Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution.

Area of Science:

• Molecular Biology
• Epigenetics
• Genomics

Background:

• Understanding gene regulation in complex tissues requires single-cell resolution analysis of chromatin state.
• Simultaneous profiling of multiple epigenetic marks is essential for comprehensive analysis.

Purpose of the Study:

• To introduce and validate a novel nanobody-based single-cell CUT&Tag (nano-CT) protocol.
• To enable simultaneous profiling of three epigenetic modalities (two histone marks and open chromatin) from individual cells.

Main Methods:

• Development of novel secondary nanobody-Tn5 fusion proteins for targeted, barcoded tagmentation.
• Utilized a commercially available platform for single-cell indexing.
• In-house production and purification of nanobody-Tn5 fusion proteins (3-4 days).

Main Results:

• Nano-CT successfully generated multimodal epigenomic profiles from thousands of brain cells at single-cell resolution.
• The protocol is efficient, requires low sample input, and offers flexibility in modality selection.
• In-house production of essential reagents is feasible within 3-4 days.

Conclusions:

• Nano-CT provides a powerful, accessible tool for multimodal single-cell epigenomic analysis.
• The method facilitates the study of epigenetic heterogeneity and chromatin dynamics in development and disease.
• Potential to reveal interactions between different chromatin modalities for deeper biological insights.