The influence of transcription in nucleosome positioning

Nucleosome positioning plays an important role in genome's function by restricting the DNA accessibility and incorporating regulatory factors. Although the role of DNA sequence in positioning nucleosomes has been widely studied, the understanding of the impact of transcription remains limited due to the complicated factors involved in this non-equilibrium process. Through numerical simulations, we investigated the influence of DNA sequence specificity, transcription factor binding, enzyme remodeling, and Pol II elongation in nucleosome positioning across species near the transcription start site (TSS). By exploring the effect of each factor, we found that a tug-of-war between two types of remodeling enzymes can reconcile the seemingly conflicting nucleosome density profiles at varying transcription levels observed in yeast and mouse embryonic stem cells.