Circadian gene expression study of SMG6 and WT mouse livers

Nonsense-mediated mRNA decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or mis-splicing. Additional roles for NMD in determining mRNA stability in regular gene expression have emerged as well, yet it is poorly known which functions the pathway has in regular mammalian physiology in vivo. Here, we report a novel conditional Smg6 mouse allele that allows converting wild-type SMG6 to a nuclease-mutant version of the protein. We analyzed the consequences of an inactive NMD pathway on the function of the circadian clock whose mechanism is known to depend on high turnover rates of their oscillating mRNAs and proteins. Fibroblast and liver clocks show strong lengthening of free-running circadian periods under Smg6 mutant conditions. We identify a specific core clock component, Cry2, as directly NMD-regulated through its long 3' UTR. Our findings indicate that NMD has been co-opted as an mRNA decay pathway to limit the temporal availability of CRY2, one of the key transcriptional repressors in the rhythm-generating feedback loop, expanding the known scope of NMD regulation in vivo. Overall design: Circadian comparative gene expression profiling analysis of RNA-seq data for WT and smg6 mutant livers.