Quantifying mRNA synthesis and decay rates using small RNAs

TL;DR

This paper introduces a method using small RNAs to simultaneously measure mRNA synthesis and decay rates, overcoming limitations of previous approaches that could cause secondary effects and require separate experiments.

Contribution

The authors develop a stochastic model linking mRNA and sRNA dynamics, enabling the estimation of transcription and decay rates from steady-state RNA levels.

Findings

Exact relationships between RNA levels and rates derived

Steady-state measurements can infer transcription and decay dynamics

Method reduces secondary effects compared to traditional approaches

Abstract

Regulation of mRNA decay is a critical component of global cellular adaptation to changing environments. The corresponding changes in mRNA lifetimes can be coordinated with changes in mRNA transcription rates to fine-tune gene expression. Current approaches for measuring mRNA lifetimes can give rise to secondary effects due to transcription inhibition and require separate experiments to estimate changes in mRNA transcription rates. Here, we propose an approach for simultaneous determination of changes in mRNA transcription rate and lifetime using regulatory small RNAs to control mRNA decay. We analyze a stochastic model for coupled degradation of mRNAs and sRNAs and derive exact results connecting RNA lifetimes and transcription rates to mean abundances. The results obtained show how steady-state measurements of RNA levels can be used to analyze factors and processes regulating changes in mRNA transcription and decay.