Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of RNA accumulation and affecting the distribution of transcripts in different subcellular compartments. Our study analysed the nuclear and cytoplasmic, poly(A) and total transcriptomes of mouse livers collected over the course of a day. These data provide a genome-wide temporal inventory of enrichment in subcellular RNA, and revealed specific signatures of splicing, nuclear export and cytoplasmic mRNA stability related to transcript and gene lengths. Combined with a mathematical model describing rhythmic RNA profiles, we could test the rhythmicity of export rates and cytoplasmic degradation rates of approximately 1400 genes. With nuclear export times usually much shorter than cytoplasmic half-lives, we found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs. This study contributes to a better understanding of the dynamic regulation of the transcriptome during the day-night cycle. Author summary Why was this study done? The circadian clock coordinates temporal gene expression programs to synchronise cellular and physiological functions with environmental time.The circadian clock impinges on many layers of gene regulation, from transcription to mRNA degradation in the cytoplasm.Specifically, whether temporal modulation of nuclear export could influence rhythmic mRNA expression was not known. What did the researchers do and find? We sequenced RNA from nuclear and cytoplasmic fractions from mouse livers sampled at different times of the day.Using a mathematical model describing temporal accumulation profiles of pre-mRNA, nuclear mRNA and cytoplasmic mRNA, we could estimate the nuclear export rates and cytoplasmic degradation rates of approximately 1400 genes.We observed rhythmic patterns in the nucleus that most likely originate from a rhythmic regulation of the nuclear export rate, affecting approximately 10% of the oscillations of the nuclear transcriptome in the liver. What do these findings mean? Our fractionated RNA analysis contributes to a better understanding of the dynamic regulation of the transcriptome during the daily cycle.The majority of the RNA transcripts are exported to the cytoplasm in less than 30 minutes, however, some are retained in the nucleus for several hours. Thus, cellular fractionation allows a finer resolution of temporal profiles in the different subcellular compartment, which is otherwise masked at bulk-level.