Sequences associated with centromere competency in the human genome

Molecular and Cellular Biology

Volumn 33, Issue 4, 2013, Pages 763-772

  Hayden, Karen E ^a,b   Strome, Erin D ^a,c   Merrett, Stephanie L ^a   Lee, Hye Ran ^a,d   Katharine Rudd, M ^a,e   Willard, Huntington F ^a  

^a DUKE UNIVERSITY   (United States)

^b University of California Santa Cruz   (United States)

^c NORTHERN KENTUCKY UNIVERSITY   (United States)

^d UNIVERSITY OF NORTH CAROLINA   (United States)

^e EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CENTROMERE PROTEIN A; SATELLITE DNA;

ARTICLE; ARTIFICIAL CHROMOSOME; CENTROMERE; DNA SEQUENCE; EPIGENETICS; GENE SEQUENCE; HUMAN; PRIORITY JOURNAL;

AUTOANTIGENS; BASE SEQUENCE; CENTROMERE; CHROMOSOMAL PROTEINS, NON-HISTONE; CHROMOSOMES, ARTIFICIAL; DATABASES, GENETIC; DNA, SATELLITE; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE DATA;

EID: 84873805996     PISSN: 02707306     EISSN: 10985549     Source Type: Journal    
DOI: 10.1128/MCB.01198-12     Document Type: Article

References (49)

1. Manuelidis L. 1978. Chromosomal localization of complex and simple repeated human DNAs. Chromosoma 66:23-32.
2. Henikoff S, Ahmad K, Malik HS. 2001. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098-1102.
3. Karpen GH, Allshire RC. 1997. The case for epigenetic effects on centromere identity and function. Trends Genet. 13:489-496.
4. Schueler MG, Sullivan BA. 2006. Structural and functional dynamics of human centromeric chromatin. Annu. Rev. Genomics Hum. Genet. 7:301-313.
5. Ugarković DI. 2009. Centromere-competent DNA: structure and evolution. Prog. Mol. Subcell. Biol. 48:53-76.
6. 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.
7. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF. 2001. Genomic and genetic definition of a functional human centromere. Science 294:109-115.
8. Vafa O, Sullivan KF. 1997. Chromatin containing CENP-A and alphasatellite DNA is a major component of the inner kinetochore plate. Curr. Biol. 7:897-900.
9. Harrington JJ, Van Bokkelen G, Mays RW, Gustashaw K, Willard HF. 1997. Formation of de novo centromeres and construction of firstgeneration human artificial microchromosomes. Nat. Genet. 15:345-355.
10. Ikeno M, Grimes B, Okazaki T, Nakano M, Saitoh K, Hoshino H, McGill NI, Cooke H, Masumoto H. 1998. Construction of YAC-based mammalian artificial chromosomes. Nat. Biotechnol. 16:431-439.
11. Nakano M, Okamoto Y, Ohzeki J, Masumoto H. 2003. Epigenetic assembly of centromeric chromatin at ectopic alpha-satellite sites on human chromosomes. J. Cell Sci. 116:4021-4034.
12. Masumoto H, Ikeno M, Nakano M, Okazaki T, Grimes B, Cooke H, Suzuki N. 1998. Assay of centromere function using a human artificial chromosome. Chromosoma 107:406-416.
13. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
14. Rudd MK, Willard HF. 2004. Analysis of the centromeric regions of the human genome assembly. Trends Genet. 20:529-533.
15. She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark RA, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE. 2004. The structure and evolution of centromeric transition regions within the human genome. Nature 430:857-864.
16. 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.
17. Willard HF, Waye JS. 1987. 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.
18. Masumoto H, Nakano M, Ohzeki J. 2004. The role of CENP-B and alpha-satellite DNA: de novo assembly and epigenetic maintenance of human centromeres. Chromosome Res. 12:543-556.
19. Warburton PE. 1999. Making CENs of mammalian artificial chromosomes. Mol. Genet. Metab. 68:152-160.
20. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AWC, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers Y-H, Frazier ME, Scherer SW, Strausberg RL, Venter JC. 2007. The diploid genome sequence of an individual human. PLoS Biol. 5:e254. doi:10.1371/journal.pbio.0050254.
21. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110:462-467.
22. 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.
23. Bao Z, Eddy SR. 2002. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12:1269-1276.
24. 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.
25. Alkan C, Cardone MF, Catacchio CR, Antonacci F, ÓBrien SJ, Ryder OA, Purgato S, Zoli M, Della Valle G, Eichler EE, Ventura M. 2011. Genome-wide characterization of centromeric satellites from multiple mammalian genomes. Genome Res. 21:137-145.
26. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19:1639-1645.
27. Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589-595.
28. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
29. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25. doi:10.1186/gb-2009-10-3-r25.
30. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. 2008. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5:829-834.
31. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9:R137. doi:10.1186/gb-2008-9-9-r137.
32. Grimes BR, Rhoades AA, Willard HF. 2002. Alpha-satellite DNA and vector composition influence rates of human artificial chromosome formation. Mol. Ther. 5:798-805.
33. 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.
34. Warburton PE, Wevrick R, Mahtani MM, Willard HF. 1992. Pulsedfield and two-dimensional gel electrophoresis of long arrays of tandemly repeated DNA: analysis of human centromeric alpha satellite. Methods Mol. Biol. 12:299-317.
35. Wevrick R, Willard HF. 1989. Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: highfrequency array-length polymorphism and meiotic stability. Proc. Natl. Acad. Sci. U. S. A. 86:9394-9398.
36. Alexandrov IA, Mitkevich SP, Yurov YB. 1988. The phylogeny of human chromosome specific alpha satellites. Chromosoma 96:443-453.
37. Alexandrov IA, Kazakov AE, Tumeneva I, Shepelev V, Yurov Y. 2001. Alpha-satelliteDNAof primates: old and new families. Chromosoma 110: 253-266.
38. Waye JS, England SB, Willard HF. 1987. Genomic organization of alpha satelliteDNAon human chromosome 7: evidence for two distinct alphoid domains on a single chromosome. Mol. Cell. Biol. 7:349-356.
39. 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.
40. Pertile MD, Graham AN, Choo KHA, Kalitsis P. 2009. Rapid evolution of mouse Y centromere repeat DNA belies recent sequence stability. Genome Res. 19:2202-2213.
41. Spence JM, Fournier REK, Oshimura M, Regnier V, Farr CJ. 2005. Topoisomerase II cleavage activity within the human D11Z1 and DXZ1 alpha-satellite arrays. Chromosome Res. 13:637-648.
42. Ohzeki J, 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.
43. Rudd MK, Mays RW, Schwartz S, Willard HF. 2003. Human artificial chromosomes with alpha satellite-based de novo centromeres show increased frequency of nondisjunction and anaphase lag. Mol. Cell. Biol. 23:7689-7697.
44. Maloney KA, Sullivan LL, Matheny JE, Strome ED, Merrett SL, Ferris A, Sullivan BA. 2012. Functional epialleles at an endogenous human centromere. Proc. Natl. Acad. Sci. U. S. A. 109:13704-13709.
45. Rudd MK, Schueler MG, Willard HF. 2003. Sequence organization and functional annotation of human centromeres. Cold Spring Harb. Symp. Quant. Biol. 68:141-149.
46. Mahtani MM, Willard HF. 1990. Pulsed-field gel analysis of alphasatellite DNA at the human X chromosome centromere: high-frequency polymorphisms and array size estimate. Genomics 7:607-613.
47. 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.
48. Prades C, Laurent MA, Puechberty J, Yurov Y, Roizès G. 1996. SINE and LINE within human centromeres. J. Mol. Evol. 42:37-43.
49. Dimitriadis EK, Weber C, Gill RK, Diekmann S, Dalal Y. 2010. Tetrameric organization of vertebrate centromeric nucleosomes. Proc. Natl. Acad. Sci. U. S. A. 107:20317-20322