Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication

Genome Biology

Volumn 9, Issue 2, 2008, Pages

  Cardone, Maria Francescs ^a   Jiang, Zhaoshi ^b,c   D'Addabbo, Pietro ^a   Archidiacono, Nicoletta ^a   Rocchi, Mariano ^a   Eichler, Evan E ^b,c   Ventura, Mario ^a  

^a UNIVERSITY OF BARI   (Italy)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; APE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHIMPANZEE; CHROMOSOME 17Q; CHROMOSOME DUPLICATION; CHROMOSOME MAP; CHROMOSOME REARRANGEMENT; CHROMOSOME SIZE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA POLYMORPHISM; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CONVERSION; GENE DELETION; GENE MAPPING; GENE SEQUENCE; GENETIC ORGANIZATION; GENOMIC INSTABILITY; GORILLA; HUMAN; HUMAN CELL; KARYOTYPE EVOLUTION; MACACA; MOLECULAR EVOLUTION; MOLECULAR MECHANICS; MONKEY; NONHUMAN; NUCLEOTIDE SEQUENCE; PAN TROGLODYTES; PARACENTRIC CHROMOSOME INVERSION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SYNTENY; ANIMAL; CAT; CHROMOSOME 17; CHROMOSOME ABERRATION; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; HAPLORHINI; KARYOTYPING;

BACTERIA (MICROORGANISMS); CERCOPITHECIDAE; GORILLA GORILLA; HOMINIDAE; HOMINOIDEA; PAN; PLATYRRHINI;

ANIMALS; CATS; CHROMOSOME ABERRATIONS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, HUMAN, PAIR 17; EVOLUTION, MOLECULAR; HAPLORHINI; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; SEQUENCE ANALYSIS, DNA;

EID: 43549099991     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-2-r28     Document Type: Article

References (56)

