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