Lineage-specific gene duplication and loss in human and great ape evolution

PLoS Biology

Volumn 2, Issue 7, 2004, Pages

  Fortna, Andrew ^a   Kim, Young ^b   MacLaren, Erik ^a   Marshall, Kriste ^a   Hahn, Gretchen ^a   Meltesen, Lynne ^a   Brenton, Matthew ^a   Hink, Raquel ^a   Burgers, Sonya ^a   Hernandez Boussard, Tina ^c   Karimpour Fard, Anis ^a   Glueck, Deborah ^a   McGavran, Loris ^a   Berry, Rebecca ^a   Pollack, Jonathan ^b   Sikela, James M ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BABOON; BRAIN FUNCTION; CELL LINEAGE; CHIMPANZEE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA MICROARRAY; FEMALE; GENE CLUSTER; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENE ISOLATION; GENE LOSS; GENE STRUCTURE; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN GENOME; HUMAN VERSUS ANIMAL COMPARISON; INTERSPECIFIC RELATIONSHIP; MALE; MAMMALIAN GENETICS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORANG UTAN; PHENOTYPIC VARIATION; SPECIES IDENTIFICATION; ANIMAL; ANTHROPOIDEA; BACTERIAL ARTIFICIAL CHROMOSOME; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DNA SEQUENCE; EVOLUTION; FLUORESCENCE IN SITU HYBRIDIZATION; GENOME; HOMINID; HUMAN; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE REPEAT; PAN TROGLODYTES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE;

ALOCASIA MACRORRHIZOS; ANIMALIA; HOMINOIDEA; MAMMALIA; PAN TROGLODYTES; PAPIO HAMADRYAS; PONGO PYGMAEUS;

COMPLEMENTARY DNA; CXYORF1 PROTEIN, HUMAN; FGF7 PROTEIN, HUMAN; KERATINOCYTE GROWTH FACTOR; PROTEIN;

ANIMALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLONING, MOLECULAR; CLUSTER ANALYSIS; DNA, COMPLEMENTARY; EVOLUTION; EVOLUTION, MOLECULAR; FIBROBLAST GROWTH FACTOR 7; GENE DUPLICATION; GENOME; HOMINIDAE; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEIC ACID HYBRIDIZATION; PAN TROGLODYTES; PONGO PYGMAEUS; PROTEINS; REPETITIVE SEQUENCES, NUCLEIC ACID; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 19344366754     PISSN: 15449173     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pbio.0020207     Document Type: Article

References (48)

