Two Ck1δ transcripts regulated by m6A methylation code for two antagonistic kinases in the control of the circadian clock

The N-6-methylation of internal adenosines (m6A) in mRNA has been quantified and localized throughout the transcriptome. However, the physiological significance of m6A in most highly methylated mRNAs is unknown. It was demonstrated previously that the circadian clock, based on transcription-translation negative feedback loops, is sensitive to the general inhibition of m6A. Here, we show that the Casein Kinase 1 Delta mRNA (Ck1 delta), coding for a critical kinase in the control of circadian rhythms, cellular growth, and survival, is negatively regulated by m6A. Inhibition of Ck1 delta mRNA methylation leads to increased translation of two alternatively spliced Ck1 delta isoforms, Ck1 delta 1 and Ck1 delta 2, uncharacterized until now. The expression ratio between these isoforms is tissuespecific, Ck1 delta 1 and Ck1 delta 2 have different kinase activities, and they cooperate in the phosphorylation of the circadian clock protein PER2. While Ck1 delta 1 accelerates the circadian clock by promoting the decay of PER2 proteins, Ck1 delta 2 slows it down by stabilizing PER2 via increased phosphorylation at a key residue on PER2 protein. These observations challenge the previously established model of PER2 phosphorylation and, given the multiple functions and targets of Ck1 delta, the existence of two isoforms calls for a re-evaluation of past research when Ck1 delta 1 and Ck1 delta 2 were simply Ck1 delta.