Human centromere genomics: Now it's personal

Chromosome Research

Volumn 20, Issue 5, 2012, Pages 621-633

  Hayden, Karen E ^a,b  

^a University of California Santa Cruz   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alpha satellite DNA; Centromere; Genomics; Kinetochore

Indexed keywords

CENTROMERE PROTEIN A; SATELLITE DNA;

CENTROMERE; EPIGENETICS; GENETIC ASSOCIATION; HUMAN; HUMAN GENOME; MICROTUBULE; MITOSIS SPINDLE; POPULATION GENETICS; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS;

CENTROMERE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME DUPLICATION; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN; DNA, SATELLITE; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; MODELS, GENETIC; PROTEIN INTERACTION MAPPING;

EID: 84864874774     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-012-9295-y     Document Type: Review

References (63)

1. Alexandrov IA, Mitkevich SP, Yurov YB (1988) The phylogeny of human chromosome specific alpha satellites. Chromosoma 96:443-453
2. Alexandrov IA, Medvedev LI, Mashkova TD, Kisselev LL, Romanova LY, Yurov YB (1993) Definition of a new alpha satellite suprachromosomal family characterized by monomeric organization. Nucleic Acids Res 21:2209-2215
3. Alexandrov IA, Kazakov AE, Tumeneva I, Shepelev V, Yurov Y (2001) Alpha-satellite DNA of primates: old and new families. Chromosoma 110:253-266
4. Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp SC, Eichler EE (2007) Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PLoS Comput Biol 3:1807-1818
5. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RVet al (2002) Recent segmental duplications in the human genome. Science 297:1003-1007
6. Baldini A, Smith DI, Rocchi M, Miller OJ, Miller DA (1989) A human alphoid DNA clone from the EcoRI dimeric family: genomic and internal organization and chromosomal assignment. Genomics 5:822-828
7. Blower MD, Stockwell TB, Karpen GH (2002) Conserved organization of centromeric chromatin in flies and humans. Developmental cell 2:319-330
8. Cavalli-Sforza LL, Kidd JR, Kidd KK, Bucci C, Bowcock AM et al (1986) DNA markers and genetic variation in the human species. Cold Spring Harb Symp Quant Biol 51 (Pt 1): 411-417
9. Cheeseman IM, Desai A (2008) Molecular architecture of the kinetochore-microtubule interface. Nat Rev Mol Cell Biol 9:33-46
10. Choo KHA (1997) Centromere DNA dynamics: latent centromeres and neocentromere formation. Am J Hum Genet 61:1225-1233
11. Dover GA (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111-117
12. Durfy SJ, Willard HF (1989) Patterns of intra-and interarray sequence variation in alpha satellite from the human X chromosome: evidence for short-range homogenization of tandemly repeated DNA sequences. Genomics 5:810-821
13. Finelli P, Antonacci R, Marzella R, Lonoce A, Archidiacono N, Rocchi M (1996) Structural organization of multiple alphoid subsets coexisting on human chromosomes 1, 4, 5, 7, 9, 15, 18, and 19. Genomics 38:325-330
14. Folco HD, Pidoux AL, Urano T, Allshire RC (2008) Heterochromatin and RNAi are required to establish CENP-A chromatin at centromeres. Science 319:94-97
15. Furuyama T, Henikoff S (2009) Centromeric nucleosomes induce positive DNA supercoils. Cell 138:104-113
16. Gray KM, White JW, Costanzi C, Gillespie D, Schroeder WT et al (1985) Recent amplification of an alpha satellite DNA in humans. Nucleic Acids Res 13:521-535
17. Guse A, Carroll CW, Moree B, Fuller CJ, Straight AF (2011) In vitro centromere and kinetochore assembly on defined chromatin templates. Nature 447:354-358
18. Haaf T, Ward DC (1994) Structural analysis of alpha-satellite DNA and centromere proteins using extended chromatin and chromosomes. Hum Mol Genet 3:697-709
19. Harrington JJ, Van Bokkelen G, Mays RW, Gustashaw K,Willard HF (1997) Formation of de novo centromeres and construction of first-generation human artificial microchromosomes. Nat Genet 15:345-355
20. Henikoff S, Ahmad K, Malik HS (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098-1102
21. Hori T, Amano M, Suzuki A, Backer CB, Welburn JP et al (2008) CCAN makes multiple contacts with centromeric DNA to provide distinct pathways to the outer kinetochore. Cell 135:1039-1052
22. Kent W, Sugnet C, Furey T, Roskin K et al (2002) The human genome browser at UCSC. Genome Res 12:996-1006
23. Kirsch S, Weiss B, Miner TL, Waterston RH, Clark RA et al (2005) Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome. Genome Res 15:195-204
24. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R et al (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639-1645
25. Lam AL, Boivin CD, Bonney CF, Rudd MK, Sullivan BA (2006) Human centromeric chromatin is a dynamic chromosomal domain that can spread over noncentromeric DNA. Proc Natl Acad Sci U S A 103:4186-4191
26. Lee C, Wevrick R, Fisher RB, Ferguson-Smith MA, Lin CC (1997) Human centromeric DNAs. Hum Genet 100:291-304
27. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV et al (2007) Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci U S A 104:19942-19947
28. Lyle R, Prandini P, Osoegawa K, ten Hallers B, Humphray S et al (2007) Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21. Genome Res 17:1690-1696
29. Malik HS, Henikoff S (2002) Conflict begets complexity: the evolution of centromeres. Curr Opin Genet Dev 12:711-718