1. Müller S Wienberg J "Bar-coding" primate chromosomes: molecular cytogenetic screening for the ancestral hominoid karyotype. Hum Genet 2001, 109:85-94 10.1007/s004390100535 11479739
2. Murphy WJ Eizirik E Johnson WE Zhang YP Ryder OA O'Brien SJ Molecular phylogenetics and the origins of placental mammals. Nature 2001, 409:614-618 10.1038/35054550 11214319
3. Murphy WJ Pevzner PA O'Brien SJ Mammalian phylogenomics comes of age. Trends Genet 2004, 20:631-639 10.1016/j.tig.2004.09.005 15522459
4. Murphy WJ Stanyon R O'Brien SJ Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biol 2001, 2 reviews0005.1 0005.8 138942 11423011 10.1186/gb-2001-2-6-reviews0005
5. Richard F Lombard M Dutrillaux B Reconstruction of the ancestral karyotype of eutherian mammals. Chromosome Res 2003, 11:605-618 10.1023/ A:1024957002755 14516069
6. Wienberg J The evolution of eutherian chromosomes. Curr Opin Genet Dev 2004, 14:657-666 10.1016/j.gde.2004.10.001 15531161
7. Yang F Alkalaeva EZ Perelman PL Pardini AT Harrison WR O'Brien PC Fu B Graphodatsky AS Ferguson-Smith MA Robinson TJ Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype. Proc Natl Acad Sci USA 2003, 100:1062-1066 298726 12552116 10.1073/pnas.0335540100
8. Carbone L Ventura M Tempesta S Rocchi M Archidiacono N Evolutionary history of chromosome 10 in primates. Chromosoma 2002, 111:267-272 10.1007/s00412-002-0205-5 12424526
9. Cardone MF Ventura M Tempesta S Rocchi M Archidiacono N Analysis of chromosome conservation in Lemur catta studied by chromosome paints and BAC/PAC probes. Chromosoma 2002, 111:348-356 10.1007/s00412-002-0215-3 12474064
10. Misceo D Cardone MF Carbone L D'Addabbo P de Jong PJ Rocchi M Archidiacono N Evolutionary history of chromosome 20. Mol Biol Evol 2005, 22:360-366 10.1093/molbev/msi021 15496555
11. Kehrer-Sawatzki H Schreiner B Tänzer S Platzer M Müller S Hameister H Molecular characterization of the pericentric inversion that causes differences between chimpanzee chromosome 19 and human chromosome 17. Am J Hum Genet 2002, 71:375-388 379169 12094327 10.1086/341963
12. Szamalek JM Goidts V Searle JB Cooper DN Hameister H Kehrer-Sawatzki H The chimpanzee-specific pericentric inversions that distinguish humans and chimpanzees have identical breakpoints in Pan troglodytes and Pan paniscus. Genomics 2006, 87:39-45 10.1016/j.ygeno.2005.09.003 16321504
13. Zody MC Garber M Adams DJ Sharpe T Harrow J Lupski JR Nicholson C Searle SM Wilming L Young SK Abouelleil A Allen NR Bi W Bloom T Borowsky ML Bugalter BE Butler J Chang JL Chen CK Cook A Corum B Cuomo CA de Jong PJ DeCaprio D Dewar K FitzGerald M Gilbert J Gibson R Gnerre S Goldstein S DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature 2006, 440:1045-1049 10.1038/nature04689 16625196
14. Bailey JA Yavor AM Viggiano L Misceo D Horvath JE Archidiacono N Schwartz S Rocchi M Eichler EE Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am J Hum Genet 2002, 70:83-100 419985 11731936 10.1086/338458
15. Dörr S Midro AT Färber C Giannakudis J Hansmann I Construction of a detailed physical and transcript map of the candidate region for Russell-Silver syndrome on chromosome 17q23-q24. Genomics 2001, 71:174-181 10.1006/geno.2000.6413 11161811
16. Eichler EE Johnson ME Alkan C Tuzun E Sahinalp C Misceo D Archidiacono N Rocchi M Divergent origins and concerted expansion of two segmental duplications on chromosome 16. J Hered 2001, 92:462-468 10.1093/jhered/ 92.6.462 11948212
17. Samonte RV Eichler EE Segmental duplications and the evolution of the primate genome. Nat Rev Genet 2002, 3:65-72 10.1038/nrg705 11823792
18. She X Jiang Z Clark RA Liu G Cheng Z Tuzun E Church DM Sutton G Halpern AL Eichler EE Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 2004, 431:927-930 10.1038/ nature03062 15496912
19. She X Liu G Ventura M Zhao S Misceo D Roberto R Cardone MF Rocchi M NISC Comparative Sequencing Program Green ED Archidiacano N Eichler EE A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res 2006, 16:576-583 1457043 16606706 10.1101/gr.4949406
