CUT&RUN Service

MtoZ Biolabs offers a CUT&RUN Service to profile protein-DNA interactions with high resolution and minimal background, using targeted cleavage and sequencing. This service is ideal for mapping transcription factor binding sites, histone modifications, chromatin regulators, and other DNA-binding proteins across the genome.

What Is CUT&RUN?

CUT&RUN (Cleavage Under Target and Release Using Nuclease) is an antibody-guided chromatin profiling method for mapping protein DNA interactions directly on native chromatin. In this approach, a specific antibody binds the protein of interest in intact nuclei, and a tethered nuclease is then recruited to cleave DNA in the immediate vicinity of the target. The resulting short DNA fragments that reflect local binding or chromatin occupancy are released, purified, and analyzed by next-generation sequencing (NGS) to generate high-resolution genomic maps with low background. In contrast to ChIP-Seq, CUT&RUN is typically performed on native chromatin without chemical crosslinking between DNA and proteins, which helps reduce artifacts.

The CUT&RUN method has gained significant popularity due to its:

🔸High Sensitivity and Low Background: The use of a micrococcal nuclease (MNase) in CUT&RUN allows for the precise cleavage of DNA-protein complexes, resulting in minimal genomic fragmentation and cleaner data compared to older techniques like ChIP-Seq.

🔸Lower Sample Requirements: CUT&RUN is particularly useful for low-input applications, requiring far fewer cells or tissue samples than ChIP-Seq, which makes it ideal for rare cell populations, primary samples, and high-throughput studies.

🔸Faster and More Cost-Effective: CUT&RUN is typically faster than ChIP-Seq and reduces costs associated with reagent usage and sequencing depth.

This approach is key to uncovering the complex relationships between DNA, histone modifications, chromatin regulators, and transcription factors in various biological processes such as gene expression regulation, epigenetic changes, and cellular responses to environmental cues.

CUT&RUN Service at MtoZ Biolabs

MtoZ Biolabs provides end-to-end CUT&RUN Services for genome-wide profiling of transcription factor binding, histone modifications, and chromatin regulator occupancy. Tell us your research objective and send your samples, and we will complete the experimental workflow, sequencing, and data analysis, delivering interpretation-ready results.

Workflow of CUT&RUN Service

1. Project Alignment

Confirm target, antibody strategy, controls, and sequencing depth based on your study goal.

2. Nuclei or Chromatin Preparation

Prepare intact nuclei or native chromatin under conditions that preserve protein–DNA interactions.

3. Antibody Binding

Bind the target protein or histone mark with a validated antibody on native chromatin.

4. Targeted Nuclease Cleavage and Fragment Release

Recruit nuclease to the antibody-bound sites to generate and release enriched DNA fragments.

5. DNA Purification

Recover CUT&RUN fragments with QC for library readiness.

6. Library Preparation and Sequencing

Construct NGS libraries and perform sequencing to generate mappable reads.

7. Bioinformatics Analysis and Reporting

Run QC, alignment, peak calling, annotation, and visualization tracks, then provide a concise report.



Source: Wikipedia

Figure 1. Visual Representation of The CUT&RUN Sequencing Workflow

Why Choose MtoZ Biolabs

✔️Advanced Technology and Platforms

MtoZ Biolabs utilizes the latest CUT&RUN protocols with optimized nuclease and antibody strategies to ensure high sensitivity and minimal background in protein-DNA interaction studies.

✔️Extensive Experience

Our team has vast experience in chromatin research, protein-DNA interaction studies, and epigenetics. We offer tailored experimental designs and provide expert guidance at each step.

✔️Customizable Services

We offer flexible service options based on your research needs, including targeted protein studies, genome-wide profiling, low-input applications, and sequencing-based analysis.

✔️Fast Turnaround

Our efficient workflows ensure a quick turnaround without compromising quality, allowing you to move forward with your research faster.

✔️Comprehensive Customer Support

MtoZ Biolabs provides end-to-end service with detailed reports, expert data analysis, and prompt communication. We're committed to ensuring that you receive the best results and guidance throughout your project.

Applications of CUT&RUN Service

CUT&RUN can be applied across a wide range of research areas:

1. Transcription Factor Binding Studies: Mapping transcription factor binding sites across the genome to understand gene regulation mechanisms.

2. Histone Modification Profiling: Identifying specific histone modifications associated with active or repressed chromatin regions to study epigenetic regulation.

3. Chromatin Regulator Interactions: Profiling chromatin-associated proteins involved in regulating gene expression, DNA repair, or cell cycle progression.

4. Epigenetic Research: Investigating the role of chromatin modifications in various biological processes such as development, disease progression, and cellular responses to environmental stimuli.

5. Cancer Research: Profiling the epigenetic landscape of cancer cells to identify biomarkers and therapeutic targets related to chromatin regulation.

6. Stem Cell Differentiation: Studying changes in protein-DNA interactions during stem cell differentiation to understand lineage commitment and gene expression changes.

7. Drug Development: Using CUT&RUN to identify how small molecules, inhibitors, or biologics affect protein-DNA interactions, aiding in drug discovery and development.

FAQ

Q1: What types of samples are suitable?

We accept various sample types, including but not limited to:

• Cultured cells
• Primary cells when sufficient input and consistent handling are available
• Fresh or frozen tissues suitable for nuclei preparation

Q2: How should I prepare my samples?

Cells

1. Provide cryopreserved cells at an appropriate scale per target, with separate tubes for each CUT&RUN reaction and comparable cell numbers (500,000-1,000,000 cells) across samples within the same project.

2. Submit cells preserved in a controlled-rate freezing workflow using a standard cryoprotectant solution, and store at -80°C. Flash-frozen dry pellets are generally not suitable for CUT&RUN.

3. For best performance, submit high-quality cells with strong post-thaw viability.

Tissues

Submit frozen tissue at an appropriate mass per target, snap-frozen promptly in liquid nitrogen and stored at -80°C.

Shipping and labeling

Ship on dry ice with secure packaging, clear sample IDs, target assignment per tube, and a sample sheet describing groups and replicates.

If you have special or limited material, we can assess feasibility and optimize a suitable workflow.

Q3: What is the service general workflow?



Q4: What data formats are provided?

1. Raw sequencing data in FASTQ

2. Alignment files in BAM plus index files when applicable

3. Peak calling outputs in BED and or tab-delimited peak tables

4. Genome browser tracks in BigWig

5. QC and summary figures in PDF plus PNG or TIFF

6. Processed result tables in XLSX or CSV, including peak annotation and comparative results when included

7. A concise PDF report documenting design, controls, key parameters, and interpretation

Additional formats can be provided upon request to meet specific analysis or publication requirements.

Start Your Project with MtoZ Biolabs

Whether you're studying transcription factors, histone modifications, or chromatin regulators, our CUT&RUN service can provide the precise data you need to move your research forward.

Contact us to discuss your project and receive expert guidance tailored to your research objectives.