IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Single-cell profiling of protein-chromatin interactions faces challenges like complex workflows, high costs, and specialized equipment needs.
• Existing methods limit throughput and accessibility for comprehensive epigenetic analysis.

Purpose of the Study:

• To develop a modular, scalable, and cost-effective method for single-cell chromatin profiling.
• To enable high-resolution analysis of histone modifications, transcription factors, and lamina-associated domains at the single-cell level.

Main Methods:

• Indexed tagmentation-based single-cell CUT&Tag-sequencing (IT-scC&T-seq) utilizing three-round combinatorial barcoding.
• A plate-based strategy designed for modularity and high throughput.

Main Results:

• IT-scC&T-seq robustly profiles histone modifications and transcription factors with high specificity.
• The method enables sensitive single-cell mapping of lamina-associated domains, resolving previously difficult-to-detect low-abundance chromatin features.
• Application to adult mouse mammary gland revealed cell-type-specific chromatin landscapes and lineage-regulatory dynamics.

Conclusions:

• IT-scC&T-seq provides a scalable, cost-effective, and broadly accessible approach for high-resolution chromatin profiling.
• The technique facilitates simultaneous analysis of multiple samples and epitopes, enhancing research capabilities.