Genome-wide detection and analysis of recent segmental duplications within mammalian organisms

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 68, Issue , 2003, Pages 115-124

  Bailey, J A ^a   Eichler, E E ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIRING; CONFERENCE PAPER; EVOLUTION; GENE DUPLICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME ANALYSIS; HUMAN GENOME; INTERSPERSED REPEAT; KARYOTYPE; MAMMAL; MOLECULAR CLONING; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; ARTICLE; CENTROMERE; CHROMOSOMAL INSTABILITY; CHROMOSOME STRUCTURE; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER MODEL; FLUORESCENCE IN SITU HYBRIDIZATION; GENOME; GENOME SIZE; GENOME-WIDE ASSOCIATION STUDY; HUMAN; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; PRIMATE; SEGMENTAL DUPLICATION; TELOMERE;

MAMMALIA;

GENOMIC DNA; REPETITIVE DNA;

EID: 3242708463     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2003.68.115     Document Type: Conference Paper

References (79)

1. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C., Rogers Y.H., Blazej R.G., Champe M., and Pfeiffer B.D., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185.
2. 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 break-points. Am. J. Hum. Genet. 65: 370.
3. Aparicio S., Chapman J., Stupka E., Putnam N., Chia J.M., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., Gelpke M.D., Roach J., Oh T., Ho I.Y., Wong M., Detter C., Verhoef F., Predki P., Tay A., Lucas S., Richardson P., Smith S.F., Clark M.S., Edwards Y.J., and Doggett N., et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301.
4. Bailey J.A., Liu G., and Eichler EE. 2003. An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73: 823.
5. 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.
6. Bailey J.A., Yavor A.M., Viggiano L., Misceo D., Horvath J.E., Archidiacono N., Schwartz S., Rocchi M., and Eichler E.E. 2002a. Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70: 83.
7. Bailey J.A., Gu Z., Clark R.A., Reinert K., Samonte R.V., Schwartz S., Adams M.D., Myers E.W., Li P.W., and Eichler E.E. 2002b. Recent segmental duplications in the human genome. Science 297: 1003.
8. 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.
9. Bridgland L., Footz T.K., Kardel M.D., Riazi M.A., and Mc Dermid H.E. 2003. Three duplicons form a novel chimeric transcription unit in the pericentromeric region of chromosome 22q11. Hum. Genet. 112: 57.
10. Chen K., Manian P., Koeuth T., Potocki L., Zhao Q., Chinault A., Lee C., and Lupski J. 1997. Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat. Genet. 17: 154.
11. 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.
12. Consortium (The C. elegans Sequencing Consortium). 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012.
13. Courseaux A. and Nahon J.L. 2001. Birth of two chimeric genes in the Hominidae lineage. Science 291: 1293.
14. Crosier M., Viggiano L., Guy J., Misceo D., Stones R., Wei W., Hearn T., Ventura M., Archidiacono N., Rocchi M., and Jackson M.S. 2002. Human paralogs of KIAA0187 were created through independent pericentromeric-directed and chromosome-specific duplication mechanisms. Genome Res. 12: 67.
15. Deininger P.L. and Schmid C.W. 1976. Thermal stability of human DNA and chimpanzee DNA heteroduplexes. Science 194: 846.
16. 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.
17. Eder A., Mario V., Ianigro M., Teti M., Rocchi M., and Archidiacono N. 2003. Chromosome 6 phylogeny in primates and centromere repositioning. Mol. Biol. Evol. 20: 1506.
18. Eichler E.E. 2001. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 17: 661.
19. 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.
20. Glusman G., Yanai I., Rubin I., and Lancet D. 2001. The complete human olfactory subgenome. Genome Res. 11: 685.
21. Graur D. and Li W.-H. 2000. Fundamentals of molecular evolution. Sinauer, Sunderland, Massachusetts.
22. Green P. 1997. Against a whole-genome shotgun. Genome Res. 7: 410.
23. Grewal P.K., van Geel M., Frants R.R., de Jong P., and Hewitt J.E. 1999. Recent amplification of the human FRG1 gene during primate evolution. Gene 227: 79.
24. Guy J., Spalluto C., McMurray A., Hearn T., Crosier M., Viggiano L., Miolla V., Archidiacono N., Rocchi M., Scott C., Lee P.A., Sulston J., Rogers J., Bentley D., and Jackson M.S. 2000. Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10q. Hum. Mol. Genet. 9: 2029.
25. 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.
26. Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.S., Toyoda A., Ishii K., Totoki Y., Choi D.K., Soeda E., Ohki M., Takagi T., Sakaki Y., Taudien S., Blechschmidt K., Polley A., Menzel U., Delabar J., Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., and Schillhabel M., et al. 2000. The DNA sequence of human chromosome 21. The chromosome 21 mapping and sequencing consortium. Nature 405: 311.
