This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Sun, X. Articles by Karpen, G. H. Search for Related Content PubMed PubMed Citation Articles by Sun, X. Articles by Karpen, G. H. Pubmed/NCBI databases Nucleotide Social Bookmarking                   What's this?

LETTER

Sequence Analysis of a Functional Drosophila Centromere

Molecular and Cell Biology Laboratory, The Salk Institute, La Jolla, CA 92037, USA

Centromeres are the site for kinetochore formation and spindle attachment and are embedded in heterochromatin in most eukaryotes. The repeat-rich nature of heterochromatin has hindered obtaining a detailed understanding of the composition and organization of heterochromatic and centromeric DNA sequences. Here, we report the results of extensive sequence analysis of a fully functional centromere present in the Drosophila Dp1187 minichromosome. Approximately 8.4% (31 kb) of the highly repeated satellite DNA (AATAT and TTCTC) was sequenced, representing the largest data set of Drosophila satellite DNA sequence to date. Sequence analysis revealed that the orientation of the arrays is uniform and that individual repeats within the arrays mostly differ by rare, single-base polymorphisms. The entire complex DNA component of this centromere (69.7 kb) was sequenced and assembled. The 39-kb "complex island" Maupiti contains long stretches of a complex A+T rich repeat interspersed with transposon fragments, and most of these elements are organized as direct repeats. Surprisingly, five single, intact transposons are directly inserted at different locations in the AATAT satellite arrays. We find no evidence for centromere-specific sequences within this centromere, providing further evidence for sequence-independent, epigenetic determination of centromere identity and function in higher eukaryotes. Our results also demonstrate that the sequence composition and organization of large regions of centric heterochromatin can be determined, despite the presence of repeated DNA.

[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos.: Beagle = AY183918, F = AY183919, 412 = AY183920, Bel = AY183921, You = AY183922, Maupiti = AY183926, AATAT = AY183925, AY183931–AY184007, and TTCTC = AY183923–AY183924, AY183927–AY183930, AY184008–AY184069].

E-MAIL karpen{at}salk.edu; FAX (858) 622-0417.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.681703.

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				M. Murata, E. Yokota, F. Shibata, and K. Kashihara Functional analysis of the Arabidopsis centromere by T-DNA insertion-induced centromere breakage PNAS, May 27, 2008; 105(21): 7511 - 7516. [Abstract] [Full Text] [PDF]

				G. Bosco, P. Campbell, J. T. Leiva-Neto, and T. A. Markow Analysis of Drosophila Species Genome Size and Satellite DNA Content Reveals Significant Differences Among Strains as Well as Between Species Genetics, November 1, 2007; 177(3): 1277 - 1290. [Abstract] [Full Text] [PDF]

				A. Villasante, J. P. Abad, and M. Mendez-Lago Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome PNAS, June 19, 2007; 104(25): 10542 - 10547. [Abstract] [Full Text] [PDF]

				C. Paris, F. Geinguenaud, C. Gouyette, J. Liquier, and J. Lacoste Mechanism of Copper Mediated Triple Helix Formation at Neutral pH in Drosophila Satellite Repeats Biophys. J., April 1, 2007; 92(7): 2498 - 2506. [Abstract] [Full Text] [PDF]

				O. V. Demakova, G. V. Pokholkova, T. D. Kolesnikova, S. A. Demakov, E. N. Andreyeva, E. S. Belyaeva, and I. F. Zhimulev The SU(VAR)3-9/HP1 Complex Differentially Regulates the Compaction State and Degree of Underreplication of X Chromosome Pericentric Heterochromatin in Drosophila melanogaster Genetics, February 1, 2007; 175(2): 609 - 620. [Abstract] [Full Text] [PDF]

				H. Yan, H. Ito, K. Nobuta, S. Ouyang, W. Jin, S. Tian, C. Lu, R.C. Venu, G.-l. Wang, P. J. Green, et al. Genomic and Genetic Characterization of Rice Cen3 Reveals Extensive Transcription and Evolutionary Implications of a Complex Centromere PLANT CELL, September 1, 2006; 18(9): 2123 - 2133. [Abstract] [Full Text] [PDF]

