The importance of DNA sequence for nucleosome positioning in the process of transcriptional regulation

Nucleosome positioning is a key factor in the regulation of transcription, as nucleosomes regulate the dynamic accessibility of chromatin for transcription factor binding and interact with the transcription machinery at every stage. Influences to steer nucleosome positioning are diverse, and the importance of the DNA sequence for this process in contrast to active chromatin remodeling has been the subject of a long discussion. In this study, we evaluate the functional role of DNA sequence for all major elements along the process of transcription. For this purpose, we developed a random forest classifier based on local DNA structure that assesses the sequence-intrinsic support for nucleosome positioning. On this basis, we created an easy-to-use data resource that can be applied in a genome-wide manner to the human genome. In our comprehensive analysis, we found a special role of DNA in mediating the competition of nucleosomes with cis-regulatory elements, in enabling steady transcription, for positioning of stable nucleosomes in exons and for nucleosome depletion during transcription termination. In contrast, we relate these findings to concurrent processes that generate strongly positioned nucleosomes in vivo that are not mediated by sequence, such as energy-dependent remodeling of chromatin. ![Figure][1] ### Competing Interest Statement The authors have declared no competing interest. [1]: pending:yes