An isochore map of the human genome based on the Z curve method

Gene

Volumn 317, Issue 1-2, 2003, Pages 127-135

  Zhang, Chun Ting ^a   Zhang, Ren ^b  

^a TIANJIN UNIVERSITY   (China)

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

Author keywords

Compositional homogeneity; Genome organization; Segmentation; Windowless technique

Indexed keywords

CHROMOSOME; CONFERENCE PAPER; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; HUMAN; HUMAN GENOME; ISOCHORE; MATHEMATICAL COMPUTING; PRIORITY JOURNAL;

EID: 0012914683     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(03)00665-6     Document Type: Conference Paper

References (31)

1. Bernardi G. The human genome, organization and evolutionary history. Annu. Rev. Genet. 29:1995;445-476.
2. Bernardi G. Isochores and the evolutionary genomics of vertebrates. Gene. 241:2000;3-17.
3. Bernardi G. Misunderstandings about isochores. Part I. Gene. 276:2001;3-13.
4. Bornish-Bowden A. Nomenclature for incompletely specified bases in nuclei sequences recommendation. Nucleic Acids Res. 13:1985;3021-3030.
5. Clay O., Bernardi G. The isochores in human chromosomes 21 and 22. Biochem. Biophys. Res. Commun. 285:2001;855-856.
6. Cuny G., Soriano P., Macaya G., Bernardi G. The major components of the mouse and human genomes, preparation, basic properties and compositional heterogeneity. Eur. J. Biochem. 115:1981;227-233.
7. Duret L., Mouchiroud D., Gautier C. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40:1995;308-317.
8. Eisenbarth I., Vogel G., Krone W., Vogel W., Assum G. An isochore transition in the Nf1 gene region coincides with a switch in the extent of linkage disequilibrium. Am. J. Hum. Genet. 67:2000;873-880.
9. Eyre-Walker A., Hurst L.D. The evolution of isochores. Nat. Rev. Genet. 2:2001;549-555.
10. Fickett J.W., Torney D.C., Wolf D.R. Base compositional structure of genomes. Genomics. 13:1992;1056-1064.
11. Fukagawa T., Sugaya K., Matsumoto K., Okumura K., Ando A., Inoko H., Ikemura T. A boundary of long-range G+C% mosaic domains in the human MHC locus: pseudoautosomal boundary-like sequence exists near the boundary. Genomics. 25:1995;184-191.
12. Fullerton S.M., Carvalho A.B., Clark A.G. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18:2001;1139-1142.
13. Haring D., Kypr J. No isochores in human chromosomes 21 and 22? Biochem. Biophys. Res. Commun. 280:2001;567-573.
14. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
15. Li W., Marr T.G., Kaneko K. Understanding long-range correlations in DNA sequences. Physics D. 75:1994;392-416.
16. Li W., Bernaola-Galvan P., Haghighi F., Grosse I. Applications of recursive segmentation to the analysis of DNA sequences. Comput. Chem. 26:2002;491-510.
17. Macaya G., Thiery J.P., Bernardi G. An approach to the organization of eukaryotic genomes at a macromolecular level. J. Mol. Biol. 108:1976;237-254.
18. Meunier-Rotival M., Soriano P., Cuny G., Strauss F., Bernardi G. Sequence organization and genomic distribution of the major family of interspersed repeats of mouse DNA. Proc. Natl. Acad. Sci. U. S. A. 79:1982;355-359.
19. Oliver J.L., Bernaola-Galvan P., Carpena P., Roman-Roldan R. Isochore chromosome maps of eukaryotic genomes. Gene. 276:2001;47-56.
20. Pavlicek A., Paces J., Clay O., Bernardi G. A compact view of isochores in the draft human genome sequence. FEBS Lett. 511:2002;165-169.
21. Saccone S., De Sario A., Della Valle G., Bernardi G. The highest gene concentrations in the human genome are in T bands of metaphase chromosomes. Proc. Natl. Acad. Sci. U. S. A. 89:1992;4913-4917.
22. Saccone S., De Sario A., Wiegant J., Rap A.K., Della Valle G., Bernardi G. Correlations between isochores and chromosomal bands in the human genome. Proc. Natl. Acad. Sci. U. S. A. 90:1993;11929-11933.
23. Sharp P.M., Averof M., Lloyd A.T., Matassi G., Peden J.F. DNA sequence evolution: the sounds of silence. Philos. Trans. R. Soc. Lond., B Biol. Sci. 349:1995;241-247.
24. Soriano P., Meunier-Rotival M., Bernardi G. The distribution of interspersed repeats is non-uniform and conserved in the mouse and human genomes. Proc. Natl. Acad. Sci. U. S. A. 80:1983;1816-1820.
25. Stephens R., Horton R., Humphray S., Rowen L., Trowsdale J., Beck S. Gene organization, sequence variation and isochore structure at the centromeric boundary of the human MHC. J. Mol. Biol. 291:1999;789-799.
26. Tenzen T., Yamagata T., Fukagawa T., Sugaya K., Ando A., Inoko H., Gojobori T., Fujiyama A., Okumura K., Ikemura T. Precise switching of DNA replication timing in the GC content transition area in the human MHC. Mol. Cell. Biol. 17:1997;4043-4050.
27. The MHC Sequencing Consortium Complete sequence and gene map of a human major histocompatibility complex. Nature. 401:1999;921-923.
28. Zhang C.T., Zhang R. Analysis of distribution of bases in the coding sequences by a diagrammatic technique. Nucleic Acids Res. 19:1991;6313-6317.
29. Zhang R., Zhang C.T. Z curves, an intuitive tool for visualizing and analyzing DNA sequences. J. Biomol. Struct. Dyn. 11:1994;767-782.
30. Zhang C.T., Wang J., Zhang R. A novel method to calculate the G+C content of genomic DNA sequences. J. Biomol. Struct. Dyn. 19:2001;333-341.
31. Zoubak S., Clay O., Bernardi G. The gene distribution of the human genome. Gene. 174:1996;95-102.