Global mRNA half-lives measurement in nonsense-mediated mRNA decay deficient ESCs
Nonsense-mediated mRNA decay (NMD) pathway promotes the degradation of several mRNA species, including transcripts containing a premature termination codon. Here,we measured global mRNA half-lives in NMD deficient and wild-type (WT) embryonic stem cells (ESCs). This allowed us to discriminate which transcripts are affected by NMD. Several transcripts had an impaired half-life in Smg5 and Smg6 KO ESCs compared to WT. They belong to different pathways and cellular processing indicating that NMD regulates multiple processes in the cells. Finally, majority of the transcripts had an impairment on the half-life in both Smg5 and Smg6 KO ESCs indicating that endo- and exonucleolityc branches of the NMD pathway target the same mRNAs. Overall design: Measurement of global mRNA half-lives in WT and NMD deficient ESCs by SLAM-Seq. We generated stable Smg5 KO and Smg6 KO ESCs. We then measured mRNAs half-lives in Smg5 and Smg6 KO and in WT ESCs.