- Cleavage Under Targets and Tagmentation (CUT&Tag) is a modern epigenomic profiling technique designed to map protein-DNA interactions and chromatin modifications with high sensitivity and resolution, even from small numbers of cells or single cells.
- CUT&Tag builds on earlier methods like ChIP-seq and CUT&RUN but introduces key innovations that simplify the workflow and enhance data quality. By integrating antibody targeting with a Tn5 transposase-mediated DNA cleavage and tagging system, CUT&Tag allows for efficient, low-background sequencing of chromatin-bound proteins such as transcription factors and histone modifications.
- The CUT&Tag procedure begins with intact, permeabilized cells or nuclei, preserving native chromatin structure. An antibody is introduced to target a specific DNA-bound protein or histone modification. This primary antibody is then bound by a secondary antibody that is pre-conjugated to a protein A/G-Tn5 transposase fusion protein, which is pre-loaded with sequencing adapters. Once tethered to the target site, the transposase is activated—typically by the addition of magnesium ions—which leads to simultaneous cleavage and insertion of sequencing adapters at those specific genomic locations.
- This tagmentation-based tagging process bypasses the need for random DNA shearing and separate ligation steps, which are required in ChIP-seq, significantly reducing sample handling, artifacts, and background noise. Because the adapter-tagged DNA fragments are ready for PCR amplification immediately after cleavage, the entire library preparation can be performed directly in the same tube. This makes CUT&Tag exceptionally well-suited for low-input samples, enabling robust chromatin profiling from as few as 100–1,000 cells or even single-cell applications.
- The resulting libraries are sequenced using next-generation sequencing platforms, and the reads are aligned to a reference genome to determine the binding locations of the target protein or the distribution of histone modifications. CUT&Tag provides high-resolution data with sharp signal peaks and minimal background, often outperforming ChIP-seq in both resolution and sensitivity. Additionally, the in situ nature of the method preserves spatial and regulatory context, enabling more accurate detection of protein-DNA interactions.
- CUT&Tag is widely used in research areas such as transcriptional regulation, epigenetics, developmental biology, and cancer biology. It is particularly advantageous in scenarios where sample quantity is limited, such as rare cell populations, primary tissues, or early embryonic stages. Moreover, it is increasingly adopted in single-cell epigenomics due to its scalable and miniaturized workflow, which is compatible with microfluidics and droplet-based systems.
