Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle

Area of Science:

• Molecular Biology
• Systems Biology
• Genomics

Background:

• Gene expression is regulated by coordinated transcriptional and post-transcriptional processes.
• Understanding these dynamics is crucial for cellular response to perturbations.

Purpose of the Study:

• To develop and validate Nanodynamo, a workflow for quantifying RNA life cycle kinetic rates.
• To investigate the interplay between nuclear and cytoplasmic RNA processing steps.
• To unravel coupling mechanisms coordinating gene expression responses.

Main Methods:

• Nanodynamo workflow combining experimental sequencing of native RNA from cellular fractions and polysomes with mathematical modeling.
• Application to triple-negative breast cancer cells.

Main Results:

• Quantified kinetic rates for nuclear and cytoplasmic RNA processing steps.
• Identified widespread post-transcriptional RNA processing mutually exclusive with co-transcriptional processing.
• Unraveled coupling interactions between transcription, processing, export, decay, and translation machineries.

Conclusions:

• Nanodynamo effectively quantifies RNA life cycle kinetics.
• Widespread post-transcriptional processing influences gene expression coordination.
• Identified nuclear-cytoplasmic coupling interactions critical for cellular response to perturbations.