The circadian demethylation of a unique intronic deoxymethylCpG-rich island boosts the transcription of its cognate circadian clock output gene

We demonstrate that there is a tight functional relationship between two highly evolu-tionary conserved cell processes, i.e., the circadian clock (CC) and the circadian DNA demethylation-methylation of cognate deoxyCpG-rich islands. We have discovered that every circadian clock-controlled output gene (CCG), but not the core clock nor its immediate-output genes, contains a single cognate intronic deoxyCpG-rich island, the demethylation-methylation of which is controlled by the CC. During the transcriptional activation period, these intronic islands are demethylated and, upon dimerization of two YY1 protein binding sites located upstream to the transcriptional enhancer and down-stream from the deoxyCpG-rich island, store activating components initially assembled on a cognate active enhancer (a RORE, a D-box or an E-box), in keeping with the gen-eration of a transcriptionally active condensate that boosts the initiation of transcription of their cognate pre-mRNAs. We report how these single intronic deoxyCpG-rich islands are instrumental in such a circadian activation/repression transcriptional process.SignificanceHow the conserved Circadian Clock (CC) and the circadian DNA demethylation of deoxyCpG islands exert a circadian transcriptional control of the CC output genes (CCG's) is unknown. We now reveal the presence of a single intronic deoxymethylCpG island in every CCG, but not in the CC nor their immediate output genes and demonstrate that these islands undergo demethylation coinciding with the circadian gene expression. Moreover, the circadian binding of the YY1 bridging protein is mandatory for an enhancer-CpG island crosstalk, leading to the generation of a transcriptionally active enhancer-CpG island condensate. In short, we reveal how the circadian DNA demethylation of intronic deoxyCpG islands cooperates with cognate CC enhancers to boost the transcription of the circadian genes and their expression.

Automated summary

This study reveals a tight functional relationship between the circadian clock and DNA demethylation-methylation of deoxyCpG islands. It is discovered that circadian clock-controlled output genes contain a specific intronic deoxyCpG island, whose demethylation-methylation is controlled by the circadian clock. These intronic islands undergo demethylation during transcriptional activation and store activating components for the initiation of transcription of their cognate pre-mRNAs. The study demonstrates how intronic deoxyCpG islands cooperate with cognate enhancers to boost circadian gene transcription and expression.