Hominoid fission of chromosome 14/15 and the role of segmental duplications

Genome Research

Volumn 23, Issue 11, 2013, Pages 1763-1773

  Giannuzzi, Giuliana ^a,d   Pazienza, Michele ^a   Huddleston, John ^b   Antonacci, Francesca ^b   Malig, Maika ^b   Vives, Laura ^b   Eichler, Evan E ^b,c   Ventura, Mario ^a,b  

^a UNIVERSITY OF BARI   (Italy)

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

^c UNIVERSITY OF WASHINGTON   (United States)

^d UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALLITRICHINAE; CHROMOSOME 14; CHROMOSOME 15; CHROMOSOME STRUCTURE; COMPARATIVE STUDY; FLUORESCENCE IN SITU HYBRIDIZATION; HETEROCHROMATIN; HUMAN; HUMAN CHROMOSOME; MACACA; NONHUMAN; PERICENTRIC CHROMOSOME INVERSION; PRIORITY JOURNAL; SEGMENTAL DUPLICATION; ANIMAL; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME; CHROMOSOME BREAKAGE; CHROMOSOME DUPLICATION; EUCHROMATIN; GENETICS; HOMINID; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY;

HOMINOIDEA;

EUCHROMATIN; HETEROCHROMATIN;

ANIMALS; CHROMOSOME BREAKPOINTS; CHROMOSOME DUPLICATION; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, HUMAN, PAIR 14; CHROMOSOMES, HUMAN, PAIR 15; CHROMOSOMES, MAMMALIAN; CLONING, MOLECULAR; EUCHROMATIN; EVOLUTION, MOLECULAR; HETEROCHROMATIN; HOMINIDAE; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEGMENTAL DUPLICATIONS, GENOMIC;

EID: 84887461864     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.156240.113     Document Type: Article

References (60)

