Chromosome landmarks as tools to study the genome of Arabidopsis thaliana

Cytogenetic and Genome Research

Volumn 120, Issue 3-4, 2008, Pages 202-209

  Siroky, J ^a  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEAR PROTEIN; REPETITIVE DNA;

ANALYTIC METHOD; ARABIDOPSIS; CENTROMERE; CYTOGENETICS; DNA SEQUENCE; DNA STRUCTURE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE SEQUENCE; GENOME ANALYSIS; IMMUNOFLUORESCENCE; MEIOSIS; NONHUMAN; PLANT CHROMOSOME; PRIORITY JOURNAL; REVIEW;

ARABIDOPSIS; CENTROMERE; CHROMOSOMES, PLANT; CYTOGENETICS; DNA, PLANT; GENOME, PLANT; HETEROCHROMATIN; IN SITU HYBRIDIZATION, FLUORESCENCE; MODELS, GENETIC; RNA, PLANT; RNA, RIBOSOMAL; TELOMERE;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 44349146736     PISSN: 14248581     EISSN: None     Source Type: Journal    
DOI: 10.1159/000121068     Document Type: Review

References (67)

1. Adams KL, Wendel JF: Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8:135-141 (2005).
2. Ali HBM, Lysak MA, Schubert I: Chromosomal localization of rDNA in the Brassicaceae. Genome 48:341-346 (2005).
3. Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815 (2000).
4. Armstrong SJ, Jones GH: Meiotic cytology and chromosome behaviour in wild-type Arabidopsis thaliana. J Exp Bot 54:1-10 (2003).
5. Armstrong SJ, Christopher F, Franklin H, Gareth H, Jones GH: Nucleolus-associated telomere clustering and pairing precede meiotic chromosome synapsis in Arabidopsis thaliana. J Cell Sci 114:4207-4217 (2001).
6. Bennett MD, Leitch IJ, Price HJ, Johnston JS: Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb. Ann Bot 91:547-557 (2003).
7. Blackburn EH: Telomeres and telomerase: their mechanisms of action and the effects of altering their functions. FEBS Lett 579:859-862 (2005).
8. Blanc G, Barakat A, Guyot A, Cooke R, Delseny M: Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12:1093-1101 (2000).
9. Bleuyard J-Y, Gallego ME, White CI: Recent advances in understanding of the DNA doublestrand break repair machinery of plants. DNA Repair 5:1-12 (2006).
10. Bloom K: Centromere dynamics. Curr Opin Genet Dev 17:151-156 (2007).
11. Brandes A, Thompson H, Dean C, Heslop-Harrison JS: Multiple repetitive DNA sequences in the paracentromeric regions of Arabidopsis thaliana L. Chromosome Res 5:238-246 (1997).
12. Bundock P, van Attikum H, Hooykaas P: Increased telomere length and hypersensitivity to DNA damaging agents in an Arabidopsis KU70 mutant. Nucleic Acids Res 30:3395-3400 (2002).
13. Chen ZJ, Wang JL, Tian L, Lee HS, Wang JYJ, et al: The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biol J Linn Soc 82:689-700 (2004).
14. Comai L, Tyagi AP, Lysak MA: FISH analysis of meiosis in Arabidopsis allopolyploids. Chromosome Res 11:217-226 (2003).
15. Copenhaver GP: Using Arabidopsis to understand centromere function: Progress and prospects. Chromosome Res 11:255-262 (2003).
16. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, et al: Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286:2468-2474 (1999).
17. de Jong JH, Fransz P, Zabel P: High resolution FISH in plants - techniques and applications. Trends Plant Sci 4:258-263 (1999).
18. Fransz PF, Armstrong S, Alonso-Blanco C, Fischer TC, Torrez-Ruiz RA, Jones G: Cytogenetics for the model system Arabidopsis thaliana. Plant J 13:867-876 (1998).
19. Fransz PF, Armstrong S, de Jong JH, Parnell LD, vanDrunen C, et al: Integrated cytogenetic map of chromosome arm 4S of A. thaliana: Structural organization of heterochromatic knob and centromere region. Cell 100:367-376 (2000).
20. Fransz P, de Jong JH, Lysak M, Castiglione MR, Schubert I: Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc Natl Acad Sci USA 99:14584-14589 (2002).
