Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana

Molecular Genetics and Genomics

Volumn 270, Issue 6, 2004, Pages 524-532

  Miura, A ^a   Kato, M ^a,b   Watanabe, K ^c   Kawabe, A ^a   Kotani, H ^d   Kakutani, T ^a,b,c  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d KAZUSA DNA RESEARCH INSTITUTE   (Japan)

Author keywords

DNA methylation; Genome organization; Heterochromatin

Indexed keywords

PRIMER DNA;

ARABIDOPSIS; ARTICLE; CHROMATIN STRUCTURE; CHROMOSOME MAP; DNA METHYLATION; DNA POLYMORPHISM; GENE INSERTION SEQUENCE; GENE LOCATION; GENE MUTATION; GENETIC VARIABILITY; GENETICS; GENOME; GENOME ANALYSIS; INTERMETHOD COMPARISON; MOLECULAR GENETICS; NATURAL SELECTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENETICS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FAMILY; PROTEIN PURIFICATION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TRANSPOSON;

ARABIDOPSIS; BASE SEQUENCE; CHROMOSOME MAPPING; DNA PRIMERS; DNA TRANSPOSABLE ELEMENTS; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; VARIATION (GENETICS);

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA; INSERTION SEQUENCES; TRANSPOSONS; UNIDENTIFIED INSERTION SEQUENCE;

EID: 1042288619     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-003-0943-y     Document Type: Article

References (44)

1. Bennetzen JL (2000) Transposable elements: contributions to plant gene and genome evolution. Plant Mol Biol 42:251-269
2. Boeke JD, Devine SE (1998) Yeast retrotransposons: finding a nice quiet neighborhood. Cell 93:1087-1089
3. Brzeski J, Jerzmanowski A (2003) Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin remodeling factors. J Biol Chem 10: 823-828
4. Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81:1991-1995
5. Cresse AD, Hulbert SH, Brown WE, Lucas JR, Bennetzen JL (1995) Mu1 -related transposable elements of maize preferentially insert into low copy number DNA. Genetics 140:315-324
6. Frank MJ, Preuss D, Mack A, Kuhlmann TC, Crawford NM (1998) The Arabidopsis transposable element Tag1 is widely distributed among Arabidopsis ecotypes. Mol Gen Genet 257:478-484
7. Fransz PF, Armstrong S, de Jong JH, Parnell LD, van Drunen G, Dean C, Zabel P, Bisseling T, Jones GH (2000) Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 100:367-376
8. Hosouchi T, Kumekawa N, Tsuruoka H, Kotani H (2002) Physical map-based sizes of the centromeric regions of Arabidopsis thaliana chromosomes 1, 2, and 3. DNA Res 9:117-121
9. Isegawa Y, Sheng J, Sokawa Y, Yamanishi K, Nakagomi O, Ueda S (1992) Selective amplification of cDNA sequence from total RNA by cassette-ligation mediated polymerase chain reaction (PCR): application to sequencing 6.5-kb genome segment of hantavirus strain B-1. Mol Cell Probes 6:467-475
10. Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22:94-97
11. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro H (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-132
12. Kakutani T, Jeddeloh J, Flowers S, Munakata K, Richards E (1996) Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci USA 93:12406-12411
13. Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol 13:421-426
14. Kumar S, Tamura K, Jacobsen I, Nei M (2000) MEGA2: Molecular Evolutionary Genetics Analysis, version 2.0. Pennsylvania and Arizona State Universities, University Park, Pennsylvania and Tempe, Arizona
15. Kurata N, et al (1994) A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet 8:365-372
16. Langley CH, Montgomery E, Hudson R, Kaplan N, Charlesworth B (1988) On the role of unequal exchange in the containment of transposable element copy number. Genet Res 52:223-235.
17. Le QH, Wright SI, Yu Z, Bureau TE (2000) Transposon diversity in Arabidopsis thaliana. Proc Natl Acad Sci USA 97:14680-14685
18. Lister C, Dean C (1993) Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J 4:745-750
19. McCombie WR, et al (2000) The complete sequence of a heterochromatic island from a higher eukaryote. Cell 100:377-386
20. Miller JT, Dong F, Jackson SA, Song J, Jiang J (1998) Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150:1615-1623
21. Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771-1780
22. Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411:212-214
23. Morgan MT (2001) Transposable element number in mixed mating populations. Genet Res 77:261-275
24. Myouga F, Tsuchimoto S, Noma K, Ohtsubo H, Ohtsubo E (2001) Identification and structural analysis of SINE elements in the Arabidopsis thaliana genome. Genes Genet Syst 76:169-179
25. Pearce SR, Pich U, Harrison G, Flavell AJ, Heslop-Harrison JS, Schubert I, Kumar A (1996) The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res 4:357-364
26. Pelissier T, Tutois S, Tourmente S, Deragon JM, Picard G (1996) DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica 97:141-151
27. Presting GG, Malysheva L, Fuchs J, Schubert I (1998) A TY3/GYPSY retrotransposon-like sequence localises to the centromeric region of cereal chromosomes. Plant J 16:721-728
28. Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, McCombie WR, Martienssen RA (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet 23:305-308
29. Round EK, Flowers SK, Richards EJ (1997) Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure. Genome Res 7:1045-1053
30. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768
31. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43-45
32. Santiago N, Herraiz C, Goni JR, Messeguer X, Casacuberta JM (2002) Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana. Mol Biol Evol 19:2285-2293
33. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
34. Schmidt T, Kubis S, Heslop-Harrison JS (1995) Analysis and chromosomal location of retrotransposons in sugar beet (Beta vulgaris): LINEs and Ty1-copia -like elements as major components of the genome. Chromosome Res 3:335-345
35. Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, Lukyanov SA (1995) An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 23:1087-1088.
36. Singer T, Yordan C, Martienssen RA (2001) Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDMI). Genes Dev 15:591-602
37. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
38. Tsay YF, Frank MJ, Page T, Dean C, Crawford NM (1993) Identification of a mobile endogenous transposon in Arabidopsis thaliana. Science 260:342-324
39. Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260:1926-1928
40. Wright SI, Agrawal N, Bureau TE (2003) Effect of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res 13:1897-1903
41. Xie W, Gai X, Zhu Y, Zappulla DC, Sternglanz R, Voytas DF (2001) Targeting of yeast Ty5 retrotransposon to silent chromatin is mediated by interaction between integrase and Sir4p. Mol Cell Biol 21:6606-6614
42. Yamazaki M, Tsugawa H, Miyao A, Yano M, Wu J, Yamamoto S, Matsumoto T, Sasaki T, Hirochika H (2001) The rice retrotransposon Tos17 prefers low-copy-number sequences as integration targets. Mol Genet Genomics 265:336-344
43. Yu Z, Wright SI, Bureau TE (2000) Mutator -like elements in Arabidopsis thaliana. Structure, diversity and evolution. Genetics 156:2019-2031
44. Zhu Y, Dai J, Fuerst PG, Voytas DF (2003) Controlling integration specificity of a yeast retrotransposon. Proc Natl Acad Sci USA 100:5891-5895