The complete sequence of a heterochromatic island from a higher eukaryote

Cell

Volumn 100, Issue 3, 2000, Pages 377-386

  McCombie, W Richard ^a   De la Bastide, Melissa ^a   Habermann, Kristina ^a   Parnell, Laurence ^a   Dedhia, Neilay ^a   Gnoj, Lidia ^a   Schutz, Kristin ^a   Huang, Emily ^a   Spiegel, Lori ^a   Yordan, Cristy ^b   Sehkon, Mundeep ^c   Murray, Jennifer ^c   Sheet, Paul ^c   Cordes, Matt ^c   Threideh, Jane ^c   Stoneking, Tamberlyn ^c   Kalicki, Joelle ^c   Graves, Tina ^c   Harmon, Gwen ^c   Edwards, Jennifer ^c   Latreille, Phil ^c   Courtney, Laura ^c   Cloud, James ^c   Abbott, Amanda ^c   Scott, Kelsi ^c   Johnson, Doug ^c   Minx, Pat ^c   Bentley, Dan ^c   Fulton, Bob ^c   Miller, Nancy ^c   Greco, Tracie ^c   Kemp, Kim ^c   Kramer, Jason ^c   Fulton, Lucinda ^c   Mardis, Elaine ^c   Dante, Mike ^c   Pepin, Kym ^c   Hillier, LaDeana ^c   Nelson, Joanne ^c   Spieth, John ^c   Simorowski, Joe ^b   May, Bruce ^b   Ma, Peter ^d   Preston, Ray ^a   Vil, Daniel ^a   Lei, Hoon See ^a   Shekher, Monica ^a   Matero, Anthony ^a   Shah, Ravi ^a   Swaby, I'Kyori ^a   O'Shaughnessy, Andrew ^a   Rodriguez, Milka ^a   Hoffman, Jane ^a   Till, Sally ^a   Granat, Susan ^a   Shohdy, Nadim ^a   Hasegawa, Amy ^a   Hameed, Aliyah ^a   Lodhi, Mohammad ^a,e   Johnson, Arthur ^a,f   Chen, Ellson ^d   Marra, Marco ^c   Wilson, Richard K ^c   Martienssen, Robert ^b   more..

^a Lita Annenberg Hazen Genome Center   (United States)

^b Watson School of Biological Sciences   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d APPLIED BIOSYSTEMS   (United States)

^e Axys Pharmaceuticals Inc   (United States)

^f NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 4; CHROMOSOME CONDENSATION; EUKARYOTE; GENE INSERTION; HETEROCHROMATIN; NONHUMAN; PRIORITY JOURNAL;

ARABIDOPSIS THALIANA;

EID: 0034603217     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)80673-X     Document Type: Article

References (90)

1. Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., et al. (1991). Complementary DNA sequencing: Expressed sequence tags and the human genome project. Science 252, 1651-1656.
2. Alfenito, M.R., and Birchler, J.A. (1993). Molecular characterization of a maize B chromosome centric sequence. Genetics 135, 589-597.
3. Ananiev, E.V., Phillips, R.L., and Rines, H.W. (1998a). Complex structure of knob DNA on maize chromosome 9. Retrotransposon invasion into heterochromatin. Genetics 149, 2025-2037.
4. Ananiev, E.V., Phillips, R.L., and Rines, H.W. (1998b). A knob-associated tandem repeat in maize capable of forming fold-back DNA segments: Are chromosome knobs megatransposons? Proc. Natl. Acad. Sci. USA 95, 10785-10790.
5. Ashburner, M., Misra, S., Roote, J., Lewis, S.E., Blazej, R., Davis, T., Doyle, C., Galle, R., George, R., Harris, N., et al. (1999). An exploration of the sequence of a 2.9 Mb region of the genome of Drosophila melanogaster. The Adh region. Genetics 153, 179-219.
6. Bennett, M.D. (1998). Plant genome values: How much do we know? Proc. Natl. Acad. Sci. USA 95, 2011-2016.
7. Bennetzen, J.L. (1996). The mutator transposable element system of maize. Curr. Top. Microbiol. Immunol. 204, 195-229.
8. Berg, C.A., and Spradling, A.C. (1991). Studies on the rate and site-specificity of P element transposition. Genetics 127, 515-524.
9. Bevan, M., Bancroft, I., Bent, E., Love, K., Goodman, H., Dean, C., Bergkamp, R., Dirkse, W., Van Staveren, M., Stiekema, W., et al. (1998). Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391, 485-488.
10. Bevan, M., Bancroft, I., Mewes, H.W., Martienssen, R., and McCombie, R. (1999). Clearing a path through the jungle: Progress in Arabidopsis genomics. Bioessays 21, 110-120.
11. Brandes, A., Thompson, H., Dean, C., and Heslop-Harrison, J.S. (1997). Multiple repetitive DNA sequences in the paracentromeric regions of Arabidopsis thaliana L. Chromosome Res. 5, 238-246.
12. Burge, C.B., and Karlin, S. (1998). Finding the genes in genomic DNA. Curr. Opin. Struct. Biol. 8, 346-354.
13. C. elegans Sequencing Consortium (1998). Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012-2018.
14. Cavalli, G., and Paro, R. (1998). Chromo-domain proteins: Linking chromatin structure to epigenetic regulation. Curr. Opin. Cell. Biol. 10, 354-360.
15. Civardi, L., Xia, Y., Edwards, K.J., Schnable, P.S., and Nikolau, B.J. (1994). The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc. Natl. Acad. Sci. USA 91, 8268-8272.
16. Cook, K.R., and Karpen, G.H. (1994). A rosy future for heterochromatin. Proc. Natl. Acad. Sci. USA 91, 5219-5221.
17. Copenhaver, G.P., and Pikaard, C.S. (1996). Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution. Plant J. 9, 273-282.
18. Copenhaver, G.P., Browne, W.E., and Preuss, D. (1998). Assaying genome-wide recombination and centromere functions with Arabidopsis tetrads. Proc. Natl. Acad. Sci. USA 95, 247-252.
19. Copenhaver, G.P., Nickel, K., Kuromori, T., Benito, M., Kaul, S., Lin, X., Bevan, M., George Murphy, G., Harris, B., McCombie, W.R., et al. (1999). Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286, 2468-2474.
20. Creighton, H., and McClintock, B. (1931). A correlation of cytological and genetical crossing over in Zea mays. Proc. Natl. Acad. Sci. USA 17, 492-497.
21. Csink, A.K., and Henikoff, S. (1996). Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature 381, 529-531.
22. Dedhia, N.N., and McCombie, W.R. (1998). Kaleidaseq: A web-based tool to monitor data flow in a high throughput sequencing facility. Genome Res. 8, 313-318.
23. Dimitri, P., and Junakovic, N. (1999). Revising the selfish DNA hypothesis: New evidence on accumulation of transposable elements in heterochromatin. Trends Genet. 15, 123-124.
24. Dorer, D.R., and Henikoff, S. (1994). Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77, 993-1002.
25. English, J., Harrison, K., and Jones, J.D. (1993). A genetic analysis of DNA sequence requirements for Dissociation state I activity in tobacco. Plant Cell 5, 501-514.
26. Fanti, L., Dorer, D.R., Berloco, M., Henikoff, S., and Pimpinelli, S. (1998). Heterochromatin protein 1 binds transgene arrays. Chromosoma 107, 286-292.
27. Fauvarque, M.O., and Dura, J.M. (1993). Polyhomeotic regulatory sequences induce developmental regulator-dependent variegation and targeted P-element insertions in Drosophila. Genes Dev. 7, 1508-1520.
28. Fransz, P., Armstrong, S., de Jong, J.H., Parnell, L.D., Van Drunen, C., Dean, C., Zabel, P., Bisseling, T., and Jones, G.H. (2000). Integrated cytogenetic map of chromosome arm 4S of A. thaliana: Structural organization of heterochromatic knob and centromeric heterochromatin. Cell 100, this issue, 367-376.
29. Grewal, S.I., and Klar, A.J. (1997). A recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating-type switching in fission yeast. Genetics 146, 1221-1238.
