Genome-wide characterization of centromeric satellites from multiple mammalian genomes

Genome Research

Volumn 21, Issue 1, 2011, Pages 137-145

  Alkan, Can ^a   Cardone, Maria Francesca ^b   Catacchio, Claudia Rita ^b   Antonacci, Francesca ^a   O'Brien, Stephen J ^c   Ryder, Oliver A ^d   Purgato, Stefania ^e   Zoli, Monica ^e   Della Valle, Giuliano ^e   Eichler, Evan E ^a   Ventura, Mario ^a,b  

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

^b UNIVERSITY OF BARI   (Italy)

^c NATIONAL CANCER INSTITUTE   (United States)

^d ZOOLOGICAL SOCIETY OF SAN DIEGO   (United States)

^e UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARMADILLO; ARTICLE; CENTROMERE; CHROMOSOME SATELLITE; CONTROLLED STUDY; DOG; ELEPHANT; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; HORSE; HUMAN; MAMMALIAN GENETICS; NONHUMAN; OPOSSUM; PLATYPUS; PRIORITY JOURNAL;

ANIMALS; ARMADILLOS; BASE SEQUENCE; CENTROMERE; COMPUTATIONAL BIOLOGY; CONSENSUS SEQUENCE; DNA, SATELLITE; DOGS; ELEPHANTS; GENOME; HORSES; MAMMALS; MOLECULAR SEQUENCE DATA; OPOSSUMS; PLATYPUS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ARMADILLO; CANIS FAMILIARIS; DIDELPHIDAE; EQUIDAE; MAMMALIA; VERTEBRATA;

EID: 78651484455     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.111278.110     Document Type: Article

References (59)