1. Alexandrov I, Kazakov A, Tumeneva I, Shepelev V, Yurov Y. 2001. a-satellite DNA of primates: Old and new families. Chromosoma 110: 253-266.
2. Armengol L, PujanaMA, Cheung J, Scherer SW, Estivill X. 2003. 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 12: 2201-2208.
3. Bailey JA, Eichler EE. 2006. Primate segmental duplications: Crucibles of evolution, diversity and disease. Nat Rev Genet 7: 552-564.
4. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. 2001. Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res 11: 1005-1017.
5. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. 2002a. Recent segmental duplications in the human genome. Science 297: 1003-1007.
6. Bailey JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, Archidiacono N, Schwartz S, Rocchi M, Eichler EE. 2002b. Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am J Hum Genet 70: 83-100.
7. Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. 2004. Hotspots of mammalian chromosomal evolution. Genome Biol 5: R23.
8. Carbone L, Ventura M, Tempesta S, Rocchi M, Archidiacono N. 2002. Evolutionary history of chromosome 10 in primates. Chromosoma 111: 267-272.
9. Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, et al. 2001. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409: 953-958.
10. Dennehey BK, Gutches DG, McConkey EH, Krauter KS. 2004. Inversion, duplication, and changes in gene context are associated with human chromosome 18 evolution. Genomics 83: 493-501.
11. Dillon N, Festenstein R. 2002. Unravelling heterochromatin: Competition between positive and negative factors regulates accessibility. Trends Genet 18: 252-258.
12. Eichler EE, Archidiacono N, Rocchi M. 1999. CAGGG repeats and the pericentromeric duplication of the hominoid genome. Genome Res 9: 1048-1058.
13. Fallin MD, Lasseter VK,Wolyniec PS,McGrath JA, Nestadt G, Valle D, Liang KY, Pulver AE. 2003. Genomewide linkage scan for schizophrenia susceptibility loci among Ashkenazi Jewish families shows evidence of linkage on chromosome 10q22. Am J Hum Genet 73: 601-611.
14. Faraone SV, Hwu HG, Liu CM, Chen WJ, Tsuang MM, Liu SK, Shieh MH, Hwang TJ, Ou-Yang WC, Chen CY, et al. 2006. Genome scan of Han Chinese schizophrenia families from Taiwan: Confirmation of linkage to 10q22.3. Am J Psychiatry 163: 1760-1766.
15. Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
16. Girirajan S, Chen L, Graves T, Marques-Bonet T, Ventura M, Fronick C, Fulton L, Rocchi M, Fulton RS, Wilson RK, et al. 2009. Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites. Genome Res 19: 178-190.
17. Hach F, Hormozdiari F, Alkan C, Birol I, Eichler EE, Sahinalp SC. 2010. mrsFAST: A cache-oblivious algorithm for short-read mapping. Nat Methods 7: 576-577.
18. Hastings PJ, Lupski JR, Rosenberg SM, Ira G. 2009. Mechanisms of change in gene copy number. Nat Rev Genet 10: 551-564.
19. Hofmann S, Franke A, Fischer A, Jacobs G, Nothnagel M, Gaede KI, Schurmann M, Muller-Quernheim J, Krawczak M, Rosenstiel P, et al. 2008. Genome-wide association study identifies ANXA11 as a new susceptibility locus for sarcoidosis. Nat Genet 40: 1103-1106.
20. IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA. 1991. Origin of human chromosome 2: An ancestral telomere-telomere fusion. Proc Natl Acad Sci 88: 9051-9055.
21. Kehrer-SawatzkiH, CooperDN. 2008.Molecularmechanisms of chromosomal rearrangement during primate evolution. Chromosome Res 16: 41-56.
22. Kehrer-Sawatzki H, Wohr G, Schempp W, Eisenbarth I, Barbi G, Assum G. 1998. Mapping of members of the low-copy-number repetitive DNA sequence family chAB4 within the p arms of human acrocentric chromosomes: Characterization of Robertsonian translocations. Chromosome Res 6: 429-435.
23. Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
24. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12: 996-1006.
25. 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.
26. Kuhl A, Melberg A, Meinl E, Nurnberg G, Nurnberg P, Kehrer-Sawatzki H, Jenne DE. 2008. Myofibrillar myopathy with arrhythmogenic right ventricular cardiomyopathy 7: Corroboration and narrowing of the critical region on 10q22.3. Eur J Hum Genet 16: 367-373.
27. Lichter P, Tang CJ, Call K, Hermanson G, Evans GA, Housman D,Ward DC. 1990. High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247: 64-69.
28. Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ. 2005. Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437: 94-100.
29. Locke DP, Archidiacono N, Misceo D, Cardone MF, Deschamps S, Roe B, Rocchi M, Eichler EE. 2003. Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. Genome Biol 4: R50.
30. Locke DP, Hillier LW,WarrenWC,Worley KC, Nazareth LV, MuznyDM, Yang SP, Wang Z, Chinwalla AT, Minx P, et al. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469: 529-533.
31. Marques-Bonet T, Kidd JM, VenturaM,Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, et al. 2009. A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457: 877-881.