20. Chen DC Saarela J Clark RA Miettinen T Chi A Eichler EE Peltonen L Palotie A Segmental duplications flank the multiple sclerosis locus on chromosome 17q. Genome Res 2004, 14:1483-1492 509257 15256512 10.1101/ gr.2340804
21. Lupski JR Genomic disorders: Structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 1998, 14:417-422 10.1016/S0168-9525(98)01555-8 9820031
22. Park SS Stankiewicz P Bi W Shaw C Lehoczky J Dewar K Birren B Lupski JR Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs. Genome Res 2002, 12:729-738 186597 11997339 10.1101/ gr.82802
23. Inoue K Dewar K Katsanis N Reiter LT Lander ES Devon KL Wyman DW Lupski JR Birren B The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes. Genome Res 2001, 11:1018-1033 311111 11381029 10.1101/gr.180401
24. Lupski JR de Oca-Luna RM Slaugenhaupt S Pentao L Guzzetta V Trask BJ Saucedo-Cardenas O Baker DF Killian JM Garcia CA Chakravarti A Patel PI DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 1991, 66:219-232 10.1016/0092-8674(91)90613-4 1677316
25. Potocki L Chen KS Koeuth T Killian J Iannaccone ST Shapira SK Kashork CD Spikes AS Shaffer LG Lupski JR DNA rearrangements on both homologues of chromosome 17 in a mildly delayed individual with a family history of autosomal dominant carpal tunnel syndrome. Am J Hum Genet 1999, 64:471-478 1377756 9973284 10.1086/302240
26. Potocki L Chen KS Park SS Osterholm DE Withers MA Kimonis V Summers AM Meschino WS Anyane-Yeboa K Kashork CD Shaffer LG Lupski JR Molecular mechanism for duplication 17p11.2- the homologous recombination reciprocal of the Smith-Magenis microdeletion. Nat Genet 2000, 24:84-87 10.1038/71743 10615134
27. Koolen DA Vissers LE Pfundt R de Leeuw N Knight SJ Regan R Kooy RF Reyniers E Romano C Fichera M Schinzel A Baumer A Anderlid BM Schoumans J Knoers NV van Kessel AG Sistermans EA Veltman JA Brunner HG de Vries BB A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat Genet 2006 ,38:999-1001 10.1038/ ng1853 16906164
28. Sharp AJ Hansen S Selzer RR Cheng Z Regan R Hurst JA Stewart H Price SM Blair E Hennekam RC Fitzpatrick CA Segraves R Richmond TA Guiver C Albertson DG Pinkel D Eis PS Schwartz S Knight SJ Eichler EE Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat Genet 2006, 38:1038-1042 10.1038/ ng1862 16906162
29. Shaw-Smith C Pittman AM Willatt L Martin H Rickman L Gribble S Curley R Cumming S Dunn C Kalaitzopoulos D Porter K Prigmore E Krepischi-Santos AC Varela MC Koiffmann CP Lees AJ Rosenberg C Firth HV de Silva R Carter NP Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability. Nat Genet 2006, 38:1032-1037 10.1038/ng1858 16906163
30. Mefford HC Clauin S Sharp AJ Moller RS Ullmann R Kapur R Pinkel D Cooper GM Ventura M Ropers HH Tommerup N Eichler EE Bellanne-Chantelot C Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy. Am J Hum Genet 2007, 81:1057-1069 10.1086/522591 17924346
31. Saarela J Schoenberg Fejzo M Chen D Finnilä S Parkkonen M Kuokkanen S Sobel E Tienari PJ Sumelahti ML Wikström J Elovaara I Koivisto K Pirttilä T Reunanen M Palotie A Peltonen L Fine mapping of a multiple sclerosis locus to 2.5 Mb on chromosome 17q22-q24. Hum Mol Genet 2002, 11:2257-2267 10.1093/hmg/11.19.2257 12217954
32. Barbouti A Stankiewicz P Nusbaum C Cuomo C Cook A Höglund M Johansson B Hagemeijer A Park SS Mitelman F Lupski JR Fioretos T The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. Am J Hum Genet 2004, 74:1-10 1181896 14666446 10.1086/380648
33. Armengol L Pujana MA Cheung J Scherer SW Estivill X Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum Mol Genet 2003, 12:2201-2208 10.1093/hmg/ddg223 12915466
34. Bailey JA Baertsch R Kent WJ Haussler D Eichler EE Hotspots of mammalian chromosomal evolution. Genome Biol 2004 5:R23 395782 15059256 10.1186/ gb-2004-5-4-r23
35. Bailey JA Church DM Ventura M Rocchi M Eichler EE Analysis of segmental duplications and genome assembly in the mouse. Genome Res 2004, 14:789-801 479105 15123579 10.1101/gr.2238404
