Michael Tolstorukov 
the Laboratory of Experimental and Computational
Biology, NCI, 

Abstract
Molecular mechanisms of the bacterial chromatin packaging are still unclear,
as bacteria lack nucleosomes or other apparent basic elements of DNA
compaction.  It was shown previously that the sequence correlations in the
genome might constitute a structural code facilitating DNA folding.  We
elaborate further this concept.  In particular, we analyze the distributions
of A-tracts and G-tracts (the sequence motifs that introduce the most
pronounced DNA curvature) in the bacterial genomes.  We have observed that
the A-tracts are over-represented in E.coli and several other bacterial
genomes and have regular patterns in their positioning, while G-tracts do
not demonstrate significant deviations from the random distribution.  First,
there is a 10-12 bp periodicity in the A-tract positioning, i.e. the
A-tracts are phased. Second, the phased A-tracts are organized in clusters
of about 100 bp long, containing several tracts, as revealed by the
specifically designed analysis algorithm.  The clusters are present
throughout the genome including the coding sequences.  Since the A-tracts
introduce bends of the DNA duplex and these bends accumulate when properly
phased, the observed clusters would facilitate forming of the DNA
mini-loops.  Also, such clusters may serve as binding sites for
nucleoid-associated proteins that have propensities for binding curved DNA
(e.g., HU, H-NS, Hfq, CbpA).  Thus, the clusters of the phased A-tracts
would facilitate DNA compaction through providing DNA intrinsic curvature
and increasing the stability to the DNA complexes with architectural
proteins.