Nucleosome positioning in vivo driven by the DNA sequence

Nucleosomes facilitate the packaging of the genome inside the nucleus and modulate the access of regulators to the DNA molecule. In yeasts, most nucleosomes occupy well-defined positions, the great majority of which are maintained under different genetic backgrounds and physiological conditions. Given this stable organization, we have studied to what extent the DNA sequence contributes to nucleosome positioning in the genomic context. Sequence analysis of mononucleosomal DNA in several species of fission and budding yeasts has revealed that the distribution of the four mononucleotides follows a highy structured pattern that is species-specific, despite the high degree of histone conservation. The incorporation of information from these nucleosomal signatures into artificial synthetic DNA molecules imposes the formation of nucleosomal patterns indistinguishable from those of endogenous sequences. That information can also be combined with coding information such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open the possibility of designing coding and non-coding DNA molecules capable of directing their own nucleosomal organization.