High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

Area of Science:

• Genomics
• Molecular Biology
• Neuroscience

Background:

• Single-cell RNA sequencing (scRNA-seq) reveals cellular transcriptional states.
• scRNA-seq offers limited insight into the upstream regulatory landscape of gene expression.
• Joint profiling of chromatin accessibility and RNA in single cells is needed to link regulation to output.

Purpose of the Study:

• To develop and demonstrate a method for joint profiling of single-cell chromatin accessibility and mRNA expression.
• To enable direct matching of transcriptional regulation with its outputs at the single-cell level.
• To apply this method to study cell types and regulatory dynamics in the mouse cerebral cortex.

Main Methods:

• Developed droplet-based single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq).
• Tn5 transposase captures accessible chromatin sites in permeabilized nuclei.
• Parallel DNA barcode tagging of accessible sites and mRNA molecules within droplets.

Main Results:

• Generated joint profiles for 5,081 neonatal and 10,309 adult mouse cerebral cortex cells.
• Reconstructed transcriptome and epigenetic landscapes for major and rare cell types.
• Identified lineage-specific accessible sites, particularly for low-abundance cells, and linked promoter accessibility dynamics to transcription levels during neurogenesis.

Conclusions:

• SNARE-seq effectively links cellular transcriptome with accessible chromatin at scale.
• The method facilitates the study of regulatory landscapes in diverse and rare cell populations.
• SNARE-seq provides insights into the relationship between epigenetic accessibility and gene expression dynamics during development.