Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC.

Area of Science:

• Epigenomics
• Transcriptomics
• Molecular Biology

Background:

• Single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) and its coassays have advanced epigenomics and transcriptomics.
• Current methods suffer from low detection efficiency, limiting the understanding of chromatin accessibility and gene expression complexity in single cells.

Purpose of the Study:

• To develop a high-sensitivity scATAC-seq method for improved detection of accessible chromatin sites.
• To precisely link enhancers to promoters without cell merging.
• To create a joint ATAC-RNA assay for simultaneous epigenomic and transcriptomic profiling.

Main Methods:

• Multiplexed end-tagging amplification of transposase accessible chromatin (METATAC) was developed for high-sensitivity scATAC-seq.
• A statistical framework was employed for precise enhancer-promoter linking.
• METATAC was combined with multiple annealing and looping based amplification cycles for digital transcriptomics (MALBAC-DT) to create M2C-seq.

Main Results:

• METATAC detects a large number of accessible sites per cell and is automation-compatible.
• Allele-specific promoter accessibility was observed in imprinted genes in the mouse cerebral cortex, with biallelic enhancer accessibility.
• M2C-seq demonstrated significant improvements in both ATAC and RNA detection compared to previous methods.

Conclusions:

• METATAC enhances the resolution of single-cell epigenomic studies.
• M2C-seq provides a powerful tool for joint single-cell epigenomic and transcriptomic analysis.
• The developed methods offer consistent performance across various biological samples.