Hominoid lineage specific amplification of low-copy repeats on 22q11.2 (LCR22s) associated with velo-cardio-facial/digeorge syndrome

Human Molecular Genetics

Volumn 16, Issue 21, 2007, Pages 2560-2571

  Babcock, Melanie ^a   Yatsenko, Svetlana ^b   Hopkins, Janet ^c   Brenton, Matthew ^c   Cao, Qing ^d   De Jong, Pieter ^d   Stankiewicz, Pawel ^b   Lupski, James R ^b   Sikela, James M ^c   Morrow, Bernice E ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CHROMOSOME 22Q; DIGEORGE SYNDROME; DNA HYBRIDIZATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; GENE DUPLICATION; GENE LOCATION; GENE MAPPING; GENETIC ASSOCIATION; GENETIC RECOMBINATION; GENETIC SCREENING; GENETIC VARIABILITY; GORILLA; HUMAN; HUMAN CELL; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RISK FACTOR; SPECIES DIFFERENCE; TELOMERE;

ALU ELEMENTS; ANIMALS; CHROMOSOMES, HUMAN, PAIR 22; DIGEORGE SYNDROME; EVOLUTION, MOLECULAR; EXONS; GENE DOSAGE; GENE DUPLICATION; GORILLA GORILLA; HOMINIDAE; HUMANS; PSEUDOGENES; REPETITIVE SEQUENCES, NUCLEIC ACID; TELOMERE;

HOMINOIDEA; PRIMATES;

EID: 35448977374     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddm197     Document Type: Article

References (41)

1. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W. et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921.
2. Stankiewicz, P. and Lupski, J.R. (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet., 18, 74-82.
3. Stankiewicz, P., Shaw, C.J., Dapper, J.D., Wakui, K., Shaffer, L.G., Withers, M., Elizondo, L., Park, S.S. and Lupski, J.R. (2003) Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am. J Hum. Genet., 72, 1101-1116.
4. Babcock, M., Pavlicek, A., Spiteri, E., Kashork, C.D., Ioshikhes, I., Shaffer, L.G., Jurka, J. and Morrow, B.E. (2003) Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. Genome Res., 13, 2519-2532.
5. Hurles, M.E. and Jobling, M.A. (2003) A singular chromosome. Nat Genet., 34, 246-247.
6. Lupski, J.R. (1998) Genomic disorders: Structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet., 14, 417-422.
7. Stankiewicz, P. and Lupski, J.R. (2002) Molecular-evolutionary mechanisms for genomic disorders. Curr. Opin. Genet. Dev., 12 312-319.
8. Potocki, L., Chen, K.S., Park, S.S., Osterholm, D.E., Withers, M.A., Kimonis, V., Summers, A.M., Meschino, W.S., Anyane-Yeboa, K., Kashork, C.D. et al. (2000) Molecular mechanism for duplication 17p 11.2- the homologous recombination reciprocal of the Smith-Magenis microdeletion. Nat. Genet., 24, 84-87.
9. Hassed, S.J., Hopcus-Niccum, D., Zhang, L., Li, S. and Mulvihill, J.J. (2004) A new genomic duplication syndrome complementary to the velocardiofacial (22q11 deletion) syndrome. Clin. Genet., 65 400-404.
10. Yobb, T.M., Somerville, M.J., Willatt, L., Firth, H.V., Harrison, K., MacKenzie, J., Gallo, N., Morrow, B.E., Shaffer, L.G., Babcock, M. et al. (2005) Microduplication and triplication of 22q11.2: A highly variable syndrome. Am. J. Hum. Genet., 76, 865-876.
11. de France, H.F., Beemer, F.A. and Ippel, P.F. (1984) Duplication in chromosome 15q in a boy with the Prader-Willi syndrome; further cytogenetic confusion. Clin. Genet., 26, 379-382.
12. Pettigrew, A.L., Gollin, S.M., Greenberg, F., Riccardi, V.M. and Ledbetter, D.H. (1987) Duplication of proximal 15q as a cause of Prader-Willi syndrome. Am. J. Med. Genet., 28, 791-802.
13. Shaikh, T.H., Kurahashi, H., Saitta, S.C., O'Hare, A.M., Hu, P., Roe, B.A., Driscoll, D.A., McDonald-McGinn, D.M., Zackai, E.H., Budarf, M.L. et al. (2000) Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: Genomic organization and deletion endpoint analysis. Hum. Mol. Genet., 9, 489-501.
14. Edelmann, L., Pandita, R.K., Spiteri, E., Funke, B., Goldberg, R., Palanisamy, N., Chaganti, R.S., Magenis, E., Shprintzen, R.J. and Morrow, B.E. (1999) A common molecular basis for rearrangement disorders on chromosome 22q11. Hum. Mol. Genet., 8, 1157-1167.
15. Schwer, H., Liu, L.Q., Zhou, L., Little, M.T., Pan, Z., Hetherington, C.J. and Zhang, D.E. (2000) Cloning and characterization of a novel human ubiquitin-specific protease, a homologue of murine UBP43 (Usp18). Genomics, 65, 44-52.
16. Heisterkamp, N., Stam, K., Groffen, J., de Klein, A. and Grosveld, G. (1985) Structural organization of the bcr gene and its role in the Ph-translocation. Nature, 315, 758-761.
17. Heisterkamp, N., Rajpert-De Meyts, E., Uribe, L., Forman, H.J. and Groffen, J. (1991) Identification of a human gamma-glutamyl cleaving enzyme related to, but distinct from, gamma-glutamyl transpeptidase. Proc. Natl Acad. Sci. USA, 88, 6303-6307.
18. Morris, C., Courtay, C.; Geurts van Kessel, A., ten Hoeve, J., Heisterkamp, N. and Groffen, J. (1993) Localization of a gamma-glutamyl-transferase-related gene family on chromosome 22. Hum. Genet., 91, 31-36.
19. Rajpert-De Meyts, E., Heisterkamp, N. and Groffien, J. (1988) Cloning and nucleotide sequence of human gamma-glutamyl transpeptidase. Proc. Natl Acad. Sci. USA, 85, 8840-8844.
20. Collins, J.E., Mungall, A.J., Badcock, K.L., Fay, J.M. and Dunham, I. (1997) The organization of the gamma-glutamyl transferase genes and other low copy repeats in human chromosome 22q11. Genome Res., 7, 522-531.
21. Edelmann, L., Pandita, R.K. and Morrow, B.E. (1999) Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. Am. J. Hum. Genet., 64, 1076-1086.
22. Bailey, J.A., Church, D.M., Ventura, M., Rocchi, M. and Eichler, E.E. (2004) Analysis of segmental duplications and genome assembly in the mouse. Genome Res., 14, 789-801.
23. Fortna, A., Kim, Y., MacLaren, E., Marshall, K., Hahn, G., Meltesen, L., Brenton, M., Hink, R. Burgers, S., Hernandez-Boussard, T. et al. (2004) Lineage-specific gene duplication and loss in human and great ape evolution. PLOS Biol., 2, E207.
24. Puech, A., Saint-Jore, B., Funke, B., Gilbert, D.J., Sirotkin, H., Copeland, N.G., Jenkins, N.A., Kucherlapati, R., Morrow, B. and Skoultchi, A.I. (1997) Comparative mapping of the human 22q11 chromosomal region and the orthologous region in mice reveals complex changes in gene organization. Proc. Natl Acad. Sci. USA, 94, 14608-14613.
25. Pavlicek, A., House, R., Gentles, A.J., Jurka, J. and Morrow, B.E. (2005) Traffic of genetic information between segmental duplications flanking, the typical 22q11.2 deletion in velo-cardio-facial syndrome/ DiGeorge syndrome. Genome Res., 15, 1487-1495.
26. Stankiewicz, P., Shaw, C.J., Withers, Y., Inoue, K. and Lupski, J.R. (2004) Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res., 14, 2209-2220.
27. Antonell, A., de Luis, O., Domingo-Roura, X. and Perez-Jurado, L.A. (2005) Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23. Genome Res., 15, 1179-1188.
28. Christian, S.L., Fantes, J.A., Mewborn, S.K., Huang, B. and Ledbetter, D.H. (1999) Large genomic duplicons map to sites of instability in the Prader-Willi/Angelman syndrome chromosome region (15q11-q13). Hum. Mol. Genet., 8, 1025-1037.
29. Valero, M.C., de Luis, O., Cruces, J. and Perez Jurado, L.A. (2000) Fine-scale comparative mapping of the human 7q11.23 region and the orthologous region on mouse chromosome 5G: The low-copy repeats that flank the Williams-Beuren syndrome deletion arose at breakpoint sites of an evolutionary inversion(s). Genomics, 69, 1-13.
30. 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.
31. Park, S.S., Stankiewicz, P., Bi, W., Shaw, C., Lehoczky, J., Dewar, K., Birren, B. and Lupski, J.R. (2002) Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs. Genome Res. 12, 729-738.
32. Ou, Z., Jarmuz, M., Sparagana, S.P., Michaud, J., Décarie, J.C., Yatsenko, S.A., Nowakowska, B., Furman, P., Shaw, C.A., Shaffer, L.G. et al. (2006) Evidence for involvement of TRE-2 (USP6) oncogene, low-copy repeat and acrocentric heterochromatin in two families with chromosomal translocations. Hum. Genet., 120, 227-237.
33. Johnson, M.E., Cheng, Z., Morrison, V.A., Scherer, S., Ventura, M., Gibbs, R.A., Green, E.D. and Eichler, E.E. (2006) Recurrent duplication-driven transposition of DNA during hominoid evolution. Proc. Natl Acad. Sci. USA, 103, 17626-17631.
34. Bailey, J.A., Liu, G. and Eichler, E.E. (2003) An A1u transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet., 73, 823-834.
35. Courseaux, A., Richard, F., Grosgeorge, J., Ortola, C., Viale, A., Turc-Carel, C., Dutrillaux, B., Gaudray, P. and Nahon, J.L. (2003) Segmental duplications in euchromatic regions of human chromosome 5: A source of evolutionary instability and transcriptional innovation. Genome Res., 13, 369-381.
36. Linardopoulou, E.V., Williams, E.M., Fan, Y., Friedman, C., Young, J.M. and Trask, B.J. (2005) Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature, 437, 94-100.
37. 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.
38. Trask, B.J., Friedman, C., Martin-Gallardo, A., Rowen, L., Akinbami, C., Blankenship, J., Collins, C., Giorgi, D., Iadonato, S., Johnson, F. 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.
39. Richardson, C., Moynahan, M.E. and Jasin, M. (1998) Double-strand break repair by interchromosomal recombination: Suppression of chromosomal translocations. Genes Dev., 12, 3831-3842.
40. Eichler, E.E., Archidiacono, N. and Rocchi, M. (1999) CAGGG repeats and the pericentromeric duplication of the hominoid genome. Genome Res. 9, 1048-1058.
41. Shaffer, L.G., Kennedy, G.M., Spikes, A.S. and Lupski, J.R. (1997) Diagnosis of CMT1A duplications and HNPP deletions by interphase FISH: implications for testing in the cytogenetics laboratory. Am. J. Med. Genet., 69, 325-331.