A high-resolution map of nucleosome positioning on a fission yeast centromere

Genome Research

Volumn 18, Issue 7, 2008, Pages 1064-1072

  Song, Jun S ^a,b,c   Liu, Xingkun ^d   Liu, X Shirley ^a,b   He, Xiangwei ^d  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c INSTITUTE FOR ADVANCED STUDY   (United States)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; CENTROMERE; CHROMATIN STRUCTURE; DNA SEQUENCE; FUNGAL GENETICS; GENE DELETION; GENE MUTATION; GENE OVEREXPRESSION; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; SCHIZOSACCHAROMYCES POMBE;

CENTROMERE; CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; DNA, FUNGAL; NUCLEOSOMES; SCHIZOSACCHAROMYCES;

SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 46449112609     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.075374.107     Document Type: Article

References (51)

1. Ando, S., Yang, H., Nozaki, N., Okazaki, T., and Yoda, K. 2002. CENP-A, -B, and -C chromatin complex that contains the I-type alpha-satellite array constitutes the prekinetochore in HeLa cells. Mol. Cell. Biol. 22: 2229-2241.
2. Appelgren, H., Kniola, B., and Ekwall, K. 2003. Distinct centromere domain structures with separate functions demonstrated in live fission yeast cells. J. Cell Sci. 116: 4035-4042.
3. Bailey, T.L. and Elkan, C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2: 28-36.
4. Bailey, T.L., Williams, N., Misleh, C., and Li, W.W. 2006. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34: W369-W373.
5. Baum, M., Sanyal, K., Mishra, P.K., Thaler, N., and Carbon, J. 2006. Formation of functional centromeric chromatin is specified epigenetically in Candida albicans. Proc. Natl. Acad. Sci. 103: 14877-14882.
6. Bernardi, F., Koller, T., and Thoma, F. 1991. The ade6 gene of the fission yeast Schizosaccharomyces pombe has the same chromatin structure in the chromosome and in plasmids. Yeast 7: 547-558.
7. Black, B.E., Foltz, D.R., Chakravarthy, S., Luger, K., Woods Jr., V.L., and Cleveland, D.W. 2004. Structural determinants for generating centromeric chromatin. Nature 430: 578-582.
8. Bloom, K.S. and Carbon, J. 1982. Yeast centromere DNA is in a unique and highly ordered structure in chromosomes and small circular minichromosomes. Cell 29: 305-317.
9. Bloom, K., Sharma, S., and Dokholyan, N.V. 2006. The path of DNA in the kinetochore. Curr. Biol. 16: R276-R278.
10. Chen, E.S., Saitoh, S., Yanagida, M., and Takahashi, K. 2003a. A cell cycle-regulated GATA factor promotes centromeric localization of CENP-A in fission yeast. Mol. Cell 11: 175-187.
11. Chen, E.S., Yanagida, M., and Takahashi, K. 2003b. Does a GATA factor make the bed for centromeric nucleosomes? Cell Cycle 2: 277-278.
12. Choe, J., Schuster, T., and Grunstein, M. 1985. Organization, primary structure, and evolution of histone H2A and H2B genes of the fission yeast Schizosaccharomyces pombe. Mol. Cell. Biol. 5: 3261-3269.
13. Clarke, L., Amstutz, H., Fishel, B., and Carbon, J. 1986. Analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. 83: 8253-8257.
14. Cleveland, D.W., Mao, Y., and Sullivan, K.F. 2003. Centromeres and kinetochores: From epigenetics to mitotic checkpoint signaling. Cell 112: 407-421.
15. Conde e Silva, N., Black, B.E., Sivolob, A., Filipski, J., Cleveland, D.W., and Prunell, A. 2007. CENP-A-containing nucleosomes: Easier disassembly versus exclusive centromeric localization. J. Mol. Biol. 370: 555-573.
16. Earnshaw, W.C. and Rothfield, N. 1985. Identification of a family of human centromere proteins using autoimmune sera from patients with scleroderma. Chromosoma 91: 313-321.
17. Espelin, C.W., Simons, K.T., Harrison, S.C., and Sorger, P.K. 2003. Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol. Biol. Cell 14: 4557-4568.
18. Fleig, U., Sen-Gupta, M., and Hegemann, J.H. 1996. Fission yeast mal2+ is required for chromosome segregation. Mol. Cell. Biol. 16: 6169-6177.
19. Foltz, D.R., Jansen, L.E., Black, B.E., Bailey, A.O., Yates III, J.R., and Cleveland, D.W. 2006. The human CENP-A centromeric nucleosome-associated complex. Nat. Cell Biol. 8: 458-469.
20. Goshima, G., Saitoh, S., and Yanagida, M. 1999. Proper metaphase spindle length is determined by centromere proteins Mis12 and Mis6 required for faithful chromosome segregation. Genes & Dev. 13: 1664-1677.
21. Hayashi, T., Fujita, Y., Iwasaki, O., Adachi, Y., Takahashi, K., and Yanagida, M. 2004. Mis16 and Mis18 are required for CENP-A loading and histone deacetylation at centromeres. Cell 118: 715-729.
22. Henikoff, S., Ahmad, K., and Malik, H.S. 2001. The centromere paradox: Stable inheritance with rapidly evolving DNA. Science 293: 1098-1102.
23. Jin, Q.W., Pidoux, A.L., Decker, C., Allshire, R.C., and Fleig, U. 2002. The mal2p protein is an essential component of the fission yeast centromere. Mol. Cell. Biol. 22: 7168-7183.
