Compositional heterogeneity within and among isochores in mammalian genomes: I. CsCl and sequence analyses

Oliver Clay, Nicolas Carels, Christophe Douady, Gabriel Macaya, Giorgio Bernardi

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

GC level distributions of a species' nuclear genome, or of its compositional fractions, encode key information on structural and functional properties of the genome and on its evolution. They can be calculated either from absorbance profiles of the DNA in CsCl density gradients at sedimentation equilibrium, or by scanning long contigs of largely sequenced genomes. In the present study, we address the quantitative characterization of the compositional heterogeneity of genomes, as measured by the GC distributions of fixed-length fragments. Special attention is given to mammalian genomes, since their compartmentalization into isochores implies two levels of heterogeneity, intra-isochore (local) and inter-isochore (global). This partitioning is a natural one, since large-scale compositional properties vary much more among isochores than within them. Intra-isochore GC distributions become roughly Gaussian for long fragments, and their standard deviations decrease only slowly with increasing fragment length, unlike random sequences. This effect can be explained by 'long-range' correlations, often overlooked, that are present along isochores.

Original languageEnglish (US)
Pages (from-to)15-24
Number of pages10
JournalGene
Volume276
Issue number1-2
DOIs
StatePublished - Oct 3 2001
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics

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