- Single-cell chromatin immunocleavage sequencing (scChIC-seq) is a powerful technique that combines the principles of chromatin profiling and single-cell resolution, enabling researchers to map histone modifications or transcription factor binding events across the genome in individual cells.
- This approach builds on the foundation of bulk chromatin immunocleavage methods, such as CUT&RUN (Cleavage Under Targets & Release Using Nuclease), but is adapted to work efficiently with the limited material available from single cells.
- The method provides insights into cell-to-cell variability in chromatin states, which is crucial for understanding gene regulation in heterogeneous tissues, developmental processes, or disease contexts like cancer.
- The core of scChIC-seq involves tethering a protein A/G-MNase (micrococcal nuclease) fusion protein to specific chromatin-bound proteins, typically histone modifications or transcription factors, through antibody targeting. Once the fusion protein binds to the target via the antibody, MNase is activated (usually with calcium ions), cleaving DNA in the vicinity of the target site. The resulting DNA fragments represent chromatin regions associated with the target protein. In the single-cell context, cells are individually encapsulated (e.g., using droplet-based microfluidics or nanowell systems), and barcoded adapters are introduced to preserve the identity of DNA fragments originating from each cell.
- After cleavage and barcoding, the DNA fragments are amplified and subjected to next-generation sequencing. Bioinformatic analysis then reconstructs the chromatin landscape at single-cell resolution by aligning reads to the genome and quantifying fragment distributions. Since the technique is highly sensitive, it allows profiling of rare chromatin features in low-abundance cell types and can detect dynamic chromatin changes during processes such as differentiation, reprogramming, or response to stimuli.
- scChIC-seq offers several advantages over traditional bulk ChIP-seq methods. It requires far fewer cells, avoids fixation (which can obscure epitope recognition), and reduces background noise due to its in situ cleavage approach. Moreover, it provides a high-resolution view of chromatin dynamics at the level of individual cells, enabling the discovery of epigenetic heterogeneity and subpopulation-specific regulatory mechanisms. This makes scChIC-seq a valuable tool in epigenomics, particularly for research involving complex tissues or developmental biology where cellular identity and state are tightly linked to chromatin architecture.
