Representing GC variation along eukaryotic chromosomes

Gene

Volumn 333, Issue SUPPL., 2004, Pages 135-141

  Pačes, Jan ^a   Zíka, Radek ^a   Pačes, Václav ^a   Pavlíček, Adam ^a   Clay, Oliver ^b   Bernardi, Giorgio ^b  

^a INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

^b STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

Author keywords

Analytical ultracentrifugation; Compositional homogeneity; GC; Genome organization; LINE; long interspersed repeat; Mammalian DNA; MAR, SAR; molar fraction of guanine and cytosine in DNA; short interspersed repeat; SINE; Software

Indexed keywords

CYTOSINE; GUANINE;

ARTICLE; CHROMOSOME; DATA BASE; EUKARYOTE; GENE MAPPING; GENE SEQUENCE; GENOME; HUMAN GENOME; ISOCHORE; PRIORITY JOURNAL;

ANIMALS; ANOPHELES; ARABIDOPSIS; BASE COMPOSITION; CAENORHABDITIS ELEGANS; CHROMOSOMES; DNA; DROSOPHILA MELANOGASTER; EUKARYOTIC CELLS; GENOME; HUMANS; ISOCHORES; MICE; REPETITIVE SEQUENCES, NUCLEIC ACID; SACCHAROMYCES CEREVISIAE; SOFTWARE;

EUKARYOTA; MAMMALIA;

EID: 2942565994     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.02.041     Document Type: Article

References (34)

1. Arabidopsis Genome Initiative (AGI) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408:2000;796-815
2. Bernardi G. The compositional evolution of vertebrate genomes. Gene. 259:2000;31-43
3. Bernardi G. Misunderstandings about isochores: Part I. Gene. 276:2001;3-13
4. Carels N., Bernardi G. The compositional organization and the expression of the Arabidopsis genome. FEBS Lett. 472:2000;302-306
5. Clay O., Carels N., Douady C., Macaya G., Bernardi G. Compositional heterogeneity within and among isochores in mammalian genomes: I. CsCl and sequence analyses. Gene. 276:2001;15-24
6. Douady C., Carels N., Clay O., Catzeflis F., Bernardi G. Diversity and phylogenetic implications of CsCl profiles from rodent DNAs. Mol. Phylogenet. Evol. 17:2000;219-230
7. Gentles A.J., Karlin S. Genome-scale compositional comparisons in eukaryotes. Genome Res. 11:2001;540-546
8. Holt R.A., Subramanian G.M., Halpern A., et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science. 298:2002;129-149
9. International Human Genome Sequencing Consortium (IHGSC) Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921
10. Jabbari K., Bernardi G. The distribution of genes in the Drosophila genome. Gene. 247:2000;287-292
11. Jacq C., Alt-Morbe J., Andre B., et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature. 387:1997;75-78
12. Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16:2000;418-420
13. Karolchik D., Baertsch R., Diekhans M., Furey T.S., Hinrichs A., Lu Y.T., Roskin K.M., Schwartz M., Sugnet C.W., Thomas D.J., Weber R.J., Haussler D., Kent W.J. The UCSC genome browser database. Nucleic Acids Res. 31:2003;51-54
14. 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
15. Mahy N.L., Perry P.E., Bickmore W.A. Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J. Cell Biol. 159:2002;753-763
16. Mouchiroud D., D'Onofrio G., Aïssani B., Macaya G., Gautier C., Bernardi G. The distribution of genes in the human genome. Gene. 100:1991;181-187
17. Mouse Genome Sequencing Consortium (MGSC) Initial sequencing and comparative analysis of the mouse genome. Nature. 420:2002;520-562
18. Myers E.W., Sutton G.G., Delcher A.L., et al. A whole-genome assembly of Drosophila. Science. 287:2000;2196-2204
19. Oliver J.L., Bernaola-Galván P., Carpena P., Román- Roldán R. Isochore chromosome maps of eukaryotic genomes. Gene. 276:2001;47-56
20. Pavlíc̀ek A., Jabbari K., Pac̀es J., Pac̀es V., Hejnar J., Bernardi G. Similar integration but different stability of Alus and LINEs in the human genome. Gene. 276:2001;39-45
21. Pavlíc̀ek A., Pac̀es J., Clay O., Bernardi G. A compact view of isochores in the draft human genome sequence. FEBS Lett. 511:2002;165-169
22. Pavlíc̀ek A., Clay O., Jabbari K., Pac̀es J., Bernardi G. Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17. FEBS Lett. 511:2002;175-177
23. Saccone S., De Sario A., Wiegant J., Raap 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
24. Saccone S., Cacciò S., Kusuda J., Andreozzi L., Bernardi G. Identification of the gene-richest bands in human chromosomes. Gene. 174:1996;85-94
25. Saccone S., Federico C., Bernardi G. Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene. 300:2002;169-178
26. Saitoh Y., Laemmli U.K. Metaphase chromosome structure: bands arise from a differential folding path of the highly AT-rich scaffold. Cell. 76:1994;609-622
27. Smit A.F. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9:1999;657-663
28. 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
29. 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 major histocompatibility complex. Mol. Cell. Biol. 17:1997;4043-4050
30. The C. elegans Sequencing Consortium (CSC) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 282:1998;2012-2018
31. The MHC sequencing consortium (MHCSC) Complete sequence and gene map of a human major histocompatibility complex. Nature. 401:1999;921-923
32. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., et al. The sequence of the human genome. Science. 291:2001;1304-1351
33. Wood V., Gwilliam R., Rajandream M.A., et al. The genome sequence of Schizosaccharomyces pombe. Nature. 415:2002;871-880
34. Zoubak S., Clay O., Bernardi G. The gene distribution of the human genome. Gene. 174:1996;95-102