24. Joglekar, A.P., Bouck, D., Finley, K., Liu, X., Wan, Y., Berman, J., He, X., Salmon, E.D., and Bloom, K.S. 2008. Molecular architecture of the kinetochore-microtubule attachment site is conserved between point and regional centromeres. J. Cell Biol. 181: 587-594.
25. Lee, W., Tillo, D., Bray, N., Morse, R.H., Davis, R.W., Hughes, T.R., and Nislow, C. 2007. A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet. 39: 1235-1244.
26. Levitsky, V.G. 2004. RECON: A program for prediction of nucleosome formation potential. Nucleic Acids Res. 32: W346-W349.
27. Liu, X., McLeod, I., Anderson, S., Yates III, J.R., and He, X. 2005. Molecular analysis of kinetochore architecture in fission yeast. EMBO J. 24: 2919-2930.
28. Marschall, L.G. and Clarke, L. 1995. A novel cis-acting centromeric DNA element affects S. pombe centromeric chromatin structure at a distance. J. Cell Biol. 128: 445-454.
29. Mellone, B.G. and Allshire, R.C. 2003. Stretching it: Putting the CEN(P-A) in centromere. Curr. Opin. Genet. Dev. 13: 191-198.
30. Meraldi, P., McAinsh, A.D., Rheinbay, E., and Sorger, P.K. 2006. Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins. Genome Biol. 7: R23. doi: 10.1186/gb-2006-7-3-r23.
31. Nabetani, A., Koujin, T., Tsutsumi, C., Haraguchi, T., and Hiraoka, Y. 2001. A conserved protein, Nuf2, is implicated in connecting the centromere to the spindle during chromosome segregation: a link between the kinetochore function and the spindle checkpoint. Chromosoma 110: 322-334.
32. Ozsolak, F., Song, J.S., Liu, X.S., and Fisher, D.E. 2007. High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol. 25: 244-248.
33. Palmer, D.K., O'Day, K., Trong, H.L., Charbonneau, H., and Margolis, R.L. 1991. Purification of the centromere-specific protein CENP-A and demonstration that it is a distinctive histone. Proc. Natl. Acad. Sci. 88: 3734-3738.
34. Peckham, H.E., Thurman, R.E., Fu, Y., Stamatoyannopoulos, J.A., Noble, W.S., Struhl, K., and Weng, Z. 2007. Nucleosome positioning signals in genomic DNA. Genome Res. 17: 1170-1177.
35. Pidoux, A.L. and Allshire, R.C. 2004. Kinetochore and heterochromatin domains of the fission yeast centromere. Chromosome Res. 12: 521-534.
36. Pidoux, A.L. and Allshire, R.C. 2005. The role of heterochromatin in centromere function. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360: 569-579.
37. Polizzi, C. and Clarke, L. 1991. The chromatin structure of centromeres from fission yeast: Differentiation of the central core that correlates with function. J. Cell Biol. 112: 191-201.
38. Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thastrom, A., Field, Y., Moore, I.K., Wang, J.P., and Widom, J. 2006. A genomic code for nucleosome positioning. Nature 442: 772-778.
39. Smirnova, J.B. and McFarlane, R.J. 2002. The unique centromeric chromatin structure of Schizosaccharomyces pombe is maintained during meiosis. J. Biol. Chem. 277: 19817-19822.
40. Stein, A. and Bina, M. 1999. A signal encoded in vertebrate DNA that influences nucleosome positioning and alignment. Nucleic Acids Res. 27: 848-853.
41. Sullivan, K.F., Hechenberger, M., and Masri, K. 1994. Human CENP-A contains a histone H3 related histone fold domain that is required for targeting to the centromere. J. Cell Biol. 127: 581-592.
42. Sullivan, B.A., Blower, M.D., and Karpen, G.H. 2001. Determining centromere identity: Cyclical stories and forking paths. Nat. Rev. Genet. 2: 584-596.
43. Takahashi, K., Murakami, S., Chikashige, Y., Funabiki, H., Niwa, O., and Yanagida, M. 1992. A low copy number central sequence with strict symmetry and unusual chromatin structure in fission yeast centromere. Mol. Biol. Cell 3: 819-835.
44. Takahashi, K., Chen, E.S., and Yanagida, M. 2000. Requirement of Mis6 centromere connector for localizing a CENP-A-like protein in fission yeast. Science 288: 2215-2219.
45. Takahashi, K., Takayama, Y., Masuda, F., Kobayashi, Y., and Saitoh, S. 2005. Two distinct pathways responsible for the loading of CENP-A to centromeres in the fission yeast cell cycle. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360: 595-606.
46. Takayama, Y. and Takahashi, K. 2007. Differential regulation of repeated histone genes during the fission yeast cell cycle. Nucleic Acids Res. 22: 22.
47. Tommerup, H., Dousmanis, A., and de Lange, T. 1994. Unusual chromatin in human telomeres. Mol. Cell. Biol. 14: 5777-5785.
48. Westermann, S., Drubin, D.G., and Barnes, G. 2007. Structures and functions of yeast kinetochore complexes. Annu. Rev. Biochem. 76: 563-591.
49. Yoda, K., Ando, S., Morishita, S., Houmura, K., Hashimoto, K., Takeyasu, K., and Okazaki, T. 2000. Human centromere protein A (CENP-A) can replace histone H3 in nucleosome reconstitution in vitro. Proc. Natl. Acad. Sci. 97: 7266-7271.
50. Yuan, G.C. and Liu, J.S. 2008. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput. Biol. 4: e13. doi: 10.1371/journal.pcbi.0040013.
51. Yuan, G.C., Liu, Y.J., Dion, M.F., Slack, M.D., Wu, L.F., Altschuler, S.J., and Rando, O.J. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.