Structural features of the rice chromosome 4 centromere

Nucleic Acids Research

Volumn 32, Issue 6, 2004, Pages 2023-2030

  Zhang, Yu ^c   Huang, Yuchen ^c   Zhang, Lei ^c   Li, Ying ^c   Lu, Tingting ^c   Lu, Yiqi ^c   Feng, Qi ^c   Zhao, Qiang ^c   Cheng, Zhukuan ^c   Xue, Yongbiao ^a   Wing, Rod A ^b   Han, Bin ^c  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF ARIZONA   (United States)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CENTROMERE; CHROMOSOME 4; CHROMOSOME STRUCTURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROPOSON; RICE; SEQUENCE ANALYSIS; TANDEM REPEAT;

BASE SEQUENCE; CENTROMERE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; DNA, SATELLITE; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PHYSICAL CHROMOSOME MAPPING; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; TANDEM REPEAT SEQUENCES;

BACTERIA (MICROORGANISMS);

EID: 3042513368     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh521     Document Type: Article

References (40)

1. Henikoff,S., Ahmad,K. and Malik,H.S. (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science, 293, 1098-1102.
2. Sullivan,B.A., Blower,M.D. and Karpen,G.H. (2001) Determining centromere identity: cyclical stories and forking paths. Nature Rev. Genet., 2, 584-596.
3. Harrington,J.J., Van,Bokkelen,G., Mays,R.M., Gustashaw,K. and Willard,H.F. (1997) Formation of de nova centromeres and construction of first-generation human artificial microchromosomes. Nature Genet., 15, 345-355.
4. Ikeno,M., Grimes,B., Okazaki,T., Nakano,M., Saitoh,K., Hoshino,H., McGill,N.I., Cooke,H. and Masumoto,H. (1998) Construction of YAC-based mammalian artificial chromosomes. Nat. Biotechnol., 16, 431-439.
5. Murphy,T.D. and Karpen,G.H. (1995) Localization of centromere function in a Drosophila minichromosome. Cell, 82, 599-609.
6. Kaszas,E. and Birchler,J.A. (1996) Misdivision analysis of centromere structure in maize. EMBO J., 15, 5246-5255.
7. Clarke,L. (1990) Centromeres of budding and fission yeast. Trends Genet., 6, 150-154.
8. Clarke,L. (1998) Centromeres: proteins, protein complexes, and repeated domains at centromeres of simple eukaryotes. Curr. Opin. Genet. Dev., 8, 212-218.
9. The C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science, 11, 2012-2018.
10. The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
11. Venter,J.C., Adams,M.D., Myers,E.W., Li,P.W., Mural,R.J., Sutton,G.G., Smith,H.O., Yandell,M., Evans,C.A., Holt,R.A. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
12. International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
13. Sasaki,T., Matsumoto,T., Yamamoto,K., Sakata,K., Baba,T., Katayose,Y., Wu,J., Niimura,Y., Cheng,Z., Nagamura,Y. et al. (2002) The genome sequence and structure of rice chromosome 1. Nature, 420, 312-316.
14. Feng,Q., Zhang,Y., Hao,P., Wang,S., Fu,G., Huang,Y., Li,Y., Zhu,J., Liu,Y., Hu,X. et al. (2002) Sequence and analysis of rice chromosome 4. Nature, 420, 316-320.
15. Schueler,M.G., Higgins,A.W., Rudd,M.K., Gustashaw,K. and Willard,H.F. (2001) Genomic and genetic definition of a functional human centromere. Science, 294, 109-115.
16. Copenhaver,G.P., Nickel,K., Kuromori,T., Benito,M.I., Kaul,S., Lin,X., Bevan,M., Murphy,G., Harris,B., Parnell,L.D. et al. (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science, 286, 2468-2474.
17. Sun,X., Le,H.D., Wahlstrom,J.M. and Karpen,G.H. (2003) Sequence analysis of a functional Drosophila centromere. Genome Res., 13, 182-194.
18. Cheng,Z., Dong,F., Langdon,T., Ouyang,S., Buell,C.R., Gu,M., Blattner,F.R. and Jiang,J. (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell, 14, 1691-1704.
