SHORT-RANGE ORDER IN 2 EUKARYOTIC GENOMES - RELATION TO CHROMOSOME STRUCTURE

Fourier transform techniques have been used to analyze the distributio ns of all ten independent DNA dinucleotide steps in two eukaryotic gen omes and one prokaryotic genome, for periodicities of approximate to 2 to 500 bp. The results reveal systematic deviations from random expec tation for certain dinucleotide steps over this entire range of period icities, together with striking peaks at certain spatial periodicities for particular dinucleotide steps. Several dinucleotides yield peaks at a periodicity of approximate to 10.2 bp that are unique to the euka ryotic genomes. Certain members of this set of dinucleotide signals we re previously identified as involved in nucleosome positioning, while others were previously unrecognized. In real-space, these dinucleotide s are uncorrelated or even anticorrelated (relative to random expectat ion) at distances of 10 and 11 bp, despite having greater than random spectral power at the corresponding periodicity Real-space correlation s of these dinucleotides at distances of 10 and 11 bp are suppressed b y another spectral component, a 3 bp periodicity attributed to codons, which has a local minimum probability at approximate to 10.5 bp. When the two eukaryotic genomes are encoded for the signal ''AA or TT'', t he peak at approximate to 10.2 bp periodicity is strengthened, whereas for the prokaryotic genome such a peak remains absent. For the Caenor habditis elegans genome, this peak becomes the dominant feature in the transform, surpassing a peak owing to the existence of codons in both height and integrated intensity. These results suggest that the requi rements of chromosome structure place significant constraints on eukar yotic genome organization; they reveal additional signals that may be related to nucleosome positioning; and they reveal a wealth of additio nal new non-random aspects of genome sequence organization. (C) 1996 A cademic Press Limited