36. Murphy WJ Larkin DM Everts-van der Wind A Bourque G Tesler G Auvil L Beever JE Chowdhary BP Galibert F Gatzke L Hitte C Meyers SN Milan D Ostrander EA Pape G Parker HG Raudsepp T Rogatcheva MB Schook LB Skow LC Welge M Womack JE O'brien SJ Pevzner PA Lewin HA Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 2005, 309:613-617 10.1126/science.1111387 16040707
37. Stankiewicz P Park SS Inoue K Lupski JR 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 2001, 11:1205-1210 311135 11435402 10.1101/gr.181101
38. Ventura M Archidiacono N Rocchi M Centromere emergence in evolution. Genome Res 2001, 11:595-599 311056 11282974 10.1101/gr.152101
39. Ventura M Mudge JM Palumbo V Burn S Blennow E Pierluigi M Giorda R Zuffardi O Archidiacono N Jackson MS Rocchi M Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25. Genome Res 2003, 13:2059-2068 403685 12915487 10.1101/gr.1155103
40. Rhesus Macaque (Macaca mulatta) BAC Mapping Via PGI http://brl.bcm.tmc.edu/pgi/rhesus/
41. Bailey JA Eichler EE Primate segmental duplications: Crucibles of evolution, diversity and disease. Nat Rev Genet 2006, 7:552-564 10.1038/ nrg1895 16770338
42. Rhesus Macaque Genome Sequencing and Analysis Consortium Gibbs RA Rogers J Katze MG Bumgarner R Weinstock GM Mardis ER Remington KA Strausberg RL Venter JC Wilson RK Batzer MA Bustamante CD Eichler EE Hahn MW Hardison RC Makova KD Miller W Milosavljevic A Palermo RE Siepel A Sikela JM Attaway T Bell S Bernard KE Buhay CJ Chandrabose MN Dao M Davis C Delehaunty KD Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007, 316:222-234 10.1126/science.1139247 17431167
43. Wang NJ Parokonny AS Thatcher KN Driscoll J Malone BM Dorrani N Sigman M Lasalle JM Schanen NC Multiple forms of atypical rearrangements generating supernumerary derivative chromosome 15. BMC Genet 2008, 9:2 2249594 18177502 10.1186/1471-2156-9-2
44. Conrad B Antonarakis SE Gene duplication: A drive for phenotypic diversity and cause of human disease. Annu Rev Genomics Hum Genet 2007, 8:17-35 10.1146/annurev.genom.8.021307.110233 17386002
45. Ji Y Eichler EE Schwartz S Nicholls RD Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res 2000, 10:597-610 10.1101/gr.10.5.597 10810082
46. Cáceres M National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program Sullivan RT Thomas JW A recurrent inversion on the eutherian X chromosome. Proc Natl Acad Sci USA 2007, 104:18571-18576 10.1073/pnas.0706604104 18003915
47. Lichter P Tang CJ Call K Hermanson G Evans GA Housman D Ward DC High-resolution mapping of human chromosomes 11 by in situ hybridization with cosmid clones. Science 1990, 247:64-69 10.1126/science.2294592 2294592
48. UCSC Genome Browser http://genome.ucsc.edu
49. CHORI Resources: Hybridization of High Density Filters http://bacpac.chori.org/highdensity.htm
50. CHORI Resources: CH250 Rhesus Macaque BAC Library http://bacpac.chori.org/rhesus250.htm
51. HomoloGene Home http://www.ncbi.nlm.nih.gov/sites/entrez/query.fcgi?db= homologene
52. McPherson JD Marra M Hillier L Waterston RH Chinwalla A Wallis J Sekhon M Wylie K Mardis ER Wilson RK Fulton R Kucaba TA Wagner-McPherson C Barbazuk WB Gregory SG Humphray SJ French L Evans RS Bethel G Whittaker A Holden JL McCann OT Dunham A Soderlund C Scott CE Bentley DR Schuler G Chen HC Jang W Green ED A physical map of the human genome. Nature 2001, 409:934-941 10.1038/35057157 11237014
53. Bourque G Pevzner PA Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res 2002, 12:26-36 155248 11779828
54. Genome Rearrangements in Man and Mouse http://grimm.bioprojects.org/ GRIMM/
55. Bailey JA Yavor AM Massa HF Trask BJ Eichler EE Segmental duplications: organization and impact within the current human genome project assembly. Genome Res 2001, 11:1005-1017 311093 11381028 10.1101/ gr.GR-1871R
56. Jiang Z Tang H Ventura M Cardone MF Marques-Bonet T She X Pevzner PA Eichler EE Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet 2007, 39:1361-1368 10.1038/ng.2007.9 17922013