MNase-seq analysis in human breast cancer cells

Nucleosomes are the most basic units of chromatin and are regulators of genome integrity and gene expression. The fundamental mechanism how nucleosomes are dynamically regulated is one of the main questions in chromatin organization; most of the study has, however, focused on its positioning. Here we performed HiLo-MNase-seq, which involves limit and partial digestion of chromatin by micrococcal nuclease (MNase) to identify the positioning of nucleosome array along with the kinetics of MNase digestion. We identified a subset of unique nucleosomes with fast digestion kinetics at the transcription factor binding sites that have been characterized as nucleosome depleted regions (NDRs). By inhibiting RNA polymerase II, we also showed that those nucleosomes changed its sensitivity to MNase in a context-dependent manner. These findings implicated a self-reinforcing regulatory network involving nucleosomes, Pol II, and transcription factors for fine-tuning of gene expression. MNase-seq experiment was performed in human breast cancer cells, MCF-7. Two biological replicates were prepared.