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

GC level distributions of a species' nuclear genome, or of its compositiona l fractions, encode key information on structural and functional properties of the genome and on its evolution. They can be calculated either from abs orbance profiles of the DNA in CsCl density gradients at sedimentation equi librium, or by scanning long contigs of largely sequenced genomes. In the p resent study, we address the quantitative characterization of the compositi onal heterogeneity of genomes, as measured by the GC distributions of fixed -length fragments. Special attention is given to mammalian genomes, since t heir compartmentalization into isochores implies two levels of heterogeneit y, intra-isochore (local) and inter-isochore (global). This partitioning is a natural one, since large-scale compositional properties vary much more a mong isochores than within them. Intra-isochore GC distributions become rou ghly Gaussian for long fragments, and their standard deviations decrease on ly slowly with increasing fragment length, unlike random sequences. This ef fect can be explained by 'long-range' correlations, often overlooked, that are present along isochores. (C) 2001 Published by Elsevier Science B.V.