Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

Area of Science:

• Epigenetics
• Genomics
• Cell Biology

Background:

• Single-cell epigenomic profiling is crucial for understanding cellular heterogeneity.
• Existing methods like single-cell CUT&Tag have limitations in throughput and multimodal analysis.

Purpose of the Study:

• To introduce nano-CUT&Tag (nano-CT), a novel method for high-resolution multimodal epigenomic profiling.
• To demonstrate nano-CT's capability to profile multiple histone modifications and chromatin accessibility simultaneously at the single-cell level.

Main Methods:

• Development of nano-CUT&Tag (nano-CT) utilizing nanobody-Tn5 fusion proteins.
• Simultaneous profiling of chromatin accessibility, H3K27ac, and H3K27me3 in juvenile mouse brain cells.
• Analysis of epigenetic dynamics during oligodendrocyte lineage progression.

Main Results:

• Nano-CT achieves higher sensitivity and fragment counts per cell compared to standard single-cell CUT&Tag.
• Simultaneous profiling identified more distinct cell types and states in the mouse brain.
• Chromatin velocity and sequential H3K27me3 repression waves were inferred during oligodendrocyte development.

Conclusions:

• Nano-CT provides a versatile and sensitive platform for multimodal single-cell epigenomic analysis.
• The method offers unique insights into complex epigenetic landscapes and cellular dynamics.
• Nano-CT advances the study of epigenetics in intricate biological systems at single-cell resolution.