CUT&RUN (Cleavage Under Targets & Release Using Nuclease) Resource Center


CUT&RUN (Cleavage Under Targets & Release Using Nuclease) is an epigenetic method used to investigate the genome-wide distribution of various chromatin-associated proteins and their modifications1-3. CUT&RUN is a derivative of chromatin immunocleavage (ChIC). CUT&RUN is similar to chromatin immunoprecipitation (ChIP), in that it utilizes an antibody to target chromatin-associated marks and proteins but requires less sample material and less sequencing depths than ChIP.

In CUT&RUN, a protein of interest is tagged with an antibody and bound to the chromatin in intact cells. Then, a micrococcal nuclease (MNase) is used to cleave the DNA specifically at the binding sites of the protein of interest. The released fragments are purified, sequenced, and mapped to the reference genome to determine the protein’s binding sites. Unlike ChIP, CUT&RUN does not require crosslinking of the protein to the DNA, which can introduce artifacts.

CUT&RUN is a valuable tool for studying chromatin-associated proteins because it is sensitive, specific, and requires fewer cells than ChIP, making it ideal for identifying binding patterns of chromatin-associated proteins such as transcription factors or histone modifications genome-wide. Chromatin-associated proteins play critical roles in regulating various cellular processes such as gene expression, DNA replication, DNA repair, and cell differentiation. Understanding the binding patterns of these proteins can provide insight into how these cellular processes are regulated.

1. Schmid, M. et al. Mol Cell, 16(1): 147-157 (2004)
2. Skene, P.J. et al. (2017) Elife 6, e21856
3. Skene, P.J. et al. (2018) Nat. Protoc., 13, 1006-1019






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