Single-cell nascent RNA sequencing unveils coordinated global transcription

Area of Science:

• Molecular Biology
• Genomics
• Epigenetics

Background:

• Transcription is the key regulatory step in gene expression.
• Current methods lack single-cell resolution for studying temporal transcription and enhancer-gene coordination.
• Existing nascent RNA capture assays measure gene and enhancer activity in cell populations.

Purpose of the Study:

• To develop a single-cell nascent RNA sequencing assay (scGRO-seq) for high-resolution analysis of transcription.
• To investigate the temporal regulation of transcription and enhancer-gene coordination at the single-cell level.
• To explore the episodic nature of transcription and the dynamics of enhancer-gene interactions.

Main Methods:

• Development of single-cell GRO-seq (scGRO-seq) using click chemistry for nascent RNA capture.
• Quantification of transcribing RNA polymerases in individual cells to estimate transcription burst size and frequency.
• Leveraging replication-dependent histone gene transcription for cell cycle dynamics analysis.

Main Results:

• scGRO-seq reveals coordinated transcription across the genome at single-cell resolution.
• Demonstration of the episodic nature of transcription and co-transcription of functionally related genes.
• Identification of enhancer-gene networks, with super-enhancer bursting preceding associated gene bursting.

Conclusions:

• scGRO-seq provides unprecedented insights into the dynamic nature of global transcription and enhancer function.
• The method enables investigation of transcription regulation mechanisms and the role of enhancers in gene expression.
• Findings highlight the episodic transcription and coordinated bursting dynamics between enhancers and genes.