30. Manuelidis L (1976) Repeating restriction fragments of human DNA. Nucleic Acids Res 3:3063-3076
31. Manuelidis L (1978) Chromosomal localization of complex and simple repeated human DNAs. Chromosoma 66:23-32
32. Masumoto H, Masukata H, Muro Y, Nozaki N, Okazaki T (1989) A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. J Cell Biol 109:1963-1973
33. Montefalcone G, Tempesta S, Rocchi M, Archidiacono N (1999) Centromere repositioning. Genome Res 9:1184-1188
34. Nishino T, Takeuchi K, Gascoigne KE, Suzuki A, Hori T et al (2012) CENP-T-W-S-X forms a unique centromeric chromatin structure with a histone-like fold. Cell 148:487-501
35. Oakey R, Tyler-Smith C (1990) Y chromosome DNA haplotyping suggests that most European and Asian men are descended from one of two males. Genomics 7:325-330
36. Ohta T, Dover GA (1984) The cohesive population genetics of molecular drive. Genetics 108:501-521
37. Ohzeki J-i, Nakano M, Okada T, Masumoto H (2002) CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA. J Cell Biol 159:765-775
38. Reich D, Patterson N, De Jager PL, McDonald GJ,Waliszewska A et al (2005) A whole-genome admixture scan finds a candidate locus for multiple sclerosis susceptibility. Nat Genet 37:1113-1118
39. Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K et al (2005) The DNA sequence of the human X chromosome. Nature 434:325-337
40. Rudd MK, Willard HF (2004) Analysis of the centromeric regions of the human genome assembly. Trends Genet 20:529-533
41. Saffery R, Wong LH, Irvine DV, Bateman MA, Griffiths B et al (2001) Construction of neocentromere-based human minichromosomes by telomere-associated chromosomal truncation. Proc Natl Acad Sci USA 98:5705-5710
42. Santos FR, Pandya A, Kayser M, Mitchell RJ, Liu A et al (2000) A polymorphic L1 retroposon insertion in the centromere of the human Y chromosome. Hum Mol Genet 9:421-430
43. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF (2001) Genomic and genetic definition of a functional human centromere. Science 294:109-115
44. Schueler MG, Dunn JM, Bird CP, Ross MT, Viggiano L et al (2005) Progressive proximal expansion of the primate X chromosome centromere. Proc Natl Acad Sci USA 102:10563-10568
45. Screpanti E, De Antoni A, Alushin GM, Petrovic A, Melis T et al (2011) Direct binding of Cenp-C to the Mis12 complex joins the inner and outer kinetochore. Curr Biol 21:391-398
46. She X, Horvath JE, Jiang Z, Liu G, Furey TS et al (2004) The structure and evolution of centromeric transition regions within the human genome. Nature 430:857-864
47. Shepelev VA, Alexandrov AA, Yurov YB, Alexandrov IA (2009) The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes. PLoS Genet 5: e1000641
48. Stacey SN, Manolescu A, Sulem P, Thorlacius S, Gudjonsson SA et al (2008) Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 40:703-706
49. Sullivan BA, Willard HF (1998) Stable dicentric X chromosomes with two functional centromeres. Nat Genet 20:227-228
50. Sullivan LL, Boivin CD, Mravinac B, Song IY, Sullivan BA (2011) Genomic size of CENP-A domain is proportional to total alpha satellite array size at human centromeres and expands in cancer cells. Chromosome Res. 19(4):457-470
51. Tyler-Smith C, Oakey RJ, Larin Z, Fisher RB, Crocker M et al (1993) Localization of DNA sequences required for human centromere function through an analysis of rearranged Y chromosomes. Nat Genet 5:368-375
52. Vafa O, Sullivan KF (1997) Chromatin containing CENP-A and alpha-satellite DNA is a major component of the inner kinetochore plate. Curr Biol 7:897-900
53. Vissel B, Choo KHA (1991) Four distinct alpha satellite subfamilies shared by human chromosomes 13, 14 and 21. Nucleic Acids Res 19:271-277
54. Vissel B, Choo KHA (1992) Evolutionary relationships of multiple alpha satellite subfamilies in the centromeres of human chromosomes 13, 14, and 21. J Mol Evol 35:137-146
55. Warburton PE, Greig GM, Tea H, Willard HF (1991) PCR amplification of chromosome-specific alpha satellite DNA: definition of centromeric STS markers and polymorphic analysis. Genomics 11:324-333
56. Warburton PE, Wevrick R, Mahtani MM, Willard HF (1992) Pulsed-field and two-dimensional gel electrophoresis of long arrays of tandemly repeated DNA: analysis of human centromeric alpha satellite. Methods Mol Biol 12:299-317
57. Warburton PE, Hasson D, Guillem F, Lescale C, Jin X, Abrusan G (2008) Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 9:533
58. Waye JS, Willard HF (1987) Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes. Nucleic Acids Res 15:7549-7569
59. Wevrick R, Willard HF (1989) Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: high-frequency array-length polymorphism and meiotic stability. Proc Natl Acad Sci U S A 86:9394-9398
60. Wevrick R, Willard HF (1991) Physical map of the centromeric region of human chromosome 7: relationship between two distinct alpha satellite arrays. Nucleic Acids Res 19:2295-2301
61. Willard HF (1985) Chromosome-specific organization of human alpha satellite DNA. Am J Hum Genet 37:524-532
62. Willard HF, Waye JS (1987) Hierarchical order in chromosomespecific human alpha satellite DNA. Trends Genet 3:192-198
63. Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R (2007) Localizing recent adaptive evolution in the human genome. PLoS genetics 3:e90