Isochore structures in the genome of the plant Arabidopsis thaliana

Journal of Molecular Evolution

Volumn 59, Issue 2, 2004, Pages 227-238

  Zhang, Ren ^a   Zhang, Chun Ting ^b  

^a KEY LABORATORY OF CANCER PREVENTION AND THERAPY   (China)

^b TIANJIN UNIVERSITY   (China)

Author keywords

Arabidopsis thaliana; Compositional homogeneity; Isochores; Windowless technique

Indexed keywords

DNA;

ARABIDOPSIS; ARTICLE; CENTROMERE; GENE INSERTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; INTRON; ISOCHORE; MATHEMATICAL ANALYSIS; TRANSPOSON;

ANALYSIS OF VARIANCE; ARABIDOPSIS; BASE COMPOSITION; CENTROMERE; DATABASES, NUCLEIC ACID; GENOME, PLANT; ISOCHORES; MODELS, GENETIC;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA; ILEX COOKII; INSERTION SEQUENCES; TRANSPOSONS;

EID: 4344700574     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-2617-8     Document Type: Article

References (38)

1. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker JR (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653-657
2. Barakat A, Matassi G, Bernard G (1998) Distribution of genes in the genome of Arabidopsis thaliana and its implications for the genome organization of plants. Proc Natl Acad Sci USA 95:10044-10049
3. Barakat A, Gallois P, Raynal M, Mestre-Ortega D, Sallaud C, Guiderdoni E, Delseny M, Bernardi G (2000) The distribution of T-DNA in the genomes of transgenic Arabidopsis and rice. FEBS Lett 471:161-164
4. Bernardi G (1995) The human genome: Organization and evolutionary history. Annu Rev Genet 29:445-476
5. Bernardi G (2000) Isochores and the evolutionary genomics of vertebrates. Gene 241:3-17
6. Carels N, Bernardi G (2000) Two classes of genes in plants. Genetics 154:1819-1825
7. Clay O, Caccio S, Zoubak S, Mouchiroud D, Bernardi G (1996) Human coding and noncoding DNA: compositional correlations. Mol Phylogenet Evol 5:2-12
8. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, Lin X, Bevan M, Murphy G, Harris B, Parnell LD, McCombie WR, Martienssen RA, Marra M, Preuss D (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286:2468-2474
9. Eyre-Walker A (1999) Evidence of selection on silent site base composition in mammals: Potential implications for the evolution of isochores and junk DNA. Genetics 152:675-683
10. Eyre-Walker A, Hurst LD (2001) The evolution of isochores. Nat Rev Genet 2:549-555
11. Haupt W, Fischer TC, Winderl S, Fransz P, Torres-Ruiz RA (2001) The centromere 1 (CEN1) region of Arabidopsis thaliana: Architecture and functional impact of chromatin. Plant J 27:285-296
12. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
13. Li W (2001) Delineating relative homogeneous G + C domains in DNA sequences. Gene 276:57-72
14. Li W, Bernaola-Galvan P, Haghighi F, Grosse I (2002) Applications of recursive segmentation to the analysis of DNA sequences. Comput Chem 26:491-510
15. Macaya G, Thiery JP, Bernardi G (1976) An approach on the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 108:237-254
16. Matassi G, Montero LM, Salinas J, Bernardi G (1989) The isochore organization and the compositional distribution of homologous coding sequences in the nuclear genome of plants. Nucleic Acids Res 17:5273-5290
17. McClintock B (1929) Chromosome morphology in Zea mays. Science 69:629
18. Meunier-Rotival M, Soriano P, Cuny G, Strauss F, Bernardi G (1982) Sequence organization and genomic distribution of the major family of interspersed repeats of mouse DNA. Proc Natl Acad Sci USA 79:355-359
19. Montero LM, Salinas J, Matassi Bernardi G (1990) Gene distribution and isochore organization in the nuclear genome of plants. Nucleic Acids Res 18:1859-1867
20. Nekrutenko A, Li WH (2000) Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res 10:1986-1995
21. Oliver JL, Bernaola-Galvan P, Carpena P, Roman-Roldan R (2001) Isochore chromosome maps of eukaryotic genomes. Gene 276:47-56
22. Oliver JL, Carpena P, Roman-Roldan R, Mata-Balaguer T, Mejias-Romero A, Hackenberg M, Bernaola-Galvan P (2002) Isochore chromosome maps of the human genome. Gene 300:117-127
23. Pavlicek A, Paces J, Clay O, Bernardi G (2002) A compact view of isochores in the draft human genome sequence. FEBS Lett 511:165-169
24. Peshkin L, Gelfand MS (1999) Segmentation of yeast DNA using hidden Markov models. Bioinformatics 15:980-986
25. Rhoades MM (1978) In: Waraen BD (ed) Maize breeding and genetics. Wiley, New York, pp 641-672
26. Rhoades MM, Dempsey E (1973) Cytogenetic studies on a transmissible deficiency in chromosome 3 of maize. J Hered 64:13-18
27. Saccone S, De Sario A, Wiegant J, Raap AK, Della Valle G, Bernardi G (1993) Correlations between isochores and chromosomal bands in the human genome. Proc Natl Acad Sci USA 90:11929-11933
28. Salinas J, Matassi G, Montero LM, Bernardi G (1988) Compositional compartmentalization and compositional patterns in the nuclear genomes of plants. Nucleic Acids Res 16:4269-4285
29. Schroder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F (2002) HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110:521-529
30. Tenzen T, Yamagata T, Fukagawa T, Sugaya K, Ando A, Inoko H, Gojobori T, Fujiyama A. Okumura K, Ikemura T (1997) Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex. Mol Cell Biol 17:4043-4050
31. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
32. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562
33. Wright SI, Agrawal N, Bureau TE (2003) Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res 13:1897-1903
34. Zhang CT, Zhang R (1991) Analysis of distribution of bases in the coding sequences by a diagrammatic technique. Nucleic Acids Res 19:6313-6317
35. Zhang CT, Zhang R (2003) An isochore map of the human genome based on the Z curve method. Gene 317:127-135
36. Zhang CT, Wang J, Zhang R (2001) A novel method to calculate the G + C content of genomic DNA sequences. J Biomol Struct Dyn 19:333-341
37. Zhang R, Zhang CT (1994) Z curves, an intuitive tool for visualizing and analyzing the DNA sequences. J Biomol Struct Dyn 11:767-782
38. Zoubak S, Clay O, Bernardi G (1996) The gene distribution of the human genome. Gene 174:95-102