Simultaneous quantification of protein-DNA interactions and transcriptomes in single cells with scDam&T-seq.

Area of Science:

• Molecular Biology
• Genomics
• Epigenetics

Background:

• Protein-DNA interactions are crucial for cell-specific chromatin structure and gene expression.
• Existing methods lack the ability to simultaneously assess protein-DNA contacts and transcriptional profiles at a single-cell level.

Purpose of the Study:

• To introduce scDam&T-seq, a novel multi-omics technique for simultaneous single-cell quantification of protein-DNA interactions and transcriptome.
• To enable the study of transcriptional changes induced by specific protein-DNA binding events.

Main Methods:

• scDam&T-seq integrates DNA adenine methyltransferase identification (DamID) for protein-DNA interaction mapping with CEL-Seq2 for transcriptome profiling.
• The protocol involves expressing a fusion protein of a protein of interest (POI) with Dam methyltransferase, followed by selective DNA amplification and mRNA sequencing.

Main Results:

• scDam&T-seq is the first method to provide concurrent protein-DNA contact and transcription data from individual cells.
• The protocol is feasible within 5 days with a throughput of hundreds to thousands of cells.

Conclusions:

• scDam&T-seq offers a powerful tool for dissecting the regulatory roles of protein-DNA interactions in gene expression at single-cell resolution.
• The method is adaptable to standard molecular biology laboratories equipped with FACS, robotics, and high-throughput sequencing capabilities.