CUT&RUN Chromatin Profiling for High-Resolution DNA-Protein Mapping
Unlock ultra-clean, low-input chromatin landscapes with CUT&RUN.
CD Genomics delivers fast, reproducible, and publication ready data for histone modifications, transcription factors, and chromatin remodelers—without crosslinking or high background noise.
Whether you're studying enhancer dynamics, heterochromatin, or pioneer factors, CUT&RUN empowers your research with precision and speed.
Compatible with TFs, histone marks, and chromatin complexes
Introduction
Why CUT&RUN? Efficiency at Its Core
Anyone who's run ChIP-seq knows the frustrations—harsh crosslinking, sonication variability, high input requirements, and signal drowned in background noise. CUT&RUN was developed to fix that.
This technique gives you precise, high-resolution maps of protein–DNA interactions, without the compromises. No crosslinking. No sonication. No need for millions of cells. Instead, CUT&RUN uses an antibody to guide micrococcal nuclease directly to your target, cutting only where binding actually happens. The result? Cleaner data, sharper peaks, and more confidence in what you're seeing.
If you're working with limited material, trying to map a transcription factor in rare cell types, or tired of over-sequencing just to see your signal, CUT&RUN is worth switching to. It's efficient, reproducible, and gives you back control over your experiment.
Why researchers choose CUT&RUN over ChIP:
Lower input, better data
You can start with far fewer cells and still get focused, interpretable peaks.
Much lower background
Native chromatin and targeted cleavage mean you see real signal—not artifacts.
No sonication, no crosslinking
That alone cuts down experimental time and variability.
More usable reads
You get more from every sequencing run—3 to 5 million reads is often enough.
Flexible applications
Histone marks, transcription factors, polymerases, chromatin remodelers—CUT&RUN works across the board.
When clean, efficient mapping matters—especially in low-input or high-precision settings—CUT&RUN gives you an edge ChIP simply can't match.
How It Works: The CUT&RUN Workflow
CUT&RUN relies on a simple, targeted principle: let the antibody bring the nuclease to your protein of interest, and let the nuclease do the work exactly where it matters.
Here's how the process unfolds:
Cell Immobilization
Cells are gently bound to ConA-coated magnetic beads, preserving their native chromatin structure.
Antibody Targeting
A primary antibody is added to recognize and bind your protein of interest—be it a histone modification, transcription factor, or chromatin remodeler.
pA/G-MNase Recruitment
A fusion of protein A/G and micrococcal nuclease (MNase) is introduced. It binds the antibody and remains inactive until the final step.
Targeted Cleavage
A brief addition of calcium activates MNase, triggering cleavage right at the protein-DNA interface. Only the DNA in proximity to the protein is released into solution—no need for whole-chromatin shearing.
Fragment Collection and Purification
The released DNA fragments are purified directly from the supernatant, ready for sequencing.
Because cleavage happens only where your protein binds, background is minimal and signal clarity is exceptional. There's no over-sonication, no random shearing, and no crosslinked noise—just the real binding profile, as it exists in the cell.
CUT&RUN vs. ChIP vs. CUT&Tag
If you're choosing between CUT&RUN, ChIP-seq, and CUT&Tag, the decision often comes down to what you need most: resolution, robustness, or scalability.
Here's how these methods compare where it really matters.
While ChIP-seq remains widely used and CUT&Tag has carved out a niche in high-throughput pipelines, CUT&RUN offers a practical middle ground: technically accessible, biologically accurate, and gentle enough for fragile samples.
Service Workflow
Service Workflow at CD Genomics
Bioinformatics
Data Handling: From Reads to Biological Insight
A strong CUT&RUN experiment doesn't stop at clean DNA fragments—it's the downstream analysis that turns those fragments into real insight.
At CD Genomics, we deliver more than raw reads. Our bioinformatics pipeline is tailored for CUT&RUN data, enabling you to see precisely where your protein of interest binds, and what that means for your system.
What We Analyze for You:
Read Alignment & Quality Metrics
We map your reads to the reference genome with optimized parameters for CUT&RUN datasets, ensuring minimal ambiguity and maximum specificity.
Peak Calling & Enrichment Profiling
Whether you're studying transcription factor occupancy or histone marks, we apply sensitive algorithms to detect high-confidence binding peaks with minimal background noise.
Motif Discovery & Annotation
For transcription factors, we identify DNA motifs at peak sites—so you can connect sequence preferences with functional binding.
Gene Ontology & Pathway Analysis
We link peaks to nearby genes and run GO/KEGG enrichment, helping you understand which biological processes and pathways your protein may be regulating.
Super-Enhancer Identification
Using H3K27ac or BRD4 data, we can identify super-enhancer regions, revealing regulatory hubs in development, disease, or cancer.
