DNA sequence and comparative analysis of chimpanzee chromosome 22

Nature

Volumn 429, Issue 6990, 2004, Pages 382-388

[No Author Info available]

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; CHROMOSOMES; GENETIC ENGINEERING; PROTEINS; SUBSTITUTION REACTIONS;

COGNITIVE FUNCTIONS; GENOME RESEARCH;

DNA;

DNA; GENOME; PRIMATE;

AMINO ACID SEQUENCE; CHROMOSOME 21; CHROMOSOME 22; CHROMOSOME ANALYSIS; COGNITION; COMPARATIVE STUDY; DNA SEQUENCE; GENE DELETION; GENE INSERTION; GENETIC LINE; GENOMICS; LANGUAGE; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUALITY CONTROL; RETROPOSON; REVIEW; SPECIES DIFFERENTIATION;

ANIMALS; CHROMOSOMES, HUMAN, PAIR 21; CHROMOSOMES, MAMMALIAN; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENES; GENOMICS; HUMANS; MUTAGENESIS; PAN TROGLODYTES; PHYLOGENY; PHYSICAL CHROMOSOME MAPPING; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS (GENETICS); REPETITIVE SEQUENCES, NUCLEIC ACID; RETROELEMENTS; SEQUENCE ANALYSIS, DNA;

INSERTION SEQUENCES; MAMMALIA; PAN TROGLODYTES; PRIMATES;

EID: 2642575083     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02564     Document Type: Review

References (46)

1. King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107-116 (1975).
2. Pennacchio, L. A. & Rubin, E. M. Genomic strategies to identify mammalian regulatory sequences. Nature Rev. Genet. 2, 100-109 (2001).
3. Fujiyama, A. et al. Construction and analysis of a human-chimpanzee comparative clone map. Science 295, 131-134 (2002).
4. Olson, M. V. & Varki, A. Sequencing the chimpanzee genome: insights into human evolution and disease. Nature Rev. Genet. 4, 20-28 (2003).
5. Boffelli, D. et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391-1394 (2003).
6. Hacia, J. G. et al. Evolutionary sequence comparisons using high-density oligonucleotide arrays. Nature Genet. 18, 155-158 (1998).
7. Patil, N. et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719-1723 (2001).
8. Thomas, J. W. et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424, 788-793 (2003).
9. Britten, R. J. Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc. Natl Acad. Sci. USA 99, 13633-13635 (2002).
10. Nickerson, E. & Nelson, D. L. Molecular definition of pericentric inversion breakpoints occurring during the evolution of humans and chimpanzees. Genomics 50, 368-372 (1998).
11. Bailey, J. A. et al. Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70, 83-100 (2002).
12. Hattori, M. et al. The DNA sequence of human chromosome 21. Nature 405, 311-319 (2000).
13. Frazer, K. A. et al. Evolutionarily conserved sequences on human chromosome 21. Genome Res. 11, 1651-1659 (2001).
14. Frazer, K. A. et al. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 13, 341-346 (2003).
15. McClure, H. M., Belden, K. H., Pieper, W. A. & Jacobson, C. B. Autosomal trisomy in a chimpanzee: resemblance to Down's syndrome. Science 165, 1010-1012 (1969).
16. Ewing, B., Hillier, L., Wendl, M. C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185 (1998).
17. Orti, R. et al. Conservation of pericentromeric duplications of a 200-kb part 25 of the human 21q22.1 region in primates. Cytogenet. Cell Genet. 83, 262-265 (1998).
18. Ebersberger, I., Metzler, D., Schwarz, C. & Paabo, S. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70, 1490-1497 (2002).
19. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
20. Sawada, I. et al. Evolution of Alu family repeats since the divergence of human and chimpanzee. J. Mol. Evol. 22, 316-322 (1985).
21. Myers, J. S. et al. A comprehensive analysis of recently integrated human Ta L1 elements. Am. J. Hum. Genet. 71, 312-326 (2002).
22. Liu, G. et al. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res. 13, 358-368 (2003).
23. Kim, M., Carman, C. V. & Springer, T. A. Bidirectional transmembrane signaling by cytoplasmic domain separation in integrins. Science 301, 1720-1725 (2003).
24. Roy, A. M. et al. Potential gene conversion and source genes for recently integrated Alu elements. Genome Res. 10, 1485-1495 (2000).
25. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
26. Britten, R. J., Baron, W. F., Stout, D. B. & Davidson, E. H. Sources and evolution of human Alu repeated sequences. Proc. Natl Acad. Sci. USA 85, 4770-4774 (1988).
27. Batzer, M. A. & Deininger, P. L. A human-specific subfamily of Alu sequences. Genomics 9, 481-487 (1991).
28. Leeflang, E. P., Chesnokov, I. N. & Schmid, C. W. Mobility of short interspersed repeats within the chimpanzee lineage. J. Mol. Evol. 37, 566-572 (1993).
29. Zietkiewicz, E., Richer, C., Makalowski, W., Jurka, J. & Labuda, D. A young Alu subfamily amplified independently in human and African great apes lineages. Nucleic Acids Res. 22, 5608-5612 (1994).
30. Batzer, M. A. et al. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J. Mol. Biol. 247, 418-427 (1995).
31. Roy, A. M. et al. Recently integrated human Alu repeats: finding needles in the haystack. Genetica 107, 149-161 (1999).
32. Chou, H. H. et al. Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution. Proc. Natl Acad. Sci. USA 99, 11736-11741 (2002).
33. Roy-Engel, A. M. et al. Non-traditional Alu evolution and primate genomic diversity. J. Mol. Biol. 316, 1033-1040 (2002).
34. Deininger, P. L. & Batzer, M. A. Mammalian retroelements. Genome Res. 12, 1455-1465 (2002).
35. Gojobori, T., Li, W. H. & Graur, D. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18, 360-369 (1982).
36. Fay, J. C. & Wu, C. I. Hitchhiking under positive Darwinian selection. Genetics 155, 1405-1413 (2000).
37. Brosius, J. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238, 115-134 (1999).
38. The HSA21 expression map initiative. A gene expression map of human chromosome 21 orthologues in the mouse. Nature 420, 586-590 (2002).
39. Clark, A. G. et al. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302, 1960-1963 (2003).
40. Shi, J. et al. Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units. Proc. Natl Acad. Sci. USA 100, 8331-8336 (2003).
41. Enard, W. et al. Intra- and interspecific variation in primate gene expression patterns. Science 296, 340-343 (2002).
42. Hellmann, I. et al. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13, 831-837 (2003).
43. Varki, A. A chimpanzee genome project is a biomedical imperative. Genome Res. 10, 1065-1070 (2000).
44. Suzuki, O. T. et al. Molecular analysis of collagen XVIII reveals novel mutations, presence of a third isoform, and possible genetic heterogeneity in Knobloch syndrome. Am. J. Hum. Genet. 71, 1320-1329 (2002).
45. Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. in A Model of Evolutionary Change in Proteins (ed. Dayhoff, M. O.) (Natl Biomed. Res. Found., Silver Springs, Maryland, 1978).
46. Tajima, F. & Nei, M. Biases of the estimates of DNA divergence obtained by the restriction enzyme technique. J. Mol. Evol. 18, 115-120 (1982).