Promoter nucleosome positioning in dendritic cells (DCs) and fibroblasts measured by ChIP-MNase-seq

We used ChIP-MNase to determine nucleosome positions around promoters in DCs and fibroblasts, after experimental treatment to stimulate inducible gene activation Mouse dendritic cells and 3T3 fibroblasts were treated for 1hr with LPS or with TNF-alpha, respectively. Cells were fixed for 10minutes with 4% formaldehyde and used to prepare chromatin. Chrromatin was fragmented to approximately 5-10kb fragments and used for ChIP. ChIP-enriched chromatin was then digested using micrococcal nuclease (MNase) to generate approximately 80% mononucleosomal fragments. DNA was extracted after reversion of fixation and used for sequencing.