Comparative Analysis (Optional)
Looking at treatment vs. control? Wild-type vs. knockout? We offer differential binding analysis to highlight condition-specific binding changes.
The result is not just a peak file—it's a comprehensive, interpretable view of your protein–DNA landscape. We provide annotated tracks, plots, tables, and summaries you can use directly in your downstream interpretation, publication, or next experiment.
If you're tired of black-box data processing or struggling to align CUT&RUN results with your biological questions, we're here to help you bridge that gap.
Applications
CUT&RUN Applications in Gene Regulation and Epigenomics
CUT&RUN isn't just an efficient ChIP alternative—it's a tool that unlocks questions previously constrained by sample input, resolution, or background noise.
Here's where researchers are using it most effectively:
Transcription Factor Binding Maps
CUT&RUN allows precise mapping of transcription factor occupancy, even for transient or low-abundance factors. It's particularly powerful when studying stress responses, developmental transitions, or cancer-specific regulatory rewiring.
Example: Mapping MYC binding to metabolic gene promoters in colorectal cancer cells under lipid stimulation.
Epigenetic Profiling in Neural Systems
Neuronal samples are notoriously challenging due to cellular heterogeneity and fragile chromatin. CUT&RUN provides the sensitivity and specificity needed to resolve enhancer usage, histone mark dynamics, and chromatin repression states in brain development and disease.
Example: Genome-wide CUT&RUN of MeCP2 reveals methylation-independent enhancer binding patterns linked to Rett syndrome.
Cancer Chromatin States & Repressors
In tumors, chromatin-modifying complexes often behave abnormally. CUT&RUN has been used to profile the occupancy of PRC2 components, pioneer factors, or chromatin remodelers under drug treatment or genetic perturbation.
Example: CUT&RUN of H3K27me3 and REST uncovers PBAF-mediated chromatin repression in melanoma.
Enhancer Discovery & Super-Enhancer Mapping
With H3K27ac or BRD4 antibodies, CUT&RUN enables the identification of super-enhancers—regions that regulate cell identity or drive oncogene expression. The high signal-to-noise ratio makes these regulatory hubs easier to define than with ChIP-seq.
Low-Input & Rare Sample Studies
Working with sorted populations, developmental timepoints, or limited biopsy material? CUT&RUN works reliably with as few as tens of thousands of cells—without compromising signal.
Whether you're decoding a transcriptional network or interrogating chromatin rewiring in disease, CUT&RUN helps you get there with clarity, even when material is scarce or targets are subtle.
Sample Requirements
CUT&RUN Sample Requirements and Submission Guidelines
To ensure optimal experimental outcomes, please follow these basic sample preparation guidelines. CUT&RUN is highly sensitive to sample integrity and antibody specificity.
Requirement
Details
Sample Type
Fresh, unfixed live cells
Minimum Cell Input
≥ 5 × 10⁵ cells per sample
Accepted Species
Human, mouse, and rat
Other Species
Subject to evaluation; please contact us before submission
Preservation
Keep samples on ice or in cryoprotectant; avoid freeze-thaw cycles
Antibody Requirement
Provide well-validated, CUT&RUN-compatible primary antibody
Best Practice Tip: Antibody quality is critical for success. Please ensure high affinity and minimal cross-reactivity for your target of interest.
If you're unsure about antibody compatibility or have limited starting material, our team can help assess feasibility before sample submission.
Advantages
CD Genomics: Your Global Partner for High-Quality CUT&RUN Analysis
Choosing a partner for CUT&RUN isn't just about sequencing—it's about confidence in your data. At CD Genomics, we understand the precision and nuance required for chromatin profiling studies. Our CUT&RUN service is built on rigorous quality control, expert-level execution, and responsive scientific support to help you extract meaningful biological insights from even the most challenging samples.
Proven Expertise in Chromatin Profiling
Our team has hands-on experience with CUT&RUN, ChIP-seq, and CUT&Tag across diverse sample types and targets. We offer optimized protocols tailored for histone marks, transcription factors, and chromatin modifiers.
High Signal, Low Noise
We prioritize enzymatic specificity and antibody validation to ensure sharp peak profiles with minimal background—crucial for resolving narrow binding sites and repressive chromatin regions.
Integrated Bioinformatics
From alignment to peak calling, motif discovery to functional annotation, our in-house bioinformatics pipeline turns raw reads into publication-ready insights—complete with visualizations and custom comparisons.
Sample-Sparing Workflow
We support projects with limited input material without compromising data quality, allowing you to work confidently with precious or rare cell populations.
Researcher-Centered Support
We're scientists too. That's why we offer consultation at every step—from experimental design to interpretation—ensuring your study objectives remain front and center.
Whether you're mapping enhancer usage, decoding transcription factor networks, or profiling histone dynamics during development, CD Genomics is your reliable partner in CUT&RUN epigenomics.
