Nucleosome occupancy

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Nucleosome occupancy is usually based on DNA digestion combined with ChIP-Seq. Sequences that are nucleosome-bound are protected from DNA digested and thus sequenced; this is in contrast to nucleosome-free regions, which are digested and not sequenced. For example, micrococcal nuclease (MNase), which is a endonuclease that preferentially digests linker DNA than DNA wrapped around a nucleosome, can be used to profile nucleosome occupancy. After MNase treatment, the presence of highly digested DNA suggests that most of the sequence was nucleosome-free and if the DNA was under digested, it indicates that the DNA was protected by nucleosomes. The precise position of a nucleosome with respect to an underlying sequence is known nucleosome positioning.

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