Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

Abstract

The rate at which RNA molecules decay is a key determinant of cellular RNA concentrations, yet current approaches for measuring RNA half-lives are generally labor-intensive, limited in sensitivity, and/or disruptive to normal cellular processes. Here we introduce a simple method for estimating relative RNA half-lives that is based on two standard and widely available high-throughput assays: Precision Run-On and sequencing (PRO-seq) and RNA sequencing (RNA-seq). Our method treats PRO-seq as a measure of transcription rate and RNA-seq as a measure of RNA concentration, and estimates the rate of RNA decay required for a steady-state equilibrium. We show that this approach can be used to assay relative RNA half-lives genome-wide, with good accuracy and sensitivity for both coding and noncoding transcription units. Using a structural equation model (SEM), we test several features of transcription units, nearby DNA sequences, and nearby epigenomic marks for associations with RNA stability after controlling for their effects on transcription. We find that RNA splicing-related features are positively correlated with RNA stability, whereas features related to miRNA binding, DNA methylation, and G+C-richness are negatively correlated with RNA stability. Furthermore, we find that a measure based on U1-binding and polyadenylation sites distinguishes between unstable noncoding and stable coding transcripts but is not predictive of relative stability within the mRNA or lincRNA classes. We also identify several histone modifications that are associated with RNA stability. Together, our estimation method and systematic analysis shed light on the pervasive impacts of RNA stability on cellular RNA concentrations.