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Science 24 May 1985:
Vol. 228. no. 4702, pp. 953 - 958
DOI: 10.1126/science.4001930
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Articles

Science, Vol 228, Issue 4702, 953-958
Copyright © 1985 by American Association for the Advancement of Science

articles

The mosaic genome of warm-blooded vertebrates

G Bernardi, B Olofsson, J Filipski, M Zerial, J Salinas, G Cuny, M Meunier-Rotival, and F Rodier

Most of the nuclear genome of warm-blooded vertebrates is a mosaic of very long (much greater than 200 kilobases) DNA segments, the isochores; these isochores are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content. The families of DNA molecules derived from such classes can be separated and used to study the genome distribution of any sequence which can be probed. This approach has revealed (i) that the distribution of genes, integrated viral sequences, and interspersed repeats is highly nonuniform in the genome, and (ii) that the base composition and ratio of CpG to GpC in both coding and noncoding sequences, as well as codon usage, mainly depend on the GC content of the isochores harboring the sequences. The compositional compartmentalization of the genome of warm-blooded vertebrates is discussed with respect to its evolutionary origin, its causes, and its effects on chromosome structure and function.


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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    PDF »
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   Abstract »    PDF »
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   Abstract »    PDF »
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   Abstract »    PDF »
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   Abstract »    PDF »
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   Abstract »    PDF »
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   Abstract »    PDF »
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