Prediction of replication time zones at single nucleotide resolution in the human genome

FEBS Letters

Volumn 582, Issue 16, 2008, Pages 2441-2444

  Gao, Feng ^a   Zhang, Chun Ting ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

G + C content; Human genome; Isochore; Replication timing; Segmentation

Indexed keywords

NUCLEOTIDE;

ARTICLE; COMPUTER PROGRAM; DNA REPLICATION TIMING; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; HUMAN; HUMAN GENOME; ISOCHORE; PRIORITY JOURNAL;

CHROMOSOMES, HUMAN; DNA REPLICATION; GENOME, HUMAN; HUMANS; ISOCHORES; NUCLEOTIDES;

EID: 45549102854     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2008.06.008     Document Type: Article

References (27)

1. Macaya G., Thiery J.P., and Bernardi G. An approach to the organization of eukaryotic genomes at a macromolecular level. J. Mol. Biol. 108 (1976) 237-254
2. Saccone S., De Sario A., Wiegant J., Raap A.K., Della Valle G., and Bernardi G. Correlations between isochores and chromosomal bands in the human genome. Proc. Natl. Acad. Sci. USA 90 (1993) 11929-11933
3. Bernardi G. The human genome: organization and evolutionary history. Annu. Rev. Genet. 29 (1995) 445-476
4. Bernardi G. Misunderstandings about isochores. Part 1. Gene 276 (2001) 3-13
5. Fukagawa T., Sugaya K., Matsumoto K., Okumura K., Ando A., Inoko H., and 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
6. Tenzen T., et al. Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex. Mol. Cell. Biol. 17 (1997) 4043-4050
7. Schmegner C., Hameister H., Vogel W., and Assum G. Isochores and replication time zones: a perfect match. Cytogenet. Genome Res. 116 (2007) 167-172
8. Cohen N., Dagan T., Stone L., and Graur D. GC composition of the human genome: in search of isochores. Mol. Biol. Evol. 22 (2005) 1260-1272
9. Li W., Bernaola-Galvan P., Carpena P., and Oliver J.L. Isochores merit the prefix 'iso'. Comput. Biol. Chem. 27 (2003) 5-10
10. Costantini M., Clay O., Auletta F., and Bernardi G. An isochore map of human chromosomes. Genome Res. 16 (2006) 536-541
11. Costantini M., and Bernardi G. Replication timing, chromosomal bands, and isochores. Proc. Natl. Acad. Sci. USA 105 (2008) 3433-3437
12. Costantini M., Clay O., Federico C., Saccone S., Auletta F., and Bernardi G. Human chromosomal bands: nested structure, high-definition map and molecular basis. Chromosoma 116 (2007) 29-40
13. Oliver J.L., Bernaola-Galvan P., Carpena P., and Roman-Roldan R. Isochore chromosome maps of eukaryotic genomes. Gene 276 (2001) 47-56
14. Li W., Bernaola-Galvan P., Haghighi F., and Grosse I. Applications of recursive segmentation to the analysis of DNA sequences. Comput. Chem. 26 (2002) 491-510
15. Zhang C.T., and Zhang R. Isochore structures in the mouse genome. Genomics 83 (2004) 384-394
16. Zhang C.T., and Zhang R. An isochore map of the human genome based on the Z curve method. Gene 317 (2003) 127-135
17. Zheng W.X., and Zhang C.T. Biological implications of isochore boundaries in the human genome. J. Biomol. Struct. Dynam. 25 (2008) 327-336
18. Selig S., Okumura K., Ward D.C., and Cedar H. Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J. 11 (1992) 1217-1225
19. Zink D. The temporal program of DNA replication: new insights into old questions. Chromosoma 115 (2006) 273-287
20. White E.J., et al. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc. Natl. Acad. Sci. USA 101 (2004) 17771-17776
21. Berezney R., Dubey D.D., and Huberman J.A. Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma 108 (2000) 471-484
22. Zhang C.T., Gao F., and Zhang R. Segmentation algorithm for DNA sequences. Phys. Rev. E 72 (2005) 041917
23. Gao F., and Zhang C.T. GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res. 34 (2006) W686-W691
24. Brylawski B.P., Cohen S.M., Horne H., Irani N., Cordeiro-Stone M., and Kaufman D.G. Transitions in replication timing in a 340 kb region of human chromosomal R-Band 1p36.1. J. Cell. Biochem. 92 (2004) 755-769
25. Schmegner C., Berger A., Vogel W., Hameister H., and Assum G. An isochore transition zone in the NF1 gene region is a conserved landmark of chromosome structure and function. Genomics 86 (2005) 439-445
26. Watanabe Y., Tenzen T., Nagasaka Y., Inoko H., and Ikemura T. Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands. Gene 252 (2000) 163-172
27. Karolchik D., et al. The UCSC Genome Browser Database. Nucleic Acids Res. 31 (2003) 51-54