I have seen reports that MNase has some sequence bias. Do you see this in your CUT&RUN assays and does it affect the target protein-interaction DNA profiles you get?

No, we do not observe any sequence bias in our CUT&RUN assays. Free MNase may have some sequence bias in the genome, however, in CUT&RUN, the MNase is fused with pAG and recruited by the target-specific antibody. The digestion to chromatin is directed to where the antibody locates in the genome. Therefore, the antibody specificity and not the sequence bias of MNase has more of an effect on the result.

 

Last updated: February 28, 2024