Loss of zinc finger homeobox-3 (ZFHX3) affects rhythmic gene transcription in mammalian central clock

Abstract

ABSTRACTThe mammalian suprachiasmatic nucleus (SCN), situated in the ventral hypothalamus, directs daily cellular and physiological 24-hr rhythms across the body. Spatiotemporal gene transcription in the SCN is vital for daily timekeeping to sustain the molecular circadian clock and clock-controlled genes (CCGs). A key SCN transcription factor, ZFHX3 (zinc finger homeobox-3), is implicated crucial for the synchronization and maintenance of the circadian timekeeping. So far, the resultant aberrant circadian behaviour after the loss of ZFHX3 is well-characterized, but the molecular mechanisms affecting the central clock, and the SCN transcriptome at large is poorly defined. Here, we used ZFHX3 targeted chromatin immunoprecipitation (ChIP-seq) to map the genomic localization of ZFHX3 in the SCN. In parallel, we conducted a comprehensive SCN RNA sequencing at six distinct times-of-day, and compared the transcriptional profile between the control and ZFHX3-conditional null mutants. Our rigorous efforts highlighted the genome wide occupancy of ZFHX3 predominantly around the gene transcription start site (TSS), co-localizing with the known histone modifications, and preferentially partnering with the core-clock TFs (CLOCK, BMAL1) to regulate the clock gene(s) transcription. We clearly showed a drastic effect of the loss of ZFHX3 on the SCN transcriptome, intensely reducing the level of neuropeptides responsible for inter-cellular coupling, along with abolishing rhythmic (24-h) oscillation of the clock TF,Bmal1. A systematic rhythmicity analysis further showed change in phase (peak expression) and amplitude of the various clock genes includingPer (1-3), Dbpin ZFHX3 deficient mice, corroborating with the noted atypical advancement in daily behaviour under 12hr light-12hr dark conditions. Taken together, these findings shed light on genome-wide regulation conferred by ZFHX3 in the central clock that is necessary to orchestrate daily timekeeping in mammals.