Nucleosome Dynamics

Nucleosome positioning plays a major role in transcriptional regulation and most DNA-related processes. The Nucleosome Dynamics server offers different tools to analyze nucleosome positioning from MNase-seq experimental data and to compare experiments to account for the transient and dynamic nature of nucleosomes under different cellular states.

Two specific programs, nucleR and NucDyn, were specifically developed to perform such studies.

  • nucleR performs Fourier transform filtering and peak calling, in order to efficiently and accurately define and classify the location of nucleosomes. Additionally, a list of other nucleosome related features, such as the location of nucleosome-free regions, the classification of transcription start sites based on the surrounding nucleosomes, the study of nucleosome phasing at gene level, and the stiffness of the nucleosomes derived from fitting a Gaussian function to nucleosome profiles, are also computed.
  • NucDyn is a method to detect changes in nucleosome architectures based on MNase-seq experiments. It identifies nucleosomes’ insertions, evictions and shifts between two experiments at the read level.

From this page you can access the MuGVRE and Galaxy framework, where you can upload, analyse and visualize your MNase-seq data. You can also find the link to nucleR and NucDyn as open source R/Bioconductor packages to install and execute on your computer.