Abstract
The human genome is a mosaic of long, compositionally homogeneous DNA segments, the isochores, that can be partitioned into five families, two GC-poor families (L1 and L2), representing 63% of the genome, and three GC-rich families (H1, H2 and H3), representing 24%, 7.5% and 4–5% of the genome, respectively. Gene concentration increases with increasing GC levels, reaching a level 20-fold higher in H3 compared with L isochores. In-situ hybridization of DNA from different isochore families provides, therefore, information on the chromosomal distribution of genes. Using this approach, three subsets of reverse or Giemsa-negative bands, H3+, H3* and H3-, containing large, moderate, and no detectable amounts, respectively, of the gene-richest H3 isochores were identified at a resolution of 400 bands. H3+ bands largely coincide with the most heat-denaturation-resistant bands, the chromomycin-A3-positive, DAPI-negative bands, the bands with the highest CpG island concentrations, and the earliest replicating bands. Here, we have defined the H3+ bands at a 850-band resolution, and have thus identified the human genome regions, having an average size of 4Mb, that are endowed with the highest gene density.
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References
Aïssani B, Bernardi G (1991a) CpG islands: features and distribution in the genomes of vertebrates. Gene 106: 173-183.
Aïssani B, Bernardi G (1991b) CpG islands, gene and isochores in the genomes of vertebrates. Gene 106: 185-195.
Ambros PF, Sumner AT (1987) Metaphase bands of human chromosomes, and distinctive properties of telomeric regions. Cytogenet Cell Genet 44: 223-228.
Bernardi G (1989) The isochore organization of the human genome. Annu Rev Genet 23: 637-661.
Bernardi G (1995) The human genome: organization and evolutionary history. Ann Rev Genet 29: 445-476.
Bernardi G, Olofsson B, Filipski J et al. (1985) The mosaic genome of warm-blooded vertebrates. Science 228: 953-958.
Bettecken T, Aïssani B, Mueller CR, Bernardi G (1992) Compositional mapping of the human dystrophin gene. Gene 122: 329-335.
Cacciò S, Perani P, Saccone S, Kadi F, Bernardi G (1994) Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates. J Mol Evol 39: 331-339.
Chowdhary BP, Raudsepp T, Frönicke L, Scherthan H (1998) Emerging patterns of comparative genome organization in some mammalian species as revealed by Zoo-FISH. Genome Res 8: 577-589.
Chumakov IM and 60 other authors (1995) A YAC contig map of the human genome. Nature 377(suppl): 175-297.
Collins A, Frezal J, Teague J, Morton NE (1996) A metric map of humans: 23,500 loci in 850 bands. Proc Natl Acad Sci USA 93: 14771-14775.
Craig M, Bickmore WA (1994) The distribution of CpG islands in mammalian chromosomes. Nature Genet 7: 376-382.
Cuny G, Soriano P, Macaya G, Bernardi G (1981) The major components of the mouse and human genomes: preparation, basic properties and compositional heterogeneity. Eur J Biochem 111: 227-233.
Delgado S, Gómez M, Bird A, Antequera F (1998) Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J 17: 2426-2435.
De Sario A, Geigl E-M, Bernardi G (1995) A rapid procedure for the compositional analysis of yeast artificial chromosomes. Nucl Acids Res 23: 4013-4014.
De Sario A, Geigl E-M, Palmieri G, D'Urso M, Bernardi G (1996) A compositional map of human chromosome band Xq28. Proc Natl Acad Sci USA 93: 1298-1302.
De Sario A, Roizës G, Allegre N, Bernardi G (1997) A compositional map of the cen-q21 region of human chromosome 21. Gene 194: 107-113.
Drouin R, Lemieux N, Richer CL (1991) Chromosome condensation from prophase to late metaphase: relationship to chromosome bands and their replication time. Cytogenet Cell Genet 57: 91-99.
Drouin R, Holmquist G, Richer CL (1994) High resolution replication bands compared with morphologic G-and R-bands. Adv Hum Genet 22: 47-115.
Dutrillaux B (1973) Nouveau système de marquage chromosomique: les bandes T. Chromosoma 41: 395-402.
Federico C, Saccone S, Bernardi G (1998) The gene-richest bands of human chromosomes replicate at the onset of the S-phase. Cytogenet Cell Genet 80: 83-88.
Francke W (1994) Digitized and differentially shaded human chromosome ideograms for genomic applications. Cytogenet Cell Genet 65: 206-219.
Gardiner K, Aïssani B, Bernardi G (1990) A compositional map of human chromosome 21. EMBO J 9: 1853-1858.
Jabbari K, Bernardi G (1998) CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families. Gene 224: 123-127.
Morescalchi MA, Schempp W, Consigliere S, Bigoni F, Wienberg J, Stanyon R (1997) Mapping chromosomal homology between humans and the black-handed spider monkey by fluorescence in situ hybridization. Chromosome Res 5: 527-536.
Mouchiroud D, D'Onofrio G, Aïssani B, Macaya G, Gautier C, Bernardi G (1991) The distribution of genes in the human genome. Gene 100: 181-187.
Pilia G, Little RD, Aïssani B, Bernardi G, Schlessinger D (1993) Isochores and CpG islands in YAC contigs in human Xq26.1-qter. Genomics 17: 456-462.
Raudsepp T, Frönicke L, Scherthan H, Gustavsson I, Chowdhary BP (1996) Zoo-FISH delineates conserved chromosomal segments in horse and man. Chromosome Res 4: 218-225.
Saccone S, De Sario A, Della Valle G, Bernardi G (1992) The highest gene concentrations in the human genome are in T-bands of metaphase chromosomes. Proc Natl Acad Sci USA 89: 4913-4917.
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.
Saccone S, Cacciò S, Kusuda J, Andreozzi L, Bernardi G (1996) Identification of the gene-richest bands in human chromosomes. Gene 174: 85-94.
Saccone S, Cacciò S, Perani P et al. (1997) Compositional mapping of mouse chromosomes and identification of the gene-rich regions. Chromosome Res 5: 293-300.
Scherthan H, Cremer T, Arnason U, Weier HU, Lima-de-Faria A, Fronicke L (1994) Comparative chromosome painting discloses homologous segments in distantly related mammals. Nature Genet 6: 342-347.
Zoubak S, Clay O, Bernardi G (1996) The gene distribution of the human genome. Gene 174: 95-102.
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Saccone, S., Federico, C., Solovei, I. et al. Identification of the Gene-Richest Bands in Human Prometaphase Chromosomes. Chromosome Res 7, 379–386 (1999). https://doi.org/10.1023/A:1009220131225
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DOI: https://doi.org/10.1023/A:1009220131225