Nucleosome occupancy

From Dave's wiki
Jump to navigation Jump to search

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.

Further reading

http://www.cs.cmu.edu/~sssykim/teaching/s13/slides/Lecture_NucI.pdf

http://www.sciencemag.org/content/309/5734/626.short