30. Hebsgaard, S.M., Korning, P.G., Tolstrup, N., Engelbrecht, J., Rouze, P., and Brunak, S. (1996). Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res. 24, 3439-3452.
31. Henikoff, S. (1998). Conspiracy of silence among repeated transgenes. Bioessays 20, 532-535.
32. Hennig, W. (1999). Heterochromatin. Chromosoma 108, 1-9.
33. Heslop-Harrison, J.S., Murata, M., Ogura, Y., Schwarzacher, T., and Motoyoshi, F. (1999). Polymorphisms and genomic organization of repetitive DNA from centromeric regions of Arabidopsis chromosomes. Plant Cell 11, 31-42.
34. Holmquist, G.P., Kapitonov, V.V., and Jurka, J. (1998). Mobile genetic elements, chiasmata, and the unique organization of beta-heterochromatin. Cytogenet. Cell Genet. 80, 113-116.
35. Hudson, A.D., Carpenter, R., and Coen, E.S. (1990). Phenotypic effects of short-range and aberrant transposition in Antirrhinum majus. Plant Mol. Biol. 14, 835-844.
36. Jeddeloh, J.A., Bender, J., and Richards, E.J. (1998). The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 12 1714-1725.
37. Jeddeloh, J.A., Stokes, T.L., and Richards, E.J. (1999). Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 22, 94-97.
38. Kakutani, T., Jeddeloh, J.A., Flowers, S.K., Munakata, K., and Richards, E.J. (1996). Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. USA 93, 12406-12411.
39. Kakutani, T., Munakata, K., Richards, E.J., and Hirochika, H. (1999). Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151, 831-838.
40. Kassis, J.A., Noll, E., VanSickle, E.P., Odenwald, W.F., and Perrimon, N. (1992). Altering the insertional specificity of a Drosophila transposable element. Proc. Natl. Acad. Sci. USA 89, 1919-1923.
41. Kaszas, E., and Birchler, J.A. (1996). Misdivision analysis of centromere structure in maize. EMBO J. 15, 5246-5255.
42. Lam, H.M., Chiu, J., Hsieh, M.H., Meisel, L., Oliveira, I.C., Shin, M., and Coruzzi, G. (1998). Glutamate-receptor genes in plants. Nature 396, 125-126.
43. Le, M.H., Duricka, D., and Karpen, G.H. (1995). Islands of complex DNA are widespread in Drosophila centric heterochromatin. Genetics 141, 283-303.
44. Lin, X., Kaul, S., Rounsley, S., Shea, T.P., Benito, M.I., Town, C.D., Fujii, C.Y., Mason, T., Bowman, C.L., Barnstead, M., et al. (1999). Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature, 402, 761-768.
45. Mayer, K., et al. The European Union Arabidopsis Genome Sequencing Consortium and the Cold Spring Harbor, Washington University in St. Louis and PE Biosystems Arabidopsis Sequencing Consortium (1999). Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402, 769-777.
46. Mardis, E. (1994). High-throughput detergent extraction of M13 subclones for fluorescent DNA sequencing. Nucleic Acids Res. 22, 2173-2175.
47. Marra, M., Kucaba, T., Sekhon, M., Hillier, L., Martienssen, R., Chinwalla, A., Crockett, J., Fedele, J., Grover, H., Gund, C., et al. (1999). A map for sequence analysis of the Arabidopsis thaliana genome. Nat. Genet. 22, 265-270.
48. Martienssen, R. (1996). Epigenetic phenomena: Paramutation and gene silencing in plants. Curr. Biol. 6, 810-813.
49. Martienssen, R. (1998a). Chromosomal imprinting in plants. Curr. Opin. Genet. Dev. 8, 240-244.
50. Martienssen, R. (1998b). Transposons, DNA methylation and gene control. Trends Genet. 14, 263-264.
51. Martienssen, R., and Henikoff, S. (1999). The house and garden guide to chromatin remodelling. Nat. Genet. 22, 6-7.
52. McClintock, B. (1929). Chromosome morphology in Zea mays. Science 69, 629.
53. McClintock, B. (1930). A cytological demonstration of the location of an interchange between two non-homologous chromosomes of Zea mays. Proc. Natl. Acad. Sci. USA 16, 791-796.
54. McClintock, B. (1951). Chromosome organization and genic expression. Cold Spring Harb. Symp. Quant. Biol. 16, 13-47.
55. McClintock, B. (1965). The control of gene action in maize. Brookhaven Symp. Biol. 18, 162-184.
56. McClintock, B. (1978). Mechanisms that rapidly reorganize the genome. Satadler Genet. Symp. 10, 25-48.
57. McClintock, B., Angel, T., Kato, Y., and Bluemenshein, A. (1981). Chromosomal Constitution of Races of Maize (Chapingo, Mexico: Colegio de Postgraduados).
58. McCombie, W.R., Adams, M.D., Kelley, J.M., FitzGerald, M.G., Utterback, T.R., Khan, M., Dubnick, M., Kerlavage, A.R., Venter, J.C., and Fields, C. (1992a). Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nat. Genet. 1, 124-131.
59. McCombie, W.R., Heiner, C., Kelley, J.M., Fitzgerald, M.G., and Gocayne, J.D. (1992b). Rapid and reliable fluorescent cycle sequencing of double-stranded templates. DNA Seq. 2, 289-296.
60. Mozo, T., Dewar, K., Dunn, P., Ecker, J.R., Fischer, S., Kloska, S., Lehrach, H., Marra, M., Martienssen, R., Meier-Ewert, S., and Altmann, T. (1999). A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat. Genet. 22,71-275.
