Evangelos Karousis from the University of Bern in Switzerland presented at London Calling 2019 on “Splice isoform-specific analysis of endogenous NMD targets in human cells.” Karousis explained that RNA degradation is involved in various biological functions, and nonsense-mediated decay (NMD) is not well understood. Nonsense mRNA is dangerous because it can contribute to disease. NMD works on endogenous mRNAs and can regulate stress responses. Karousis and the team wanted to learn if and how NMD targets specific mRNA targets. The group used RNA-mediated knock-down of SMG6/SMG7. They used cDNA sequencing with Nanopore and short reads to perform differential RNA splicing analyses. SQANTI software was used to filter and analyze the data. The approach allowed the team to focus on the targeted isoforms. When NMD factors were depleted, the group noticed changes in specific isoforms. Karousis concluded by sharing a model of how NMD affects specific isoforms. This session combined a simple library-prep approach and short reads to learn about a complex process.
