A study of the impact of DNA helical rise on protein-DNA interaction

Nucleosomes are not uniformly distributed along DNA and their positioning (termed “nucleosomal landscape”) can be derived using data available for several genomes. In this study we analyzed DNA helical rise profiles through a tetranucleotide code, and we defined the nucleosomal landscape of several sequences forming dinucleosomes and of the sequences of huntingtin, myotonic dystrophy type 1 and fragile mental retardation 2 genes, which contained several repeated sequences. We also analyzed the profiles of some sequences interacting with transcription factors or with RNA polymerase II. In the genomes of Cenorhabditis elegans, Mus musculus and Homo sapiens we found profiles with extremely low helical rise values, characteristic of nucleosome free regions. We defined these regions as “holes” and found that their presence correlates with lamina associated domains sequences. Altogether, this study shows that DNA helical rise profile may have a role in gene expression modulation and in shaping chromosomal structure. •Critical threshold of trinucleotide repeats in disease genes could be associated with variation in the nucleosomal landscape.•Transcription factors binding sites show specific helical rise profiles linked to distinct nucleosomal landscapes.•The binding of CCTF depends on the stability of nucleosomes bound to the surrounding genomic regions.•The access of RNA polymerase to promoter sites is inversely correlated to the stability of nucleosomes bound at TSS.•We identified genomic regions with very low helical rise values likely associated to Lamina Associated Domains.