Do I need to optimize the MNase digestion conditions in my CUT&RUN experiment for different cell types?

Our optimized digestion conditions for the CUT&RUN assay work well across multiple cell lines, both adherent and suspension. In addition, we have not observed significant changes in chromatin digestion when increasing or decreasing either the amount of pAG-MNase added or the time of digestion. Our observations are similar to those published by Peter Skene et al. (2018; PMID29651053). That said, the digestion temperature does matter. We find that digestion at 4°C can significantly increase signal strength with an acceptable background for transcription factors and cofactors compared to digestion at 0°C.

Last updated: February 26, 2024