1. Alexandrov IA, Mitkevich SP, Yurov YB. 1988. The phylogeny of human chromosome specific alpha satellites. Chromosoma 96: 443-453.
2. Alexandrov I, Kazakov A, Tumeneva I, Shepelev V, Yurov Y. 2001. Alpha-satellite DNA of primates: Old and new families. Chromosoma 110: 253-266.
3. Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp SC, Eichler E.E. 2007. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PLoS Comput Biol 3: 1807-1818.
4. Alves G, Seuanez HN, Fanning T. 1994. Alpha satellite DNA in neotropical primates (Platyrrhini). Chromosoma 103: 262-267.
5. Benson G. 1999. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res 27: 573-580.
6. Breen M, Thomas R, Binns MM, Carter NP, Langford CF. 1999. Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog (Canis familiaris) and human. Genomics 61: 145-155.
7. Bulazel K, Metcalfe C, Ferreri GC, Yu J, Eldridge MD, O'Neill RJ. 2006. Cytogenetic and molecular evaluation of centromere-associated DNA sequences from a marsupial (Macropodidae: Macropus rufogriseus) X chromosome. Genetics 172: 1129-1137.
8. Bulazel KV, Ferreri GC, Eldridge MD, O'Neill RJ. 2007. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biol 8: R170. doi: 10.1186/gb-2007-8-8-r170.
9. Carbone L, Nergadze SG, Magnani E, Misceo D, Francesca Cardone M, Roberto R, Bertoni L, Attolini C, Francesca Piras M, de Jong P. et al. 2006. Evolutionary movement of centromeres in horse, donkey, and zebra. Genomics 87: 777-782.
10. Cardone MF, Alonso A, Pazienza M, Ventura M, Montemurro G, Carbone L, de Jong PJ, Stanyon R, D'Addabbo P, Archidiacono N, et al. 2006. Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs. Genome Biol 7: R91. doi: 10.1186/gb-2006-7-10-r91.
11. Cellamare A, Catacchio CR, Alkan C, Giannuzzi G, Antonacci F, Cardone MF, Della Valle G, Malig M, Rocchi M, Eichler EE, et al. 2009. New insights into centromere organization and evolution from the white-cheeked gibbon and marmoset. Mol Biol Evol 26: 1889-1900.
12. Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, Gu M, Blattner FR, Jiang J. 2002. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14: 1691-1704.
13. Cleveland DW, Mao Y, Sullivan KF. 2003. Centromeres and kinetochores. From epigenetics to mitotic checkpoint signaling. Cell 112: 407-421.
14. Dong F, Miller JT, Jackson SA, Wang GL, Ronald PC, Jiang J. 1998. Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc Natl Acad Sci 95: 8135-8140.
15. Earnshaw WC, Tomkiel JE. 1992. Centromere and kinetochore structure. Curr Opin Cell Biol 4: 86-93.
16. Eckardt NA. 2008. Defining a functional centromere. Plant Cell 20: 7.
17. Eichler EE, Clark RA, She X. 2004. An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat Rev Genet 5: 345-354.
18. Fowler JC, Skinner JD, Burgoyne LA, Drinkwater RD. 1989. Satellite DNA and higher-primate phylogeny. Mol Biol Evol 6: 553-557.
19. Fratkin E, Naughton BT, Brutlag DL, Batzoglou S. 2006. MotifCut: Regulatory motifs finding with maximum density subgraphs. Bioinformatics 22: e150-e157.
20. Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J. 2007. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res 17: 992-1004.
21. Gopalakrishnan S, Sullivan BA, Trazzi S, Della Valle G, Robertson KD. 2009. DNMT3B interacts with constitutive centromere protein CENPC to modulate DNA methylation and the histone code at centromeric regions. Hum Mol Genet 18: 3178-3193.
22. Grady DL, Ratliff RL, Robinson DL, McCanlies EC, Meyne J, Moyzis RK. 1992. Highly conserved repetitive DNA sequences are present at human centromeres. Proc Natl Acad Sci 89: 1695-1699.
23. Haaf T, Willard HF. 1998. Orangutan alpha-satellite monomers are closely related to the human consensus sequence. Mamm Genome 9: 440-447.
24. 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.
25. Kawabe A, Hansson B, Hagenblad J, Forrest A, Charlesworth D. 2006. Centromere locations and associated chromosome rearrangements in Arabidopsis lyrata and A. thaliana. Genetics 173: 1613-1619.
26. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal Wand Clustal X version 2.0. Bioinformatics 23: 2947-2948.
27. Lee C, Wevrick R, Fisher RB, Ferguson-Smith MA, Lin CC. 1997. Human centromeric DNAs. Hum Genet 100: 291-304.
28. Longo MS, Carone DM, Green ED, O'Neill MJ, O'Neill RJ. 2009. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics 10: 334. doi: 10.1186/1471-2164-10-334.
29. Maddox PS, Oegema K, Desai A, Cheeseman IM. 2004. "Holo"er than thou: Chromosome segregation and kinetochore function in C. elegans. Chromosome Res 12: 641-653.
30. McMillan D, Miethke P, Alsop AE, Rens W, O'Brien P, Trifonov V, Veyrunes F, Schatzkamer K, Kremitzki CL, Graves T, et al. 2007. Characterizing the chromosomes of the platypus (Ornithorhynchus anatinus). Chromosome Res 15: 961-974.
31. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-177.