19. Dong,F., Miller,J.T., Jackson,S.A., Wang,G.L., Ronald,P.C. and Jiang,J. (1998) Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc. Natl Acad. Sci. USA, 95, 8135-8140.
20. Nomomura,K.I. and Kurata,N. (1999) Organization of the 1.9-kb repeat unit RCE1 in the centromeric region of rice chromosomes. Mol. Gen. Genet., 261, 1-10.
21. Langdon,T., Seago,C., Mende,M., Leggett,M., Thomas,H., Forster,J.W., Thomas,H., Jones,R.N. and Jenkins,G. (2000) Retrotransposon evolution in diverse plant genomes. Genetics, 156, 313-325.
22. Kumekawa,N., Ohmido,N., Fukui,K., Ohtsubo,E. and Ohtsubo,H. (2001) A new gypsy-type retrotransposon, RIRE7: preferential insertion into the tandom repeat sequence TrsD in pericentromeric heterochromatin regions of rice chromosomes. Mol. Genet. Gemomics, 265, 480-488.
23. Nonomura,K.T. and Kurata,N. (2001) The centromere composition of multiple repetitive sequences on rice chromosome 5. Chromosoma, 110, 284-291.
24. Zhao,Q., Zhang,Y., Cheng,Z., Chen,M., Wang,S., Feng,Q., Huang,Y., Li,Y., Tang,Y., Zhou,B. et al. (2002) A fine physical map of the rice chromosome 4. Genome Res., 12, 817-823.
25. Ewing,B. and Green,P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
26. SanMiguel,P., Gaut,B.S., Tikhonov,A., Nakajima,Y. and Bennetzen,J.L. (1998) The paleontology of intergene retrotransposons of maize. Nature Genet., 20, 43-45.
27. Gaut,B.S., Morton,B.R., McCaig,B.C. and Clegg,M.T. (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl Acad. Sci. USA, 93, 10274-10279.
28. Chen,M., Presting,G., Barbazuk,W.B., Goicoechea,J.L., Blackmon,B., Fang,G., Kim,H., Frisch,D., Yu,Y., Sun,S. et al. (2002) An integrated physical and genetic map of the rice genome. Plant Cell, 14, 537-545.
29. Harushima,Y., Yano,M., Shomura,A., Sato,M., Shimano,T., Kuboki,Y., Yamamoto,T., Lin,S.Y., Antonio,B.A., Parco,A. et al. (1998). A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics, 148, 479-494.
30. Wu,J., Maehara,T., Shimokawa,T., Yamamoto,S., Harada,C., Takazaki,Y., Ono,N., Mukai,Y., Koike,K., Yazaki,J. et al. (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell, 14, 525-535.
31. Nagaki,K., Talbert,P.B., Zhong,C.X., Dawe,R.K., Henikoff,S. and Jiang,J. (2003) Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics, 163, 1221-1225.
32. Zhong,C.X., Marshall,J.B., Topp,C., Mroczek,R., Kato,A., Nagaki,K., Birchler,J.A., Jiang,J. and Dawe,R.K. (2002) Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell, 14, 2825-2836.
33. Jiang,J., Birchler,J.A., Parrott,W.A. and Dawe,R.K. (2003) A molecular view of plant centromeres. Trends Plant Sci., 8, 570-575.
34. Cheng,Z., Buell,C.R., Wing,R.A., Gu,M. and Jiang,J. (2001) Toward a cytological characterization of the rice genome. Genome Res., 11, 2133-2141.
35. Ananiev,E.V., Phillips,R.L. and Rines,H.W. (1998) Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc. Natl Acad. Sci. USA, 95, 13073-13078.
36. Miller,J.T., Dong,F., Jackson,S.A., Song,J. and Jiang,J. (1998) Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics, 150, 1615-1623.
37. Hudakova,S., Michalek,W., Presting,G.G., ten Hoopen,R., dos Santos,K., Jasencakova,Z. and Schubert,I. (2001) Sequence organization of barley centromeres. Nucleic Acids Res., 29, 5029-5035.
38. Volpe,T., Schramke,V., Hamilton,G.L., White,S.A., Teng,G., Martienssen,R.A. and Allshire,R.C. (2003) RNA interference is required for normal centromere function in fission yeast. Chromosome Res., 11, 137-146.
39. Martienssen,R.A. (2003) Maintenance of heterochromatin by RNA interference of tandem repeats. Nature Genet., 35, 213-214.
40. Schramke,V. and Allshire,R. (2003) Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science, 301, 1069-1074.