Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome

In the yeast genome, a large proportion of nucleosomes occupy well-defined positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genomic context remains controversial. Through genome-wide, quantitative analysis of nucleosome positioning and high-resolution mutagenenesis of mononucleosomal DNA, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes. This effect is equally detected in transcribed and non-transcribed regions, suggesting the existence of sequence elements contributing to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open up the possibility of designing coding and non-coding DNA molecules capable of directing their own nucleosomal organization. Overall design: Samples from mononucleosomal DNA from S. pombe strains (h- 972) and S. cerevisiae (W303) harbouring different mutant sequences, were sequenced (Illumina NextSeq 500 platform) using the pair-end read protocol