32. Morris CA, Moazed D. 2007. Centromere assembly and propagation. Cell 128: 647-650.
33. Muro Y, Masumoto H, Yoda K, Nozaki N, Ohashi M, Okazaki T. 1992. Centromere protein B assembles human centromeric alpha-satellite DNA at the 17-bp sequence, CENP-B box. J Cell Biol 116: 585-596.
34. Pluta AF, Mackay AM, Ainsztein AM, Goldberg IG, Earnshaw WC. 1995. Centromere: Hub of chromosomal activities. Science 270: 1591-1594.
35. Prasad AB, Allard MW, Green ED. 2008. Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol Biol Evol 25: 1795-1808.
36. Rens W, O'Brien PC, Yang F, Solanky N, Perelman P, Graphodatsky AS, Ferguson MW, Svartman M, De Leo AA, Graves JA, et al. 2001. Karyotype relationships between distantly related marsupials from South America and Australia. Chromosome Res 9: 301-308.
37. Roizes G. 2006. Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning. Nucleic Acids Res 34: 1912-1924.
38. Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP, et al. 2005. The DNA sequence of the human X chromosome. Nature 434: 325-337.
39. Rudd MK, Willard HF. 2004. Analysis of the centromeric regions of the human genome assembly. Trends Genet 20: 529-533.
40. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF. 2001. Genomic and genetic definition of a functional human centromere. Science 294: 109-115.
41. Schueler MG, Dunn JM, Bird CP, Ross MT, Viggiano L, Rocchi M, Willard HF, Green ED. 2005. Progressive proximal expansion of the primate X chromosome centromere. Proc Natl Acad Sci 102: 10563-10568.
42. She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, et al. 2004. The structure and evolution of centromeric transition regions within the human genome. Nature 430: 857-864.
43. Stitou S, Diaz de la Guardia R, Jimenez R, Burgos M. 1999. Isolation of a species-specific satellite DNA with a novel CENP-B-like box from the North African rodent Lemniscomys barbarus. Exp Cell Res 250: 381-386.
44. Sullivan BA, Blower MD, Karpen GH. 2001. Determining centromere identity: Cyclical stories and forking paths. Nat Rev Genet 2: 584-596.
45. Suzuki N, Nakano M, Nozaki N, Egashira S, Okazaki T, Masumoto H. 2004. CENP-B interacts with CENP-CCENPC domains containing Mif2 regions responsible for centromere localization. J Biol Chem 279: 5934-5946.
46. Torras-Llort M, Moreno-Moreno O, Azorin F. 2009. Focus on the centre: The role of chromatin on the regulation of centromere identity and function. EMBO J 28: 2337-2348.
47. Trazzi S, Perini G, Bernardoni R, Zoli M, Reese JC, Musacchio A, Della Valle G. 2009. The C-terminal domain of CENP-C displays multiple and critical functions for mammalian centromere formation. PLoS ONE 4: e5832. doi: 10.1371/journal.pone.0005832.
48. Umlauf D, Goto Y, Cao R, Cerqueira F, Wagschal A, Zhang Y, Feil R. 2004. Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nat Genet 36: 1296-1300.
49. Vagnarelli P, Ribeiro SA, Earnshaw WC. 2008. Centromeres: Old tales and new tools. FEBS Lett 582: 1950-1959.
50. Ventura M, Archidiacono N, Rocchi M. 2001. Centromere emergence in evolution. Genome Res 11: 595-599.
51. Ventura M, Mudge JM, Palumbo V, Burn S, Blennow E, Pierluigi M, Giorda R, Zuffardi O, Archidiacono N, Jackson MS, et al. 2003. Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25. Genome Res 13: 2059-2068.
52. Ventura M, Antonacci F, Cardone MF, Stanyon R, D'Addabbo P, Cellamare A, Sprague LJ, Eichler EE, Archidiacono N, Rocchi M. 2007. Evolutionary formation of new centromeres in macaque. Science 316: 243-246.
53. Warburton PE, Haaf T, Gosden J, Lawson D, Willard HF. 1996. Characterization of a chromosome specific chimpanzee alpha satellite subset: Evolutionary relationship to subsets on human chromosomes. Genomics 33: 220-228.
54. Waye JS, Willard HF. 1989. Concerted evolution of alpha satellite DNA: Evidence for species specificity and a general lack of sequence conservation among alphoid sequences of higher primates. Chromosoma 98: 273-279.
55. Willard HF, Waye JS. 1987a. 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.
56. Willard HF, Waye JS. 1987b. Hierarchical order in chromosome-specific human alpha satellite DNA. Trends Genet 3: 192-198.
57. Willard HF, Wevrick R, Warburton PE. 1989. Human centromere structure: Organization and potential role of alpha satellite DNA. Prog Clin Biol Res 318: 9-18.
58. Yang F, Fu B, O'Brien PCM, Nie W, Ryder OA, Ferguson-Smith MA. 2004. Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: Insight into the occasional fertility of mules. Chromosome Res 12: 65-76.
59. Yoda K, Kitagawa K, Masumoto H, Muro Y, Okazaki T. 1992. A human centromere protein, CENP-B, has a DNA binding domain containing four potential alpha helices at the NH2 terminus, which is separable from dimerizing activity. J Cell Biol 119: 1413-1427.