Circadian rhythms in mouse choroid plexus identified by time-resolved RNAseq require clock in the suprachiasmatic nucleus

The aim of our study was to investigate the circadian regulation of cellular processes in mouse choroid plexus (ChP) and to determine their dependence on signals from the clock in the suprachiasmatic nuclei (SCN). We performed time-resolved transcriptomics of ChP samples from C57Bl6J mice with intact (Ctrl) or surgically removed SCN (SCNx) collected every 4 h over 2 days in constant darkness and from FoxJ1-ERT2-Cre+/-; Bmal1fl/fl mice with ChP-specific clock disruption (Bmal1-KO) collected at 2 time points. We found widespread circadian gene expression in Ctrl mice that was not present in SCNx mice, and the SCNx day/night ratios were reduced similarly to Bmal1-KO. Overall design: ChP samples were collected every 4 h over 2 days in constant darkness from 12 Ctrl and 12 SCNx mice, and at 2 time points (day, night) from 2 Bmal1-KO mice. Total RNA was purified and submitted for sequencing. We performed gene expression profiling, comparing time-resolved transcriptome of Ctrl and SCNx samples after circadian rhythmicity analysis. We also compared day-night differences of top rhythmic genes between Ctrl, SCNx and Bmal1-KO samples.