Background in open chromatin may indicate digestion of accessible chromatin by pAG-MNase, due to prolonged incubation and/or incorrect temperature. However, it can also indicate over-sequencing of CUT&RUN libraries.
To resolve this:
Sequence libraries to 3-8 million reads.
Repeat assay using fresh buffers.
Ensure pAG-MNase digestion is performed at 4˚C.