21. Fransz P, ten Hoopen R, Tessadori F: Composition and formation of heterochromatin in Arabidopsis thaliana. Chromosome Res 14:71-82 (2006).
22. Gallego ME, White CI: DNA repair and recombination functions in Arabidopsis telomere maintenance. Chromosome Res 13:481-491 (2005).
23. Gallego ME, Jeanneau M, Granier F, Bouchej D, Bechtold N, White CI: Disruption of the Arabidopsis RAD50 gene leads to plant sterility and MMS sensitivity. Plant J 25:31-41 (2001).
24. Hall AE, Keith KC, Hall SE, Copenhaver GP, Preuss D: The rapidly evolving field of plant centromeres. Curr Opin Plant Biol 7:108-114 (2004).
25. Heacock M, Spangler E, Riha K, Puizina J, Shippen DE: Molecular analysis of telomere fusions in Arabidopsis: multiple pathways for chromosome end-joining. EMBO J 23:2304-2313 (2004).
26. Henry Y, Bedhomme M, Blanc G: History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement. Trends Plant Sci 11:267-273 (2006).
27. Jasencakova Z, Soppe WJ, Meister A, Gernand D, Turner BM, Schubert I: Histone modifications in Arabidopsis - high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J 33:471-480 (2003).
28. Jiang J, Gill BS: Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057-1068 (2006).
29. Jiang J, Birchler JA, Parrott WA, Dawe RK: A molecular view of plant centromeres. Trends Plant Sci 8:570-575 (2003).
30. Jones GH, Armstrong SJ, Caryl AP, Franklin FCH: Meiotic chromosome synapsis and recombination in Arabidopsis thaliana; an integration of cytological and molecular approaches. Chromosome Res 11:205-215 (2003).
31. Koornneef M, Fransz P, de Jong H: Cytogenetic tools for Arabidopsis thaliana. Chromosome Res 11:183-194 (2003).
32. Laibach F: Zur Frage nach der Individualität der Chromosomen im Pflanzenreich. Beih Bot Centralbl 22:191-210 (1907).
33. Leitch AR: Higher levels of organization in the interphase nucleus of cycling and differentiated cells. Microbiol Mol Biol R 64:138-152 (2000).
34. Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, et al: Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23:4286-4296 (2004).
35. Lysak MA, Fransz PF, Ali HBM, Schubert I: Chromosome painting in Arabidopsis thaliana. Plant J 28:689-697 (2001).
36. Lysak MA, Pecinka A, Schubert I: Recent progress in chromosome painting of Arabidopsis and related species. Chromosome Res 11:195-204 (2003).
37. Lysak M, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I: Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl Acad Sci USA 103:5224-5229 (2006).
38. Maillet G, White CI, Gallego ME: Telomere-length regulation in interecotype crosses of Arabidopsis. Plant Mol Biol 62:859-866 (2006).
39. Maluszynska J, Heslop-Harrison JS: Localization of tandemly repeated DNA sequences in Arabidopsis thaliana. Plant J 1:159-166 (1991).
40. Martinez-Zapater JM, Estelle MA, Somerville CR: A highly repeated DNA sequence in Arabidopsis thaliana. Mol Gen Genet 204:417-423 (1986).
41. McClintock B: The stability of broken ends of chromosomes in Zea mays. Genetics 26:234-282 (1941).
42. McCombie WR, et al. (CSHL/WUGSC/PEB Arabidopsis Sequencing Consortium): The complete sequence of a heterochromatic island from a higher eukaryote. Cell 100:377-386 (2000).
43. Mokros P, Vrbsky J, Siroky J: Identification of chromosomal fusion sites in Arabidopsis mutants using sequential bicolour BAC-FISH. Genome 49:1036-1042 (2006).
44. Pearson PL: Historical development of analysing large-scale changes in the human genome. Cytogenet Genome Res 115:198-204 (2006).
