What is CUT&RUN?
1. Sample preparation. Cells (or nuclei) are bound to Concanavalin A (ConA) magnetic beads and permeabilized with Digitonin to facilitate antibody and pAG-MNase binding.
2. Antibody binding. A target-specific antibody is added, which binds the chromatin feature of interest. Cells are washed several times following incubation to reduce nonspecific antibody binding.
3. Targeted cleavage using pAG-MNase. pAG-MNase is added to the reaction. Protein A/G binds immunoglobulin proteins, tethering MNase to antibody-bound chromatin loci. Calcium is added to activate MNase, which cleaves nearby genomic DNA.
4. DNA purification and sequencing. Digested chromatin fragments (antibody-bound complex; see figure) are released into solution and bead-bound cells are removed using a magnet. Target-enriched DNA is purified and prepared for sequencing
For further introduction to CUT&RUN, watch the video below or see this blog.
Watch the video above for an introduction to CUT&RUN.
What is the difference between CUT&RUN and ChIP-seq?
Is CUT&RUN better than ChIP-seq?
CUT&RUN is superior to ChIP-seq in terms of cell input, sequencing depth, throughput, and cost. CUT&RUN assays are also more user-friendly, generate more reliable data, and work with a a diverse array of sample types, processing methods, and targets.
A full comparison of CUT&RUN technology and ChIP-seq can be found in the camparison table.
Advantages of CUT&RUN
Low-input chromatin mapping
CUT&RUN enables epigenomic analysis of low-abundance targets and rare sample types, opening new avenues of research. With CUT&RUN:
- Produce high on-target, low background epigenomic maps
- Profile historically inaccessible cell types (biopsies, FACS-isolated cells)
Map challenging targets with ease
Dysregulation of histone PTMs and chromatin-bound proteins is strongly linked to disease, making them key biomedical targets. Use CUT&RUN to study:
- Nucleosome remodelers – inaccessible by ChIP!
- Transcription factors, chromatin readers, and histone PTMs
Reveal dynamic chromatin changes
Chromatin-interacting proteins are emerging drug targets, but validating their therapeutic potential remains challenging. Ultra-sensitive CUT&RUN assays can:
- Detect epigenomic changes in response to drugs or stimuli
- Uncover novel drug targets or explore therapeutic mechanism of action
Broad sample type compatibility
CUT&RUN has been used in various research areas (see Key Publications and Example Applications). Specifically, CUT&RUN is:
- Compatible with fresh, frozen, or fixed cell lines, primary cells, and tissues
- Flexible to meet the needs of your project – including those using archived material
CUT&RUN Frequently Asked Questions
Why choose CUTANA CUT&RUN?
All-in-one Kits for CUT&RUN and Library Prep
Our CUT&RUN and Library Prep kits deliver a streamlined solution for CUT&RUN experiments.
- The CUTANA CUT&RUN kit includes everything you need to go from cells to DNA, including an extensive manual and key experimental controls
- CUTANA CUT&RUN Library Prep kit harness the power of NEBNext® reagents and are specifically optimized for CUT&RUN experiments
Exclusive spike-in control technology
Standard epigenomics controls can only validate part of your experiment. SNAP-CUTANA Spike-ins Controls use purified nucleosomes, which replicate the natural target of CUT&RUN, allowing you to:
- Directly monitor assay success
- Troubleshoot experiments
- Examine histone PTM antibody specificity
High-confidence epigenomic profiling
There are enough variables in experiments – let EpiCypher worry about the controls. Our CUTANA CUT&RUN kit and protocol include controls at every step, saving both time and resources.
- Quick methods to confirm quality sample prep
- Control reactions to monitor experimental success
- Clear metrics for confidence in proceeding to sequencing