27. 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.
28. Horvath J., Schwartz S., and Eichler E. 2000. The mosaic structure of a 2p11 pericentromeric segment: A strategy for characterizing complex regions of the human genome. Genome Res. 10: 839.
29. 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.
30. Horvath J.E., Gulden C.L., Bailey J.A., Yohn C., McPherson J.D., Prescott A., Roe B.A., De Jong P.J., Ventura M., Misceo D., Archidiacono N., Zhao S., Schwartz S., Rocchi M., and Eichler E.E. 2003. Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. Mol. Biol. Evol. 20: 1463.
31. Jackson M.S., Rocchi M., Thompson G., Hearn T., Crosier M., Guy J., Kirk D., Mulligan L., Ricco A., Piccininni S., Marzella R., Viggiano L., and Archidiacono N. 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.
32. Ji Y., Eichler E.E., Schwartz S., and Nicholls R.D. 2000. Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res. 10: 597.
33. Johnson M.E., Viggiano L., Bailey J.A., Abdul-Rauf M., Goodwin G., Rocchi M., and Eichler E.E. 2001. Positive selection of a gene family during the emergence of humans and African apes. Nature 413: 514.
34. Kehrer-Sawatzki H., Schreiner B., Tanzer S., Platzer M., Muller S., and Hameister H. 2002. Molecular characterization of the pericentric inversion that causes differences between chimpanzee chromosome 19 and human chromosome 17. Am. J. Hum. Genet. 71: 375.
35. Kunkel H.G., Natvig J.B., and Joslin F.G. 1969. A "Lepore" type of hybrid gamma-globulin. Proc. Natl. Acad. Sci. 62: 144.
36. 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.
37. Loftus B.J., Kim U.J., Sneddon V.P., Kalush F., Brandon R., Fuhrmann J., Mason T., Crosby M.L., Barnstead M., Cronin L., Deslattes Mays A., Cao Y., Xu R.X., Kang H.L., Mitchell S., Eichler E.E., Harris P.C., Venter J.C., and Adams M.D. 1999. Genome duplications and other features in 12 Mbp of DNA sequence from human chromosome 16p and 16q. Genomics 60: 295.
38. Lopez-Correa C., Dorschner M., Brems H., Lazaro C., Clementi M., Upadhyaya M., Dooijes D., Moog U., Kehrer-Sawatzki H., Fryns J.P., Rutkowski J.L., Marynen P., Stephens K., and Legius E. 2001. Recombination hotspot in NF1 microdeletion patients. Hum. Mol. Genet. 10: 1387.
39. Luijten M., Wang Y., Smith B.T., Westerveld A., Smink L.J., Dunham I., Roe B.A., and Hulsebos T.J. 2000. Mechanism of spreading of the highly related neurofibromatosis type 1 (NF1) pseudogenes on chromosomes 2, 14 and 22. Eur. J. Hum. Genet. 8: 209.
40. Lupski J.R. 1998. Genomic disorders: Structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14: 417.
41. Mazzarella R. and Schlessinger D. 1997. Duplication and distribution of repetitive elements and non-unique regions in the human genome. Gene 205: 29.
42. -. 1998. Pathological consequences of sequence duplications in the human genome. Genome Res. 8: 1007.
43. McPherson J.D., Marra M., Hillier L., Waterston R.H., Chinwalla A., Wallis J., Sekhon M., Wylie K., Mardis E.R., Wilson R.K., Fulton R., Kucaba T.A., Wagner-McPherson C., Barbazuk W.B., Gregory S.G., Humphray S.J., French L., Evans R.S., Bethel G., Whittaker A., Holden J.L., McCann O.T., Dunham A., Soderlund C., and Scott C.E., et al. (International Human Genome Mapping Consortium). 2001. A physical map of the human genome. Nature 409: 934.
44. Mefford H.C. and Trask B.J. 2002. The complex structure and dynamic evolution of human subtelomeres. Nat. Rev. Genet. 3: 91.
45. 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.
46. Monfouilloux S., Avet-Loiseau H., Amarger V., Balazs I., Pourcel C., and Vergnaud G. 1998. Recent human-specific spreading of a subtelomeric domain. Genomics 51: 165.
47. Morrow B., Edelmann L., Ferreira J., Pandita R., Carlson C., Procter J., Jackson M., Wilson D., Goldberg R., Shprintzen R., and Kucherlapati R. 1997. A duplication of chromosome 22q11 is the basis for the common deletion that occurs in velo-cardiofacial syndrome patients. Am. J. Hum. Genet. (suppl.) 61: A7.
48. Muller H.J. 1936. Bar duplication. Science 83: 528.
49. Murphy W.J., Stanyon R., and O'Brien S.J. 2001. Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biol. 2: REVIEWS0005.
50. Nei M. 1968. The frequency distribution of lethal chromosomes in finite populations. Proc. Natl. Acad. Sci. 60: 517.
51. Nickerson E., Gibbs R.A., and Nelson D.L. 1999. Sequence analysis of the breakpoints of a pericentric inversion distinguishing the human and chimpanzee chromosomes 12. Am. J. Hum. Genet. 65: A291.
52. Ohno S. 1972. So much "junk" DNA in our genome. Brookhaven Symp. Biol. 23: 366.