				V. Boeva, M. Regnier, D. Papatsenko, and V. Makeev Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression Bioinformatics, March 15, 2006; 22(6): 676 - 684. [Abstract] [Full Text] [PDF]

				J. Ma and S. A. Jackson Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice Genome Res., February 1, 2006; 16(2): 251 - 259. [Abstract] [Full Text] [PDF]

				J. Ma and J. L. Bennetzen Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice PNAS, January 10, 2006; 103(2): 383 - 388. [Abstract] [Full Text] [PDF]

				M. D. Cervantes, X. Xi, D. Vermaak, M.-C. Yao, and H. S. Malik The CNA1 Histone of the Ciliate Tetrahymena thermophila Is Essential for Chromosome Segregation in the Germline Micronucleus Mol. Biol. Cell, January 1, 2006; 17(1): 485 - 497. [Abstract] [Full Text] [PDF]

				T. Ebersole, Y. Okamoto, V. N. Noskov, N. Kouprina, J.-H. Kim, S.-H. Leem, J. C. Barrett, H. Masumoto, and V. Larionov Rapid generation of long synthetic tandem repeats and its application for analysis in human artificial chromosome formation Nucleic Acids Res., September 1, 2005; 33(15): e130 - e130. [Abstract] [Full Text] [PDF]

				N. Mugnier, C. Biemont, and C. Vieira New Regulatory Regions of Drosophila 412 Retrotransposable Element Generated by Recombination Mol. Biol. Evol., March 1, 2005; 22(3): 747 - 757. [Abstract] [Full Text] [PDF]

				F. Shibata and M. Murata Differential localization of the centromere-specific proteins in the major centromeric satellite of Arabidopsis thaliana J. Cell Sci., June 15, 2004; 117(14): 2963 - 2970. [Abstract] [Full Text] [PDF]

				B. Wickstead, K. Ersfeld, and K. Gull The Small Chromosomes of Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes Genome Res., June 1, 2004; 14(6): 1014 - 1024. [Abstract] [Full Text] [PDF]

				Y. Zhang, Y. Huang, L. Zhang, Y. Li, T. Lu, Y. Lu, Q. Feng, Q. Zhao, Z. Cheng, Y. Xue, et al. Structural features of the rice chromosome 4 centromere Nucleic Acids Res., April 2, 2004; 32(6): 2023 - 2030. [Abstract] [Full Text] [PDF]

				J. Wu, H. Yamagata, M. Hayashi-Tsugane, S. Hijishita, M. Fujisawa, M. Shibata, Y. Ito, M. Nakamura, M. Sakaguchi, R. Yoshihara, et al. Composition and Structure of the Centromeric Region of Rice Chromosome 8 PLANT CELL, April 1, 2004; 16(4): 967 - 976. [Abstract] [Full Text] [PDF]

				S. H. Myster, F. Wang, R. Cavallo, W. Christian, S. Bhotika, C. T. Anderson, and M. Peifer Genetic and Bioinformatic Analysis of 41C and the 2R Heterochromatin of Drosophila melanogaster: A Window on the Heterochromatin-Euchromatin Junction Genetics, February 1, 2004; 166(2): 807 - 822. [Abstract] [Full Text] [PDF]

				M. K. Rudd, R. W. Mays, S. Schwartz, and H. F. Willard Human Artificial Chromosomes with Alpha Satellite-Based De Novo Centromeres Show Increased Frequency of Nondisjunction and Anaphase Lag Mol. Cell. Biol., November 1, 2003; 23(21): 7689 - 7697. [Abstract] [Full Text] [PDF]

				V. Schramke and R. Allshire Hairpin RNAs and Retrotransposon LTRs Effect RNAi and Chromatin-Based Gene Silencing Science, August 22, 2003; 301(5636): 1069 - 1074. [Abstract] [Full Text] [PDF]