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Elife. 2019 Jun 24;8. pii: e46314. doi: 10.7554/eLife.46314.

Improved CUT&RUN chromatin profiling tools.

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Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
Howard Hughes Medical Institute, United States.


Previously, we described a novel alternative to chromatin immunoprecipitation, CUT&RUN, in which unfixed permeabilized cells are incubated with antibody, followed by binding of a protein A-Micrococcal Nuclease (pA/MNase) fusion protein (Skene and Henikoff, 2017). Here we introduce three enhancements to CUT&RUN: A hybrid protein A-Protein G-MNase construct that expands antibody compatibility and simplifies purification, a modified digestion protocol that inhibits premature release of the nuclease-bound complex, and a calibration strategy based on carry-over of E. coli DNA introduced with the fusion protein. These new features, coupled with the previously described low-cost, high efficiency, high reproducibility and high-throughput capability of CUT&RUN make it the method of choice for routine epigenomic profiling.


chromatin; chromosomes; epigenomics; gene expression; genetics; genomics; human; spike-in calibration

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