61. Parsons, J.D. (1995). Miropeats: Graphical DNA sequence comparisons. Comput. Appl. Biosci. 11, 615-619.
62. Paszkowski J., and Mittelsten Scheid, O. (1998). Plant genes: The genetics of epigenetics. Curr. Biol. 8, R206-R208.
63. Pelissier, T., Tutois, S., Tourmente, S., Deragon, J.M., and Picard, G. (1996). DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica 97, 141-151.
64. Pirrotta, V., and Rastelli, L. (1994). White gene expression, repressive chromatin domains and homeotic gene regulation in Drosophila. Bioessays 16, 549-556.
65. Plasterk, R.H., Izsvak, Z., and Ivics, Z. (1999). Resident aliens: The Tc1/mariner superfamily of transposable elements. Trends Genet. 15, 326-332.
66. Richards, E.J., and Dawe, R.K. (1998). Plant centromeres: Structure and control. Curr. Opin. Plant Biol. 1, 130-135.
67. Round, E.K., Flowers, S.K., and Richards, E.J. (1997). Arabidopsis thaliana centromere regions: Genetic map positions and repetitive DNA structure. Genome Res. 7 1045-1053.
68. Rubin, G.M. (1998). The Drosophila genome project: A progress report. Trends Genet. 14, 340-343.
69. San Miguel, P., Tikhonov, A., Jin, Y.K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P.S., Edwards, K.J., Lee, M., et al. (1996). Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765-768.
70. Schmidt, R., West, J., Love, K., Lenehan, Z., Lister, C., Thompson, H., Bouchez, D., and Dean, C. (1995). Physical map and organization of Arabidopsis thaliana chromosome 4. Science 270, 480-483.
71. Schnable, P.S., Hsia, A.P., and Nikolau, B.J. (1998). Genetic recombination in plants. Curr. Opin. Plant Biol. 1, 123-129.
72. Springer, P.S., McCombie, W.R., Sundaresan, V., and Martienssen, R.A. (1995). Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis. Science 268, 877-880.
73. Sulston J., Du, Z., Thomas, K., Wilson, R., Hillier, L., Staden, R., Halloran, N., Green, P., Thierry-Mieg, J., Qiu, L., et al. (1992). The C. elegans genome sequencing project: A beginning. Nature 356, 37-41.
74. Sun, X., Wahlstrom, J., and Karpen, G. (1997). Molecular structure of a functional Drosophila centromere. Cell 91, 1007-10 19.
75. Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J.D., Dean, C., Ma, H., and Martienssen, R. (1995). Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9, 1797-18 10.
76. Taillebourg, E., and Dura, J.-M. (1999). A novel mechanism for P element homing in Drosophila. Proc. Acad. Natl. Sci. USA 96, 6956-6961.
77. Thompson, H., Schmidt, R., Brandes, A., Heslop-Harrison, J.S., and Dean, C. (1996). A novel repetitive sequence associated with the centromeric regions of Arabidopsis thaliana chromosomes. Mol. Gen. Genet. 253, 247-252.
78. Thompson-Stewart, D., Karpen, G.H., and Spradling, A.C. (1994). A transposable element can drive the concerted evolution of tandemly repetitious DNA. Proc. Natl. Acad. Sci. USA 91, 9042-9046.
79. Thuriaux, P. (1977). Is recombination confined to structural genes on the eukaryotic genome? Nature 268, 460-462.
80. Timmermans, M.C., Das, O.P., and Messing, J. (1996). Characterization of a meiotic crossover in maize identified by a restriction fragment length polymorphism-based method. Genetics 143, 1771-1783.
81. Tsugeki, R., Kochieva, E.Z., and Fedoroff, N.V. (1996). A transposon insertion in the Arabidopsis SSR16 gene causes an embryo-defective lethal mutation. Plant J. 10, 479-489.
82. Vongs, A., Kakutani, T., Martienssen, R.A., and Richards, E.J. (1993). Arabidopsis thaliana DNA methylation mutants. Science 260, 1926-1928.
83. Wallrath, L.L. (1998). Unfolding the mysteries of heterochromatin. Curr. Opin. Genet. Dev. 8, 147-153.
84. Waterston, R., Martin, C., Craxton, M., Huynh, C., Coulson, A., Hillier, L., Durbin, R., Green, P., Shownkeen, R., Halloran, N., et al. (1992). A survey of expressed genes in Caenorhabditis elegans. Nat. Genet. 1, 114-123.
85. Weil, C.F., and Wessler, S.R. (1993). Molecular evidence that chromosome breakage by Ds elements is caused by aberrant transposition. Plant Cell 5, 515-522.
86. Wilson, R., Ainscough, R., Anderson, K., Baynes, C., Berks, M., Bonfield, J., Burton, J., Connell, M., Copsey, T., et al. (1994). 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature 368, 32-38.
87. Wolffe, A.P. (1998). When more is less. Nat. Genet. 18, 5-6.
88. Wolffe, A.P., and Hayes, J.J. (1999). Chromatin disruption and modification. Nuc. Acids Res. 27, 711-720.
89. Xu, X., Hsia, A.P., Zhang, L., Nikolau, B.J., and Schnable, P.S. (1995). Meiotic recombination break points resolve at high rates at the 5′ end of a maize coding sequence. Plant Cell 7, 2151-2161.
90. Zhang, M. (1998). Identification of protein-coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis. Plant Mol. Biol. 37, 803-806.