53. Ohno S., Wolf U., and Atkin N. 1968. Evolution from fish to mammals by gene duplication. Hereditas 59: 169.
54. Park H.S., Nogami M., Okumura K., Hattori M., Sakaki 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.
55. Paulding C.A., Ruvolo M., and Haber D.A. 2003. The Tre2 (USP6) oncogene is a hominoid-specific gene. Proc. Natl. Acad. Sci. 100: 2507.
56. Pentao L., Wise C., Chinault A., Patel P., and Lupski J. 1992. Charcot-Marie-Tooth type 1A duplication appears to arise from recombination at repeat sequences flanking the 1.5 Mb monomer unit. Nat. Genet. 2: 292.
57. Phillips J.A., III, Vik T.A., Scott A.F., Young K.E., Kazazian H.H., Jr., Smith K.D., Fairbanks V.F., and Koenig H.M. 1980. Unequal crossing-over: A common basis of single alpha-globin genes in Asians and American blacks with hemoglobin-H disease. Blood 55: 1066.
58. 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.
59. Reiter L.T., Hastings P.J., Nelis E., De Jonghe P., Van Broeckhoven C., and Lupski J.R. 1998. Human meiotic recombination products revealed by sequencing a hotspot for homologous strand exchange in multiple HNPP deletion patients. Am. J. Hum. Genet. 62: 1023.
60. Reiter L., Murakami T., Koeuth T., Pentao L., Muzny D., Gibbs R., and Lupski J. 1996. A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nat. Genet. 12: 288.
61. 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.
62. Rouquier S., Taviaux S., Trask B.J., Brand-Arpon V., van den Engh G., Demaille J., and Giorgi D. 1998. Distribution of olfactory receptor genes in the human genome. Nat. Genet. 18: 243.
63. Ruault M., Trichet V., Gimenez S., Boyle S., Gardiner K., Rolland M., Roizes G., and De Sario A. 1999. Juxta-centromeric region of human chromosome 21 is enriched for pseudogenes and gene fragments. Gene 239: 55.
64. Schmid C.W. and Deininger P.L. 1975. Sequence organization of the human genome. Cell 6: 345.
65. 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., and Emanuel B.S. 2000. Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: Genomic organization and deletion endpoint analysis. Hum. Mol. Genet. 9: 489.
66. Stankiewicz P. and Lupski J.R. 2002. Genome architecture, rearrangements and genomic disorders. Trends Genet. 18: 74.
67. Stankiewicz P., Park S.S., Inoue K., and Lupski J.R. 2001. The evolutionary chromosome translocation 4;19 in Gorilla gorilla is associated with microduplication of the chromosome fragment syntenic to sequences surrounding the human proximal CMT1A-REP. Genome Res. 11: 1205.
68. Trask B.J., Massa H., Brand-Arpon V., Chan K., Friedman C., Nguyen O.T., Eichler E.E., van den Engh G., Rouquier S., Shizuya H., and Giorgi D. 1998a. Large multi-chromosomal duplications encompass many members of the olfactory receptor gene family in the human genome. Hum Mol. Genet. 7: 2007.
69. Trask B., Friedman C., Martin-Gallardo A., Rowen L., Akinbami C., Blankenship J., Collins C., Giorgi D., Iadonato S., Johnson F., Kuo W., Massa H., Morrish T., Naylor S., Nguyen O., Rouquier S., Smith T., Wong D., Younglbom J., and van den Engh G. 1998b. 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.
70. van Geel M., Eichler E.E., Beck A.F., Shan Z., Haaf T., van Der Maarel S.M., Frants R.R., and de Jong P.J. 2002. A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomes. Am. J. Hum. Genet. 70: 269.
71. van Geel M., van Deutekom J.C., van Staalduinen A., Lemmers R.J., Dickson M.C., Hofker M.H., Padberg G.W., Hewitt J.E., de Jong P.J., and Frants R.R. 2000. Identification of a novel beta-tubulin subfamily with one member (TUBB4Q) located near the telomere of chromosome region 4q35. Cytogenet. Cell Genet. 88: 316.
72. 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.
73. 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. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520.
74. Weber J.L. and Myers E.W. 1997. Human whole-genome shotgun sequencing. Genome Res. 7: 401.
75. Wienberg J., Stanyon R., Nash W.G., O'Brien P.C., Yang F., O'Brien S.J., and Ferguson-Smith M.A. 1997. Conservation of human vs. feline genome organization revealed by reciprocal chromosome painting. Cytogenet. Cell Genet. 77: 211.
76. Wong A.C., Shkolny D., Dorman A., Willingham D., Roe B.A., and McDermid H.E. 1999. Two novel human RAB genes with near identical sequence each map to a telomere-associated region: The subtelomeric region of 22q13.3 and the ancestral telomere band 2q13. Genomics 59: 326.
77. Yunis J.J. 1976. High resolution of human chromosomes. Science 191: 1268.
78. Yunis J.J. and Prakash O. 1982. The origin of man: A chromosomal pictorial legacy. Science 215: 1525.
79. 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. 94: 11461.