45. Pecinka A, Schubert V, Meister A, Kreth G, Klatte M, et al: Chromosome territory arrangement and homologous pairing in nuclei of Arabidopsis thaliana are predominantly random except for NOR-bearing chromosomes. Chromosoma 113:258-269 (2004).
46. Pelissier T, Tutois S, Tourmente S, Deragon JM, Pickard G: DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica 97:141-151 (1996).
47. Pradillo M, López E, Romero C, Sánchez-Morán E, Cuñado N, Santos JL: An analysis of univalent segregation in meiotic mutants of Arabidopsis thaliana: A possible role for synaptonemal complex. Genetics 175:505-511 (2007).
48. Puizina J, Siroky J, Mokros P, Schweizer D, Riha K: Mre11 deficiency in Arabidopsis is associated with chromosomal instability in somatic cells and Spo11-dependent genome fragmentation during meiosis. Plant Cell 16:1968-1978 (2004).
49. Riha K, McKnight TD, Griffing LR, Shippen DE: Living with genome instability: plant responses to telomere dysfunction. Science 291:1797-1800 (2001).
50. Riha K, Watson JM, Parkey J, Shippen DE: Telomere length deregulation and enhanced sensitivity to genotoxic stress in Arabidopsis mutants deficient in Ku70. EMBO J 21:2819-2826 (2002).
51. Riha K, Heacock ML, Shippen DE: The role of the nonhomologous end-joining DNA doublestrand break repair pathway in telomere biology. Annu Rev Genet 40:237-277 (2006).
52. Ross K, Fransz PF, Jones GH: A light microscopic atlas of meiosis in Arabidopsis thaliana. Chromosome Res 4:507-516 (1996).
53. Round EK, Flowers SK, Richards EJ: Arabidopsis thaliana centromere regions: Genetic map positions and repetitive DNA structure. Genome Res 7:1045-1053 (1997).
54. Sanchez Moran E, Armstrong SJ, Santos JL, Franklin FCH, Jones GH: Chiasma formation in Arabidopsis thaliana accession Wassileskija and in two meiotic mutants. Chromosome Res 9:121-128 (2001).
55. Sanchez-Moran E, Armstrong SJ, Santos JL, Franklin FCH, Jones GH: Variation in chiasma frequency among eight accessions of Arabidopsis thaliana. Genetics 162:1415-1422 (2002).
56. Schranz ME, Lysak MA, Mitchell-Olds T: The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci 11:535-542 (2006).
57. Shibata F, Murata M: Differential localization of the centromere-specific proteins in the major centromeric satellite of Arabidopsis thaliana. J Cell Sci 117:2963-2970 (2004).
58. Siroky J, Zluvova J, Riha K, Shippen DE, Vyskot B: Rearrangements of ribosomal DNA clusters in late generation telomerase-deficient Arabidopsis. Chromosoma 112:116-123 (2003).
59. Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, et al: DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21:6549-6559 (2002).
60. Steinitz-Sears LM: Chromosome studies in Arabidopsis thaliana. Genetics 48:483-490 (1963).
61. Talbert PB, Masuelli R, Tyagi AP, Comai L, Henikoff S: Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell 14:1053-1066 (2002).
62. Tessadori F, van Driel R, Fransz P: Cytogenetics as a tool to study gene regulation. Trends Plant Sci 9:147-153 (2004).
63. Vannier JB, Depeiges A, White C, Gallego ME: Two roles for Rad50 in telomere maintenance. EMBO J 25:4577-4585 (2006).
64. Vespa L, Couvillion M, Spangler E, Shippen DE: ATM and ATR make distinct contributions to chromosome end protection and the maintenance of telomeric DNA in Arabidopsis. Genes Dev 19:2111-2115 (2005).
65. Wang J, Tian L, Lee H-S, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Chen ZJ: Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507-517 (2006).
66. Zellinger B, Riha K: Composition of plant telomeres. Biochim Biophys Acta 1769:399-409 (2007).
67. Zijlmans JM, Martens UM, Poon SS, Raap AK, Tanke HJ, et al: Telomeres in the mouse have larger inter-chromosomal variations in the number of T2AG3 repeats. Proc Natl Acad Sci USA 94:7423-7428 (1997).