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Improved CUT&RUN chromatin profiling and analysis tools

Michael P. Meers, Terri Bryson, View ORCID ProfileSteven Henikoff
doi: https://doi.org/10.1101/569129
Michael P. Meers
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109
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Terri Bryson
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109
2Howard Hughes Medical Institute, USA
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Steven Henikoff
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109
2Howard Hughes Medical Institute, USA
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  • ORCID record for Steven Henikoff
  • For correspondence: steveh@fhcrc.org
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Abstract

We previously described a novel alternative to Chromatin Immunoprecipitation, Cleavage Under Targets & Release Using Nuclease (CUT&RUN), in which unfixed permeabilized cells are incubated with antibody, followed by binding of a Protein A-Micrococcal Nuclease (pA/MNase) fusion protein (1). Upon activation of tethered MNase, the bound complex is excised and released into the supernatant for DNA extraction and sequencing. Here we introduce four enhancements to CUT&RUN: 1) a hybrid Protein A-Protein G-MNase construct that expands antibody compatibility and simplifies purification; 2) a modified digestion protocol that inhibits premature release of the nuclease-bound complex; 3) a calibration strategy based on carry-over of E. coli DNA introduced with the fusion protein; and 4) a novel peak-calling strategy customized for the low-background profiles obtained using CUT&RUN. 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 16, 2019.
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Improved CUT&RUN chromatin profiling and analysis tools
Michael P. Meers, Terri Bryson, Steven Henikoff
bioRxiv 569129; doi: https://doi.org/10.1101/569129
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Improved CUT&RUN chromatin profiling and analysis tools
Michael P. Meers, Terri Bryson, Steven Henikoff
bioRxiv 569129; doi: https://doi.org/10.1101/569129

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