  Nucleosome organization in eukaryotic genomes has a deep impact on gene
function. Although progress has been recently made in the identification of
various concurring factors influencing nucleosome positioning, it is still
unclear whether nucleosome positions are sequence dictated or determined by a
random process. It has been postulated for a long time that,in the proximity of
TSS, a barrier determines the position of the +1 nucleosome and then geometric
constraints alter the random positioning process determining nucleosomal
phasing. Such a pattern fades out as one moves away from the barrier to become
again a random positioning process. Although this statistical model is widely
accepted,the molecular nature of the barrier is still unknown. Moreover,we are
far from the identification of a set of sequence rules able:to account for the
genome-wide nucleosome organization;to explain the nature of the barriers on
which the statistical mechanism hinges;to allow for a smooth transition from
sequence-dictated to statistical positioning and back. We show that sequence
complexity,quantified via various methods, can be the rule able to at least
partially account for all the above.In particular, we have conducted our
analyses on 4 high resolution nucleosomal maps of the model eukaryotes and
found that nucleosome depleted regions can be well distinguished from
nucleosome enriched regions by sequence complexity measures.In particular, (a)
the depleted regions are less complex than the enriched ones, (b) around TSS
complexity measures alone are in striking agreement with in vivo nucleosome
occupancy,in particular precisely indicating the positions of the +1 and -1
nucleosomes. Those findings indicate that the intrinsic richness of
subsequences within sequences plays a role in nucleosomal formation in genomes,
and that sequence complexity constitutes the molecular nature of nucleosome
barrier.
