan, P., Friedman, C., Fertitta, A.L., Garcia, E., Carrano, A., Negorev, D., Macina, R.A., Trask, B.J., et al. 1995. Molecular analysis of a novel subtelomeric repeat with polymorphic chromosomal distribution. Cytogenet. Cell Genet. 71: 289-295.
26. Mefford, H. and Trask, B.J. 2002. The complex structure and dynamic evolution of human subtelomeres. Nat. Rev. Genet. 3: 91-102.
27. Mefford, H.C., Linardopoulou, E., Coil, D., van den Engh, G., and Trask, B.J. 2001. Comparative sequencing of a multicopy subtelomeric region containing olfactory receptor genes reveals multiple interactions between non-homologous chromosomes. Hum. Mol. Genet. 10: 2363-2372.
28. Mondello, C., Pirzio, L., Azzalin, C.M., and Giulotto, E. 2000. Instability of interstitial telomeric sequences in the human genome. Genomics 68: 111-117.
29. Musio, A. and Mariani, T. 1999. Distribution of interstitial telomere-related sequences in the human genome and their relationship with fragile sites. J. Environ. Pathol. Toxicol. Oncol. 18: 11-15.
30. Ning, Y., Rosenberg, M., Biesecker, L.G., and Ledbetter, D.H. 1996. Isolation of the human chromosome 22q telomere and its application to detection of cryptic chromosomal abnormalities. Hum. Genet. 97: 765-769.
31. Park, H.S., Nogami, M., Okumura, K., Hattori, M., Sakakia, Y., and Fujiyama, A. 2000. Newly identified repeat sequences, derived from human chromosome 21qter, are also localized in the subtelomeric region of particular chromosomes and 2q13, and are conserved in the chimpanzee genome. FEBS Lett. 475: 167-169.
32. Riethman, H.C., Xiang, Z., Paul, S., Morse, E., Hu, X.L., Flint, J., Chi, H.C., Grady, D.L., and Moyzis, R.K. 2001. Integration of telomere sequences with the draft human genome sequence. Nature 409: 948-951.
33. Roy-Engel, A.M., Carroll, M.L., Vogel, E., Garber, R.K., Nguyen, S.V., Salem, A.H., Batzer, M.A., and Deininger, P.L. 2001. Alu insertion polymorphisms for the study of human genomic diversity. Genetics 159: 279-290.
34. Samonte, R.V., Conte, R.A., Ramesh, K.H., and Verma, R.S. 1996. Molecular cytogenetic characterization of breakpoints involving pericentric inversions of human chromosome 9. Hum. Genet. 98: 576-580.
35. Simi, S., Attolini, C., and Giulotto, E. 1998. Intrachromosomal telomeric repeats and stabilization of truncated chromosomes in V79 Chinese hamster cells. Mutat. Res. 397: 229-233.
36. Slijepcevic, P., Xiao, Y., Dominguez, I., and Natarajan, A.T. 1996. Spontaneous and radiation-induced chromosomal breakage at interstitial telomeric sites. Chromosoma 104: 596-604.
37. Sutherland, G.R. and Mattel, J.F. 1987. Report of the committee on cytogenetic markers. Cytogenet. Cell Genet. 46: 316-324.
38. Trask, B. 1999. Fluorescence In Situ Hybridization. In Genome analysis: A laboratory manual (eds. B. Birren, E.D. Green, P. Hieter; S. Klapholz, R.M. Myers, H. Riethman, and J. Roskams), pp. 303-413. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
39. Trask, B.J., van den Engh, G., Christensen, M., Massa, H.F., Gray, J.W., and Van Dilla, M. 1991. Characterization of somatic cell hybrids by bivariate flow karyotyping and fluorescence in situ hybridization. Somat. Cell Mol. Genet. 17: 117-136.
40. Trask, B., Fertitta, A., Christensen, M., Youngblom, J., Bergmann, A., Copeland, A., de Jong, P., Mohrenweiser, H., Olsen, A., Carrano, A., et al. 1993. Fluorescence in situ hybridization mapping of human chromosome 19: Cytogenetic band location of 540 cosmids and 70 genes or DNA markers. Genomics 15: 133-145.
41. Wienberg, J., Stanyon, R., Jauch, A., and Cremer, T. 1992. Homologies in human and Macaca fuscata chromosomes revealed by in situ suppression hybridization with human chromosome specific DNA libraries. Chromosoma 101: 265-270.
42. Wienberg, J., Jauch, A., Ludecke, H.J., Senger, G., Horsthemke, B., Claussen, U., Cremer, T., Arnold, N., and Lengauer, C. 1994. The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary. Chromosome Res. 2: 405-410.
43. Williams, A.J. and Howell, R.T. 1977. A fragile secondary constriction on chromosome 2 in a severely mentally retarded patient. J. Ment. Defic. Res. 21: 227-239.
44. Yu, N., Zhao, Z., Fu, Y.X., Sambuughin, N., Ramsay, M., Jenkins, T., Leskinen, E., Patthy, L., Jorde, L.B., Kuromori, T., et al. 2001. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol. Biol. Evol. 18: 214-222.
45. Yunis, J.J. and Prakash, O. 1982. The origin of man: A chromosomal pictorial legacy. Science 215: 1525-1530.