Gene regulatory landscape dissected by single-cell four-omics sequencing.

Area of Science:

• Genomics
• Epigenetics
• Cell Biology

Background:

• Cellular diversity arises from complex gene regulation beyond the transcriptome.
• Epigenomic layers like nucleosome occupancy, chromatin states, and genome architecture are crucial for cellular identity.

Purpose of the Study:

• To develop a method for simultaneously profiling multiple epigenomic layers and genome conformation at single-cell resolution.
• To comprehensively understand how diverse epigenomic regulatory modalities converge to define cellular identity.

Main Methods:

• Developed a novel single-cell four-omics sequencing technology named CHARM (Chromatin Architecture, Histone modification, Accessibility, and gene Expression).
• Applied CHARM to mouse embryonic stem cells and cortical tissues.
• Utilized an interpretable machine learning model to identify enhancer-promoter linkages.

Main Results:

• Integrated epigenome profiles were reconstructed at single-cell resolution.
• Distinct cell-cycle dynamics of chromatin accessibility and histone modifications were uncovered.
• Spatial clustering of regulatory elements within the 3D nuclear space was observed.
• Thousands of cell-type- and subtype-specific enhancer-promoter linkages modulating gene expression were identified with high accuracy.

Conclusions:

• CHARM enables the integrative dissection of the 3D epigenome at single-cell resolution.
• This technology provides a versatile platform for decoding regulatory landscapes in complex tissues.
• The findings offer new insights into the epigenetic basis of cellular diversity and identity.