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. 1. Introduction It is generally accepted that the chromatin organization of eukaryotic DNA is strongly governed by a code inherent to the DNA sequence. Modulating the accessibility of individual DNA sequences involves many complex interactions, the most prevalent of which are the interactions between histone octamers and DNA in compacted chromosomes [1, 2]. The condensation of DNA into an ordered chromatin structure allows the cell to solve the topological problems associated with storing huge amount of information of chromosomal DNA within the nucleus. In Eukaryotes and Archaea, DNA is packaged into chromatin in orderly repetitive protein-DNA complexes called nucleosomes. Each nucleosome consists of approximately 146-147？bp of dsDNA wound 1.7-1.8 times around a histone octamer [3–5] to form the basic unit of chromatin structure, the nucleosome. Each octamer is composed of two H3-H4 histone dimers bridged together as a stable tetramer that is flanked by two separate H2A-H2B dimers [6]. Stretches of DNA called linker up to 100？bp, often with an increment of 10？bp, separate adjacent nucleosomes. Multiple nuclear proteins bind to this linker region, some of which may be responsible for the ordered wrapping of strings of
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