Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR

Cellular RNA abundance reflects synthesis and decay rates, which can differ among transcripts of the same gene. Understanding nonsense-mediated mRNA decay and other RNA turnover pathways requires isoform-resolved kinetic measurements, but existing bioinformatic tools cannot robustly estimate isoform-specific degradation rate constants. We extend the EZbakR-suite to infer isoform-level kinetics from nucleotide-recoding RNA-seq data, uncovering unexpected variability in nonsense-mediated decay efficiency among transcripts with premature termination codons and rapid decay of select mRNAs lacking premature termination codons. Our findings highlight the competition between nonsense-mediated decay and other decay pathways and provide mechanistic insights into transcript features promoting efficient decay.