GSE182856
Characterisation of the temporal hepatic transcriptome at subcellular level
In eukaryotes, RNA is synthesized 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, generating daily fluctuations of RNA accumulation and impacting the distribution of transcripts in different subcellular compartments. Here, we performed a comprehensive analysis of nuclear and cytoplasmic, polyA and total, transcriptomes of mouse livers sampled along the daily cycle. These data provide a genome-wide temporal inventory of RNA subcellular enrichments, 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 rhyhtmicity of export rates and cytoplasmic degradation rates of ~1400 genes. While nuclear export times  are usually much shorter than cytoplasmic half-lives, we found that that nuclear export contributes to the modulation and generation of rhythmic profiles of ~10% of the cycling nuclear mRNAs. This study provides an estimation of the nuclear and cytoplasmic life times in the liver  and contributes to a better understanding of the dynamic regulation of the transcriptome during the feeding-fasting cycle. Overall design: RNA-seq of mouse liver tissues sampled during the diurnal cycle (6 time points, 2 WT and 2 Cry1/Cry2 KO animals per time points), at ZT0, 4, 8, 12, 16 and 20. ZT0 is the onset of the light phase (rest phase, without food access) and ZT12 is onset of the dark phase (active phase, with food access). RNA from nuclear fraction, cytoplasmic fraction and total liver tissue were sequenced