32. McConkey EH. 2004. Orthologous numbering of great ape and human chromosomes is essential for comparative genomics. Cytogenet Genome Res 105: 157-158.
33. Melberg A, Oldfors A, Blomstrom-Lundqvist C, Stalberg E, Carlsson B, Larrson E, Lidell C, Eeg-Olofsson KE, Wikstrom G, Henriksson G, et al. 1999. Autosomal dominant myofibrillar myopathy with arrhythmogenic right ventricular cardiomyopathy linked to chromosome 10q. Ann Neurol 46: 684-692.
34. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, et al. 2013. The UCSC Genome Browser database: Extensions and updates 2013. Nucleic Acids Res 41: D64-D69.
35. Murphy WJ, Larkin DM, Everts-van derWind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309: 613-617.
36. Niimura Y, Nei M. 2007. Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS ONE 2: e708.
37. O'Meara E, Stack D, Lee CH, Garvin AJ, Morris T, Argani P, Han JS, Karlsson J, Gisselson D, Leuschner I, et al. 2012. Characterization of the chromosomal translocation t(10;17)(q22;p13) in clear cell sarcoma of kidney. J Pathol 227: 72-80.
38. Pontius JU, Mullikin JC, Smith DR, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, et al. 2007. Initial sequence and comparative analysis of the cat genome. Genome Res 17: 1675-1689.
39. Pujana MA, NadalM, GratacosM, Peral B, Csiszar K, Gonzalez-Sarmiento R, Sumoy L, Estivill X. 2001. Additional complexity on human chromosome 15q: Identification of a set of newly recognized duplicons (LCR15) on 15q11-q13, 15q24, and 15q26. Genome Res 11: 98-111.
40. Pujana MA, Nadal M, Guitart M, Armengol L, Gratacos M, Estivill X. 2002. Human chromosome 15q11-q14 regions of rearrangements contain clusters of LCR15 duplicons. Eur J Hum Genet 10: 26-35.
41. Quintero-Del-Rio AI, Kelly JA, Kilpatrick J, James JA, Harley JB. 2002. The genetics of systemic lupus erythematosus stratified by renal disease: Linkage at 10q22.3 (SLEN1), 2q34-35 (SLEN2), and 11p15.6 (SLEN3). Genes Immun (Suppl 1) 3: S57-S62.
42. Roberto R, Misceo D, D'Addabbo P, Archidiacono N, Rocchi M. 2008. Refinement ofmacaque synteny arrangement with respect to the official rheMac2 macaque sequence assembly. Chromosome Res 16: 977-985.
43. Rudd MK, Endicott RM, Friedman C, Walker M, Young JM, Osoegawa K, de Jong PJ, Green ED, Trask BJ. 2009. Comparative sequence analysis of primate subtelomeres originating from a chromosome fission event. Genome Res 19: 33-41.
44. Schein J, Kucaba T, Sekhon M, Smailus D,Waterston R, MarraM. 2004. Highthroughput BAC fingerprinting. Methods Mol Biol 255: 143-156.
45. Smit AFA, Hubley R, 2010. RepeatMasker Open-3.2.9. http://www. repeatmasker.org/.
46. Stanyon R, Rocchi M, Capozzi O, Roberto R, Misceo D, Ventura M, Cardone MF, Bigoni F, Archidiacono N. 2008. Primate chromosome evolution: Ancestral karyotypes, marker order and neocentromeres. Chromosome Res 16: 17-39.
47. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
48. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTALW: 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.
49. Venken T, Alaerts M, Souery D, Goossens D, Sluijs S, Navon R, Van Broeckhoven C,Mendlewicz J, Del-Favero J, Claes S. 2008. Chromosome 10q harbors a susceptibility locus for bipolar disorder in Ashkenazi Jewish families. Mol Psychiatry 13: 442-450.
50. Ventura M, Mudge JM, Palumbo V, Burn S, Blennow E, Pierluigi M, Giorda R, Zuffardi O, Archidiacono N, JacksonMS, et al. 2003. Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25. Genome Res 13: 2059-2068.
51. Ventura M, Antonacci F, Cardone MF, Stanyon R, D'Addabbo P, Cellamare A, Sprague LJ, Eichler EE, Archidiacono N, Rocchi M. 2007. Evolutionary formation of new centromeres in macaque. Science 316: 243-246.
52. VenturaM, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, et al. 2011. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res 21: 1640-1649.
53. Ventura M, Catacchio CR, Sajjadian S, Vives L, Sudmant PH, Marques-Bonet T, Graves TA,Wilson RK, Eichler EE. 2012. The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. Genome Res 22: 1036-1049.
54. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, et al. 2009. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326: 865-867.
55. Wienberg J, Stanyon R. 1995. Chromosome painting in mammals as an approach to comparative genomics. Curr Opin Genet Dev 5: 792-797.
56. Wienberg J, Stanyon R. 1997. Comparative painting of mammalian chromosomes. Curr Opin Genet Dev 7: 784-791.
57. Wienberg J, Jauch A, Ludecke HJ, Senger G, Horsthemke B, Claussen U, Cremer T, Arnold N, Lengauer C. 1994. The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary. Chromosome Res 2: 405-410.
58. Yunis JJ, Prakash O. 1982. The origin of man: A chromosomal pictorial legacy. Science 215: 1525-1530.
59. Yunis JJ, Sawyer JR, Dunham K. 1980. The striking resemblance of highresolution G-banded chromosomes of man and chimpanzee. Science 208: 1145-1148.
60. Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O'Neill K, Whittaker CA, Kamal M, Chang JL, Cuomo CA, et al. 2006. Analysis of the DNA sequence and duplication history of human chromosome 15. Nature 440: 671-675.