Nascent-Seq analysis of Drosophila cycling gene expression

RhythmicmRNA expression is a hallmark of circadian biology and has been described in numerous experimental systems including mammals. A small number of core clock gene mRNAs and a much larger number of output mRNAs are under circadian control. The rhythmic expressionof core clock genes is regulated at the transcriptional level, and this regulation is important for the timekeeping mechanism. However, the relative contribution of transcriptional and posttranscriptional regulation to global circadian mRNA oscillations is unknown. To address this issue in Drosophila, we isolated nascent RNA fromadult fly heads collected at different time points andsubjected it to high-throughput sequencing. mRNA was isolated and sequenced in parallel. Some genes had cycling nascent RNAs with no cycling mRNA, caused,most likely, by light-mediated read-through transcription. Most genes with cycling mRNAs had significant nascent RNA cyclingamplitudes, indicating a prominent role for circadian transcriptional regulation.However, a considerable fraction had higher mRNA amplitudes than nascent RNA amplitudes. The same comparison for core clock genemRNAs gives rise to a qualitatively similar conclusion. The data therefore indicate a significant quantitative contribution of posttranscriptional regulation to mRNA cycling.