Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds

Gene

Volumn 300, Issue 1-2, 2002, Pages 169-178

  Saccone, Salvatore ^a,b   Federico, Concetta ^a   Bernardi, Giorgio ^c  

^a UNIVERSITY OF CATANIA   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

^c STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

Author keywords

Chicken; Chromatin condensation; Chromosomal band; Human; Isochore; Nuclear architecture

Indexed keywords

DNA;

CELL NUCLEUS MEMBRANE; CHICKEN; CHROMOSOME; CONFERENCE PAPER; CONFORMATION; DENSITY; GENE LOCATION; GENETIC ANALYSIS; GENETIC PARAMETERS; INTERPHASE; PRIORITY JOURNAL; VERTEBRATE;

ANIMALS; BASE COMPOSITION; CELL NUCLEUS; CHICKENS; CHROMATIN; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 12; CHROMOSOMES, HUMAN, PAIR 6; GC RICH SEQUENCE; GENOME; HUMANS; INTERPHASE; ISOCHORES; METAPHASE;

AVES; GALLUS GALLUS; MAMMALIA; VERTEBRATA;

EID: 0037202372     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(02)01038-7     Document Type: Conference Paper

References (32)

1. Andreozzi L., Federico C., Motta S., Saccone S., Sazanova A., Sazanov A., Smirnov A., Galkina S.A., Lukina N.A., Rodionov A.V., Carels N., Bernardi G. Compositional mapping of chicken chromosomes and identification of the gene-richest regions. Chromosome Res. 9:2001;521-532.
2. Bernardi G. Isochores and the evolutionary genomics of vertebrates. Gene. 241:2000;3-17.
3. Bernardi G., Olofsson B., Filipski J., Zerial M., Salinas J., Cuny G., Meunier-Rotival M., Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 228:1985;953-958.
4. Boyle S., Gilchrist S., Bridger J.M., Mahy N.L., Ellis J.A., Bickmore W.A. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum. Mol. Genet. 10:2001;211-219.
5. Bridger J.M., Boyle S., Kill I.R., Bickmore W.A. Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr. Biol. 10:2000;149-152.
6. Cacciò S., Perani P., Saccone S., Kadi F., Bernardi G. Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates. J. Mol. Evol. 39:1994;331-339.
7. Cortadas J., Olofsson B., Meunier-Rotival M., Macaya G., Bernardi G. The DNA components of the chicken genome. Eur. J. Biochem. 99:1979;179-186.
8. Croft J.A., Bridger J.M., Boyle S., Perry P., Teague P., Bickmore W.A. Differences in the localization and morphology of chromosomes in the human nucleus. J. Cell Biol. 145:1999;1119-1131.
9. Cuny G., Soriano P., Macaya G., Bernardi G. The major components of the mouse and human genomes. 1. Preparation, basic properties and compositional heterogeneity. Eur. J. Biochem. 115:1981;227-233.
10. Dutrillaux B. Nouveau système de marquage chromosomique: les bandes T. Chromosoma. 41:1973;395-402.
11. Federico C., Saccone S., Bernardi G. The gene-richest bands of human chromosomes replicate at the onset of the S-phase. Cytogenet. Cell Genet. 80:1998;83-88.
12. Federico C., Andreozzi L., Saccone S., Bernardi G. Gene density in the Giemsa bands of human chromosomes. Chromosome Res. 8:2000;737-746.
13. Ferreira J., Paolella G., Ramos C., Lamond A.I. Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. Cell Biol. 139:1997;1597-1610.
14. 4-Ag density gradient centrifugation. J. Mol. Biol. 80:1973;177-197.
15. Francke U. Digitized and differentially shaded human chromosome ideograms for genomic applications. Cytogenet. Cell Genet. 6:1994;206-219.
16. Hori T., Suzuki Y., Solovei I., Saitoh Y., Hutchinson N., Ikeda J.E., Macgregor H., Mizumo S. Characterization of DNA sequences constituting the terminal heterochromatin of the chicken Z chromosome. Chromosome Res. 4:1996;411-426.
17. Kadi F., Mouchiroud D., Sabeur G., Bernardi G. The compositional patterns of the avian genomes and their evolutionary implications. J. Mol. Evol. 37:1993;544-551.
18. Lander E., et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
19. 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.
20. 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.
21. Olofsson B., Bernardi G. Organization of nucleotide sequences in the chicken genome. Eur. J. Biochem. 130:1983;241-245.
22. Pavliček A., Paces J., Clay O., Bernardi G. A compact view of isochores in the draft human genome sequence. FEBS Lett. 511:2002;165-169.
23. 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. USA. 89:1992;4913-4917.
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., Solovei I., Croquette M.F., Della Valle G., Bernardi G. Identification of the gene-richest bands in human prometaphase chromosomes. Chromosome Res. 7:1999;379-386.
26. Saccone S., Pavliček A., Federico C., Paces J., Bernardi G. Genes, isochores and bands in human chromosomes 21 and 22. Chromosome Res. 9:2001;533-539.
27. Sadoni N., Langer S., Fauth C., Bernardi G., Cremer T., Turner B.M., Zink D. Nuclear organization of mammalian genomes: polar chromosome territories build up functionally distinct higher order compartments. J. Cell Biol. 146:1999;1211-1226.
28. Strouboulis J., Wolffe A.P. Functional compartmentalization of the nucleus. J. Cell Science. 109:1996;1991-2000.
29. Venter C., et al. The sequence of the human genome. Science. 291:2001;1304-1351.
30. Volpi E.V., Chevret E., Jones T., Vatcheva R., Williamson J., Beck S., Campbell R.D., Goldsworthy M., Powis S.H., Ragoussis J., Trowsdale J., Sheer D. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J. Cell Sci. 113:2000;1565-1576.
31. Yokota H., Singer M.J., van den Engh G.J., Trask B.J. Regional differences in the compaction of chromatin in human G0/G1 interphase nuclei. Chromosome Res. 5:1997;157-166.
32. Zoubak S., Clay O., Bernardi G. The gene distribution of the human genome. Gene. 174:1996;95-102.