Usually there are slight differences in the protocols when we use DNase or MNase qPCR/ seq in analysing genome accessibility. Is it known if DNase sensitivity and MNase sensitivity (i.e. accessibility and nucleosome occupancy) are exactly the same? Are nucleosome occupancy and chromatin accessibility the same thing or just two correlated phenomena ?
Hi, I am also reading on this and my understanding is that MNase will keep only the DNA sequence in a nucleosome, therefore testing the nucleosome occupancy. usually when there is a protein other than histones (e.g.: transcription factors) binding to the chromatin, the nucleosome is loosen up. so from a MNase-seq data, you can deduce transcription factor binding site from the absence of certain sequence. but DNase I digestion will keep the sequence where the transcription factor binds. I hope I get this right.
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