The structure and evolution of centromeric transition regions within the human genome

Nature

Volumn 430, Issue 7002, 2004, Pages 857-864

  She, Xinwei ^a,b   Horvath, Julie E ^a   Jiang, Zhaoshi ^a,b   Liu, Ge ^a   Furey, Terrence S ^c   Christ, Laurie ^a   Clark, Royden ^a   Graves, Tina ^d   Gulden, Cassy L ^a   Alkan, Can ^a   Bailey, Jeff A ^a   Sahinalp, Cenk ^a,e   Rocchi, Mariano ^f   Haussler, David ^c   Wilson, Richard K ^d   Miller, Webb ^g   Schwartz, Stuart ^a   Eichler, Evan E ^a,b  

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

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

^c Santa Cruz   (United States)

^d WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e SIMON FRASER UNIVERSITY   (Canada)

^f UNIVERSITY OF BARI   (Italy)

^g PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOMES; DNA;

CENTROMERIC TRANSITION; DRAFT GENOME SEQUENCE;

GENES;

BIOLOGY; GENOME;

ARTICLE; CENTROMERE; CHROMOSOME ARM; CHROMOSOME DUPLICATION; CHROMOSOME STRUCTURE; EXON; GENETIC TRANSCRIPTION; HUMAN; HUMAN GENOME; NONHUMAN; PRIORITY JOURNAL;

ANIMALS; BASE COMPOSITION; CENTROMERE; DNA; EUCHROMATIN; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENE DUPLICATION; GENOME, HUMAN; HUMANS; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

PRIMATES;

EID: 4344672526     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02806     Document Type: Article

References (40)

1. Nagaki, K. et al. Sequencing of a rice centromere uncovers active genes. Nature Genet. 36, 138-145 (2004).
2. Horvath, J. et al. Molecular structure and evolution of an alpha/non-alpha satellite junction at 16p11. Hum. Mol. Genet. 9, 113-123 (2000).
3. Jackson, M. Duplicate, decouple, disperse: the evolutionary transience of human centromeric regions. Curr. Opin. Genet. Dev. 13, 629-635 (2003).
4. International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
5. Eichler, E. E. Masquerading repeats: Paralogous pitfalls of the Human Genome. Genome Res. 8, 758-762 (1998).
6. Bailey, J. A., Yavor, A. M., Massa, H. F., Trask, B. J. & Eichler, E. E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 11, 1005-1017 (2001).
7. Istrail, S. et al. Whole-genome shotgun assembly and comparison of human genome assmblies. Proc. Natl Acad. Sci. USA 101, 1916-1921 (2004).
8. 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).
9. Bailey, J. A., Giu, L. & Eichler, E. E. An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73, 823-834 (2003).
10. Horvath, J. E., Bailey, J. A., Locke, D. P. & Eichler, E. E. Lessons from the human genome: transitions between euchromatin and heterochromatin. Hum. Mol. Genet. 10, 2215-2223 (2001).
11. Schueler, M. G., Higgins, A. W., Rudd, M. K., Gustashaw, K. & Willard, H. F. Genomic and genetic definition of a functional human centromere. Science 294, 109-115 (2001).
12. Horvath, J. E. et al. Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. Mol. Biol. Evol. 20, 1463-1479 (2003).
13. Ventura, M. et al. Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25. Genome Res. 13, 2059-2068 (2003).
14. Yunis, J. J. & Prakash, O. The origin of man: a chromosomal pictorial legacy. Science 215, 1525-1530 (1982).
15. Baldini, A. et al. An alphoid DNA sequence conserved in all human and great ape chromosomes: evidence for ancient centromeric sequences at human chromosomal regions 2q21 and 9q13. Hum. Genet. 90, 577-583 (1993).
16. Liu, G. et al. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res. 13, 358-368 (2003).
17. Ventura, M., Archidiacono, N. & Rocchi, M. Centromere emergence in evolution. Genome Res. 11, 595-599 (2001).
18. Eder, V. et al. Chromosome 6 phylogeny in primates and centromere repositioning. Mol. Biol. Evol. 20, 1506-1512 (2003).
19. Eichler, E. E. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 17, 661-669 (2001).
20. Locke, D. P. et al. Molecular evolution of the human chromosome 15 pericentromeric region. Cytogenet. Genome Res. (in the press).
21. Golfier, G. et al. The 200-kb segmental duplication on human chromosome 21 originates from a pericentromeric dissemination involving human chromosomes 2,18 and 13. Gene 312, 51-59 (2003).
22. Courseaux, A. et al. Segmental duplications in euchromatic regions of human chromosome 5: a source of evolutionary instability and transcriptional innovation. Genome Res. 13, 369-381 (2003).
23. Horvath, J., Schwartz, S. & Eichler, E. The mosaic structure of a 2p11 pericentromeric segment: A strategy for characterizing complex regions of the human genome. Genome Res. 10, 839-852 (2000).
24. Bailey, J. A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002).
25. Guy, J. et al. Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p. Genome Res. 13, 159-172 (2003).
26. Hillier, L. W. et al. The DNA sequence of human chromosome 7. Nature 424,157-164 (2003).
27. Crosier, M. et al. Human paralogs of KIAA0187 were created through independent pericentromeric-directed and chromosome-specific duplication mechanisms. Genome Res. 12, 67-80 (2002).
28. Jackson, M. S. et al. 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, 205-215 (1999).
29. Locke, D. P. et al. Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res. 13, 347-357 (2003).
30. Thomas, J. W. et al. Pericentromeric duplications in the laboratory mouse. Genome Res. 13, 55-63 (2003).
31. Tuzun, E., Bailey, J. & Eichler, E. E. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res. 14, 493-506 (2004).
32. Bailey, J. A., Baertsch, R., Kent, W. J., Haussler, D. & Eichler, E. E. Hotspots of mammalian chromosomal evolution. Genome Biol. 5, R23 (2004).
33. Copenhaver, G. P. et al. Genetic definition and sequence analysis of Arabidopsis centromeres. Science: 286, 2468-2474 (1999).
34. Schneider, H. et al. Molecular phylogeny of the New World monkeys (Platyrrhini, primates) based on two unlinked nuclear genes: IRBP intron I and epsilon-globin sequences. Am. J. Phys. Anthropol. 100, 153-179 (1996).
35. Willard, H. F. & Waye, J. S. Chromosome-specific subsets of human alpha satellite DNA: analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat. J. Mol. Evol. 25, 207-214 (1987).
36. Alexandrov, I., Kazakov, A., Tumeneva, I., Shepelev, V. & Yurov, Y. Alpha-satellite DNA of primates: old and new families. Chromosoma 110, 253-266 (2001).
37. Lee, C., Wevrick, R., Fisher, R. B., Ferguson-Smith, M. A. & Lin, C. C. Human centromeric DNAs. Hum. Genet. 100, 291-304 (1997).
38. An International System for Human Cytogenetic Nomenclature, High resolution-banding. Cytogenet. Cell Genet. 31, 1-23 (1981).
39. Leem, S. H. et al. Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements. Genome Res. 14, 239-246 (2004).
40. Rudd, M. K. & Willard, H. F. Analysis of the centromeric regions of the human genome assembly. Trends Genet. (in the press).