CUT&RUN Service

CUT&RUN (Cleavage Under Targets and Release Using Nuclease) is an advanced, antibody-guided chromatin profiling method that uses tethered MNase to selectively cleave and release DNA fragments adjacent to target protein binding sites, achieving high-resolution mapping with exceptionally low background. CD BioSciences's CUT&RUN service harnesses this powerful technology through an optimized, industry-grade workflow—delivering precise protein–DNA interaction maps, minimal sequencing requirements, and robust performance across both abundant and low-input samples.

Introduction to CUT&RUN

CUT&RUN profiles chromatin-bound proteins by anchoring a Protein A/G–MNase (pA/pAG-MNase) fusion to a target-specific antibody. Upon calcium activation, MNase selectively cleaves DNA near the protein-binding site, releasing only desired fragments for sequencing. This targeted cleavage approach produces:

1. Extremely low background
2. High-resolution footprints (often single-nucleosome or sub-nucleosomal)
3. Accurate, native-state protein–DNA binding maps
4. Superior performance for both abundant and low-abundance chromatin targets

CUT&RUN eliminates the need for crosslinking and sonication, avoiding many of the confounding artifacts associated with traditional ChIP-seq.

Fig.1 An improved fusion protein for CUT&RUN. (Meers, M. P., et al., 2019)

Advantages of CUT&RUN

Our Services

To ensure high specificity and low-background chromatin profiling, CD BioSciences has established a streamlined CUT&RUN workflow optimized for both histone modifications and transcription factor targets. From sample preparation to sequencing-ready libraries and data analysis, our protocol emphasizes reproducibility, sensitivity, and compatibility with low-input or precious samples.

Sample Preparation & Antibody Binding

1. Mild permeabilization and ConA bead immobilization
2. Primary antibody incubation (rabbit, mouse, goat, etc.)
3. Optional secondary antibody enhancement for difficult epitopes

Targeted MNase Tethering

1. pA/G-MNase binding to antibody–chromatin complexes
2. High specificity with minimized off-target DNA digestion

Controlled MNase Cleavage

1. Calcium activation under optimized 0 °C High-Ca / Low-Salt conditions
2. Prevents premature chromatin release and dramatically lowers background

DNA Release & Purification

1. 37 °C release of target-specific fragments
2. Efficient recovery of short fragments (<120 bp for TF footprints; mono-nucleosomes for histones)

Library Preparation & Sequencing

1. Low-input library construction
2. Paired-end sequencing
3. Spike-in–free normalization incorporating E. coli carry-over DNA from MNase preparation

Bioinformatics Analysis

1. Read alignment, filtering, QC
2. Peak calling (MACS2 optimized for CUT&RUN)
3. Motif analysis
4. Size-fractionated TF footprint analysis
5. Sample-to-sample normalization

Supported Sample Types

1. Cultured Cells (e.g., mammalian)
2. Fresh-Frozen Tissue
3. FFPE Tissue Sections

1. Low-Input and Micro-Dissected Samples
2. Small Model Organisms (e.g., C. elegans)
3. Other Types (Please Inquire)

Our Advantages

1. High Specificity with Low Background: pA/G-MNase and native conditions reduce off-target cleavage.
2. Low Input Compatibility: Effective with as few as 1,000 cells per target.
3. Flexible Target Types: Supports transcription factors, histone marks, and chromatin remodelers.
4. Spike-in–Free Normalization: Uses intrinsic E. coli DNA as an internal control.
5. Footprinting Enabled: Detects sub-nucleosomal fragments for TF occupancy mapping.
6. Clinically Applicable: Validated on needle biopsies and frozen patient samples.

Unlock high-resolution chromatin profiling without the limitations of ChIP-seq. Our scientific team will assist with project planning, antibody selection, input recommendations, and complete data interpretation. Contact us to initiate your CUT&RUN project.

References

1. Meers, M. P., et al. (2019). Improved CUT&RUN chromatin profiling tools. eLife, 8, e46314.
2. Kaya-Okur, H. S., et al. (2020). Efficient low-cost chromatin profiling with CUT&Tag. Nature protocols, 15(10), 3264–3283.