Short-range Order in Two Eukaryotic Genomes:
Relation to Chromosome Structure
J. Widom
Journal of Molecular Biology, 259, 579--588 (1996)
Abstract
Fourier transform techniques have been used to analyze the distributions
of all ten independent DNA dinucleotide steps in two eukaryotic genomes
and one prokaryotic genome, for periodicities of ~2 to 500 bp. The
results reveal systematic deviations from random expectation for
certain dinucleotide steps over this entire range of periodicities,
together with striking peaks at certain spatial periodicity of ~10.2 bp
that are unique to the eukaryotic genomes. Certain members of this set
of dinucleotide signals were previously identified as involved in nucleosome
positioning, while others were previously unrecognized. In real-space,
these dinucleotides are uncorrelated or even anticorrelated (relative to
random expectation) at distances of 10 and 11 bp, despite having greater
than random spectral power at the corresponding periodicity. Real-space
correlations of these dinucleotides at distances of 10 and 11 bp are
suppressed by another spectral component, a 3 bp periodicity attributed
to codons, which has a local minimum probability at ~ 10.5 bp. When
the two eukaryotic genomes are encoded for the signal "AA or TT", the
peak at ~10.2 bp periodicity is strengthened, whereas for the
prokaryotic genome such as peak remains absent. For the 