Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells

Area of Science:

• Molecular Biology
• Genomics
• Epigenetics

Background:

• Protein-DNA interactions are crucial for gene expression regulation.
• Understanding cell-to-cell variability in these interactions and its impact on gene expression is challenging.

Purpose of the Study:

• To develop a novel method for simultaneously quantifying protein-DNA contacts and gene expression at the single-cell level.
• To investigate the relationship between genome organization, chromatin accessibility, and gene expression variability.

Main Methods:

• Developed and applied single-cell DNA adenine methyltransferase identification with messenger RNA sequencing (scDam&T-seq).
• Simultaneously quantified protein-DNA contacts and transcriptome in individual cells.
• Analyzed genome-wide interactions of polycomb-group protein RING1B.

Main Results:

• scDam&T-seq successfully distinguished mouse embryonic stem cells under different culture conditions based on their chromatin landscapes.
• Revealed correlations between genome-lamina contacts, chromatin accessibility, and gene expression in individual cells.
• Provided single-cell genome-wide interaction data for RING1B and its associated transcriptome.

Conclusions:

• scDam&T-seq is a sensitive method for analyzing cell-to-cell heterogeneity in protein-DNA interactions and gene expression.
• The method enables the study of protein-mediated gene regulation in complex biological systems.
• Facilitates analysis of mechanisms driving cell-type-specific transcriptional programs.