Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics

Area of Science:

• Genomics and Molecular Biology
• Single-cell Multiomics
• Gene Regulation

Background:

• Enhancers and transcription factors (TFs) are critical for cellular processes.
• Existing multiomic technologies lack multiplexing and scalability for studying gene regulatory mechanisms.
• Need for high-throughput, cost-effective single-cell multiomic solutions.

Purpose of the Study:

• Introduce single-cell ultra-high-throughput multiplexed sequencing (SUM-seq) for co-assaying chromatin accessibility and gene expression.
• Demonstrate SUM-seq's capability for large-scale, cost-effective single-cell multiomic profiling.
• Apply SUM-seq to resolve gene regulation in macrophage polarization, T helper cell subsets, and TF perturbation studies.

Main Methods:

• Developed SUM-seq, a novel single-cell ultra-high-throughput multiplexed sequencing method.
• Co-assayed chromatin accessibility and gene expression in single nuclei.
• Applied SUM-seq to profile hundreds of samples at the million-cell scale.

Main Results:

• SUM-seq enables profiling of millions of cells, outperforming current high-throughput single-cell methods.
• Successfully resolved temporal gene regulation in macrophage polarization, linking TF networks to immune disease variants.
• Defined regulatory landscapes in T helper cell subsets and dissected TF perturbation effects in iPSCs.

Conclusions:

• SUM-seq provides a scalable and cost-effective solution for ultra-high-throughput single-cell multiomic sequencing.
• Accelerates the understanding of complex gene regulatory networks in differentiation, perturbation responses, and disease.
• Enables deeper insights into cellular mechanisms through simultaneous chromatin accessibility and gene expression analysis.