1. 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. Find this article online
2. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, et al. (2002a) Recent segmental duplications in the human genome. Science 297: 1003-1007. Find this article online
3. Bailey JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, et al. (2002b) Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am J Hum Genet 70: 83-100. Find this article online
4. Bieche I, Olivi M, Champeme MH, Vidaud D, Lidereau R, et al. (1998) Novel approach to quantitative polymerase chain reaction using real-time detection: Application to the detection of gene amplification in breast cancer. Int J Cancer 78: 661-666. Find this article online
5. Chen FC, Li WH (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. Find this article online
6. Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, et al. (2003) Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol 4: R25. Find this article online
7. Ciccodicola A, D'Esposito M, Esposito T, Gianfrancesco F, Migliaccio C, et al. (2000) Differentially regulated and evolved genes in the fully sequenced Xq/Yq pseudoautosomal region. Hum Mol Genet 9: 395-401. Find this article online
8. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: R60. Find this article online
9. DiAntonio A, Haghighi AP, Portman SL, Lee JD, Amaranto AM, et al. (2001) Ubiquitination-dependent mechanisms regulate synaptic growth and function. Nature 412: 449-452. Find this article online
10. Fan Y, Linardopoulou E, Friedman C, Williams E, Trask BJ (2002) Genomic structure and evolution of the ancestral chromosome fusion site in 2q13-2q14.1 and paralogous regions on other human chromosomes. Genome Res 12: 1651-1662. Find this article online
11. Frazer KA, Chen X, Hinds DA, Pant PV, Patil N, et al. (2003) Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res 13: 341-346. Find this article online
12. Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, et al. (1999) Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397: 436-441. Find this article online
13. Gilad Y, Bustamante CD, Lancet D, Pääbo S (2003) Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am J Hum Genet 73: 489-501. Find this article online
14. Heid CA, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Res 6: 986-994. Find this article online
15. Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, et al. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423: 91-96. Find this article online
16. Horvath JE, Schwartz S, Eichler EE (2000) The mosaic structure of human pericentromeric DNA: A strategy for characterizing complex regions of the human genome. Genome Res 10: 839-852. Find this article online
17. Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA (2003) Identifying biological themes within lists of genes with EASE. Genome Biol 4: R70. Find this article online
18. 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 U S A 88: 9051-9055. Find this article online
19. Johnson ME, Viggiano L, Bailey JA, Abdul-Rauf M, Goodwin G, et al. (2001) Positive selection of a gene family during the emergence of humans and African apes. Nature 413: 514-519. Find this article online
20. Kaessmann H, Wiebe V, Pääbo S (1999) Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-1162. Find this article online
21. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, et al. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818-821. Find this article online
22. Lamprecht R, Farb CR, LeDoux JE (2002) Fear memory formation involves p190 RhoGAP and ROCK proteins through a GRB2-mediated complex. Neuron 36: 727-738. Find this article online
23. Lefebvre S, Burglen L, Reboullet S, Clermont O, Burlet P, et al. (1995) Identification and characterization of a spinal muscular atrophy-determining gene. Cell 80: 155-165. Find this article online
24. Li WH (1997) Molecular evolution. Sunderland, Massachusetts: Sinauer Associates. 432 p.
25. Liston P, Roy N, Tamai K, Lefebvre C, Baird S, et al. (1996) Suppression of apoptosis in mammalian cells by NAIP and a related family of IAP genes. Nature 379: 349-353. Find this article online
26. Livak KJ, Flood SJ, Marmaro J, Giusti W, Deetz K (1995) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl 4: 357-362. Find this article online
27. Locke DP, Segraves R, Carbone L, Archidiacono N, Albertson DG, et al. (2003) Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res 13: 347-357. Find this article online
28. Mefford HC, Trask BJ (2002) The complex structure and dynamic evolution of human subtelomeres. Nat Rev Genet 3: 91-102. Find this article online
29. Muchmore EA, Diaz S, Varki A (1998) A structural difference between the cell surfaces of humans and the great apes. Am J Phys Anthropol 107: 187-198. Find this article online
30. Novembre FJ, Saucier M, Anderson DC, Klumpp SA, O'Neil SP, et al. (1997) Development of AIDS in a chimpanzee infected with human immunodeficiency virus type 1. J Virol 71: 4086-4091. Find this article online
31. Ohno S (1970) Evolution by gene duplication. Berlin: Springer. 160 p.
32. Pääbo S (2003) The mosaic that is our genome. Nature 421: 409-412. Find this article online
33. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20: 207-211. Find this article online
34. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, et al. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23: 41-46. Find this article online
35. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, et al. (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A 99: 12963-12968. Find this article online
36. Ramakers GJ (2000) Rho proteins and the cellular mechanisms of mental retardation. Am J Med Genet 94: 367-371. Find this article online
37. Rieder MJ, Taylor SL, Tobe VO, Nickerson DA (1998) Automating the identification of DNA variations using quality-based fluorescence resequencing: Analysis of the human mitochondrial genome. Nucleic Acids Res 26: 967-973. Find this article online
38. Rochette CF, Gilbert N, Simard LR (2001) SMN gene duplication and the emergence of the SMN2 gene occurred in distinct hominids: SMN2 is unique to Homo sapiens. Hum Genet 108: 255-266. Find this article online
39. Samonte RV, Eichler EE (2002) Segmental duplications and the evolution of the primate genome. Nat Rev Genet 3: 65-72. Find this article online
40. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470. Find this article online
41. SLI Consortium (2002) A genomewide scan identifies two novel loci involved in specific language impairment. Am J Hum Genet 70: 384-398. Find this article online
42. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29: 263-264. Find this article online
43. Stankiewicz P, Lupski JR (2002) Molecular-evolutionary mechanisms for genomic disorders. Curr Opin Genet Dev 12: 312-319. Find this article online
44. Stanyon R, Wienberg J, Romagno D, Bigoni F, Jauch A, et al. (1992) Molecular and classical cytogenetic analyses demonstrate an apomorphic reciprocal chromosomal translocation in Gorilla gorilla. Am J Phys Anthropol 88: 245-250. Find this article online
45. Wildman DE, Uddin M, Liu G, Grossman LI, Goodman M (2003) Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo. Proc Natl Acad Sci U S A 100: 7181-7188. Find this article online
46. Xu M, Okada T, Sakai H, Miyamoto N, Yanagisawa Y, et al. (2002) Functional human NAIP promoter transcription regulatory elements for the NAIP and PsiNAIP genes. Biochim Biophys Acta 1574: 35-50. Find this article online
47. Yunis JJ, Prakash O (1982) The origin of man: A chromosomal pictorial legacy. Science 215: 1525-1530. Find this article online
48. Zimonjic DB, Kelley MJ, Rubin JS, Aaronson SA, Popescu NC (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 U S A 94: 11461-11465. Find this article online