Gene-Specific Linear Trends Constrain Transcriptional Variability of the Toll-like Receptor Signaling

Area of Science:

• Immunology
• Molecular Biology
• Systems Biology

Background:

• Single-cell gene expression exhibits inherent variability.
• Control mechanisms for this variability in response to stimulation are not fully understood.

Purpose of the Study:

• Investigate the regulation of inducible gene expression variability in immune cells.
• Determine how mRNA counts of specific immune genes are controlled.

Main Methods:

• Employed single-cell RNA sequencing (scRNA-seq) and single-molecule fluorescence in situ hybridization (smFISH).
• Studied the toll-like receptor system in immune cells.
• Utilized mathematical modeling and chromatin state perturbation.

Main Results:

• Tumor necrosis factor α (TNF-α) mRNA counts follow a standard stochastic switch model.
• Interleukin-1β (IL-1β) transcription shows increased heterogeneity due to an additional regulatory step.
• Single-cell transcript counts are linearly constrained by the mean response across various conditions.
• Transcriptional bursting modulates these linear constraints.

Conclusions:

• Transcriptional bursting is a key mechanism constraining variability in inducible single-cell mRNA responses.
• Different genes exhibit distinct regulatory strategies for managing expression variability.
• The interplay between transcriptional bursting and gene-specific factors dictates expression heterogeneity.