Genetic variants affecting RNA stability influence complex traits and disease risk I

Gene expression is jointly modulated by transcriptional regulation and mRNA stability, yet the latter is often overlooked in studies on genetic variants. Leveraging metabolic labeling data (Bru/BruChase-seq) and a new computational pipeline, RNAtracker, we distinguished allele-specific RNA stability (asRS) from allele-specific RNA transcription (asRT) events. Our analysis identified >5,000 asRS variants, revealing comparable impact of stability on allelic imbalance as transcriptional regulation. This study highlights RNA stability as a critical, yet understudied mechanism linking genetic variation and disease. Overall design: We performed prime editing in HEK293T cells to evaluate the effect of asRS variants. After introducing the edits, total RNA was harvested from cells 0h (pre-treatment), 2h, 8h, and 24h after treatment with 10 ug/ml of ActD (3 replicates per timepoint). After reverse transcription using the SuperScript™ IV Reverse Transcriptase (Thermo Fisher Scientific, Cat# 18090010), the cDNA was amplified using gene-specific primers to generate amplicons containing the variant of interest. Amplicons containing different variants from the same timepoint were pooled together before a second round of PCR to add Illumina adaptors for sequencing. The PCR reactions were stopped before the plateau of the amplification curves. The libraries were purified using 2% agarose gel and sequenced with NovaSeq X Plus 150 PE.