Single-cell nascent transcription reveals sparse genome usage and plasticity

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• Cell diversification in metazoans relies on understanding transcriptional regulation at the single-cell level.
• Existing methods struggle to capture genome-wide nascent transcription in individual cells.

Purpose of the Study:

• To introduce a novel single-cell nascent RNA sequencing method, scFLUENT-seq, for genome-wide transcription analysis.
• To investigate the extent of genome engagement and transcriptional heterogeneity across diverse cell types.

Main Methods:

• Developed single-cell full-length EU-labeled nascent RNA sequencing (scFLUENT-seq).
• Utilized brief 10-minute metabolic labeling to capture active transcription.
• Applied the method to various cell types, including lymphocytes and stem cells.

Main Results:

• Individual cells transcribe a surprisingly small fraction of the genome (0.02%-3.1%), contrasting with bulk analysis (>80%).
• Identified pervasive, stochastic intergenic transcription, particularly from heterochromatin.
• Observed poor coordination between mRNA transcription and decay in single cells, suggesting noise-buffering.

Conclusions:

• scFLUENT-seq reveals limited genome engagement and significant cell-to-cell transcriptional heterogeneity.
• Intergenic transcription dynamics correlate with cellular plasticity and state transitions.
• The findings challenge bulk transcription assumptions and highlight complex regulatory mechanisms in single cells.