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Short answer: CUT&RUN (Cleavage Under Targets and Release Using Nuclease) is a chromatin profiling method that uses an antibody to guide micrococcal nuclease to one chosen protein or histone mark in unfixed nuclei, cutting out the bound DNA so it can be sequenced. It was introduced by Skene and Henikoff in 2017. (In everyday speech “cut and run” is an idiom for abandoning a situation; this page covers only the laboratory assay.)
Definition and scope
What does the term “cut and run” mean in the lab?
In molecular biology, “cut and run” refers to CUT&RUN, a method for mapping where a protein sits on DNA or where a histone modification occurs. The original paper describes it as “antibody-targeted controlled cleavage by micrococcal nuclease” that “releases specific protein-DNA complexes into the supernatant” (Skene and Henikoff, eLife 2017;6:e21856). Targets include transcription factors, cofactors and histone marks. The assay answers one question: where is this particular protein or mark bound in the genome?
How a CUT&RUN experiment works
What does CUT&RUN do, and how is an experiment performed?
At the conceptual level, as described in the eLife paper and in vendor overviews from EpiCypher and Cell Signaling Technology:
- Unfixed cells or nuclei are immobilised on magnetic beads (lectin- or concanavalin A-coated beads).
- A primary antibody against the target binds in situ; in the original paper, nuclei were then incubated with protein A-micrococcal nuclease (pA-MN). EpiCypher describes a Protein A/G-MNase fusion (pAG-MNase) in its version.
- Calcium triggers the nuclease. In the paper, cleavage was started on ice and stopped by chelation after seconds to minutes.
- The cut fragments diffuse out of the nucleus, the beads are removed magnetically, and DNA from the supernatant goes to sequencing library preparation. No crosslinking is used.
This overview deliberately omits reagent volumes, times and temperatures. Use the published protocol or your kit’s instructions for those.
What is the difference between ATAC-seq, ChIP-seq and CUT&RUN?
The three methods ask different questions. ChIP-seq and CUT&RUN both profile a chosen protein or mark with an antibody; ATAC-seq does not use an antibody and instead reports accessible chromatin (editorial summary; see the ATAC-seq guide). The table attributes each CUT&RUN entry to its source; items marked “vendor-reported” are manufacturer claims, not independent benchmarks.
| Aspect | CUT&RUN | ChIP-seq | ATAC-seq |
|---|---|---|---|
| What it maps | Binding of a chosen protein or histone mark (Skene and Henikoff 2017) | Binding of a chosen protein or mark (see ChIP-seq) | Accessible chromatin, not a specific protein (editorial) |
| Antibody needed | Yes, validated for in situ use | Yes | No (editorial) |
| Crosslinking | None; unfixed nuclei (Skene and Henikoff 2017; EpiCypher) | Contrasted with the crosslinking-free CUT&RUN workflow (EpiCypher) | Not applicable |
| Sequencing depth | About one tenth of ChIP; about 10 million reads sufficed for CTCF versus about 100 million for ChIP-exo (Skene and Henikoff 2017). Vendor-reported: roughly 3 to 8 million reads per reaction (EpiCypher) | Higher (as at left) | Not compared in the sources used |
| Input cells | 600,000 to 10 million K562 cells in the paper’s titration. Vendor-reported: validated from 500,000 down to 5,000 cells (EpiCypher) | Vendor-reported: up to 40-fold more cells (EpiCypher) | Not compared in the sources used |
Where it matters for labs: decisions before ordering
CUT&RUN is built from a few distinct components, and each is a decision a lab makes before the first run. This checklist is drawn from the sources above and does not replace a protocol.
- Target and antibody. The method depends on one antibody binding its target in unfixed nuclei. EpiCypher notes that standard epigenomics controls “can only validate part of your experiment” and offers spike-in nucleosomes (SNAP-CUTANA) to monitor success and check histone-modification antibody specificity.
- Cell or nuclei source. The paper used yeast and human nuclei; plan input numbers against the ranges in the table.
- Immobilisation beads and nuclease fusion. Lectin- or ConA-coated magnetic beads and a protein A or protein A/G-MNase fusion are the consumable and reagent classes named in the sources.
- Normalisation. Cell Signaling Technology describes Drosophila spike-in and fragmented yeast DNA normalisation.
- Negative control. The original paper’s main control omitted the primary antibody and gave a near-flat track; the paper’s text does not describe an IgG control. Check what your chosen kit specifies.
- Readout. qPCR or next-generation sequencing (Cell Signaling Technology); see NGS DNA sequencing and depth versus breadth of coverage.
Common misunderstandings
- “It replaces ChIP-seq everywhere.” The sources show lower input and depth requirements, not that every target works with every antibody; antibody performance still has to be validated.
- “Lower depth means no sequencing planning.” It lowers the read count but not the need to choose a library and sequencing strategy.
- “Vendor numbers are guarantees.” Cell-number and read figures from vendor pages are the vendors’ own validation claims.
- “CUT&RUN and CUT&Tag are the same.” They are related but separate methods; this page covers CUT&RUN only.
FAQ
What is a CUT&RUN experiment?
An experiment in which an antibody-guided nuclease cuts the DNA around a chosen protein in unfixed nuclei, and the released fragments are sequenced to map where the protein binds.
What is the difference between ATAC-seq and CUT&RUN?
ATAC-seq reports accessible chromatin without an antibody; CUT&RUN maps a specific protein or histone mark and requires an antibody (editorial summary).
How do I perform CUT&RUN?
Follow the published protocol (Skene and Henikoff 2017) or the instructions for the kit you use. This page gives the concept, not step-by-step conditions. Background: what is epigenetics.
Sources
- Skene PJ, Henikoff S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 2017;6:e21856. doi:10.7554/eLife.21856. elifesciences.org/articles/21856 (read 2026-11-08).
- EpiCypher, CUT&RUN overview (vendor page). epicypher.com (read 2026-11-08).
- Cell Signaling Technology, CUT&RUN (vendor page). cellsignal.com (read 2026-11-08).
