Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis.

Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequence-based nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats.