Zinc finger homeobox-3 (ZFHX3) exerts genome-wide regulation of dailygene expression in the suprachiasmatic nucleus [RNA-seq]
The mammalian suprachiasmatic nucleus (SCN), situated in the ventral hypothalamus, directs daily cellular and physiological 24-hr rhythms across the body. The cell-autonomous timing mechanism is based on a self-sustaining transcriptional-translational feedback loop (TTFL) that in turn co-ordinates the expression of clock-controlled genes (CCGs) that direct circadian programmes of SCN cellular activity.  In the mouse, the transcription factor, ZFHX3 (zinc finger homeobox-3), is necessary for the development of the SCN and influences circadian behaviour in the adult.  The molecular mechanisms by which ZFHX3 affects the SCN at transcriptome and genome levels are, however, poorly defined. Here, we used chromatin immunoprecipitation (ChIP-seq) to map the genomic localization of ZFHX3 sites in the SCN. In parallel, we conducted a comprehensive SCN RNA sequencing at six distinct times-of-day, and then compared the transcriptional profile between the control and ZFHX3-conditional null mutants. We show that the genome wide occupancy of ZFHX3 occurs 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. Correspondingly, we show that the conditional loss of ZFHX3 in the adult has a dramatic effect on the SCN transcriptome,  reducing the level of neuropeptides-encoding transcripts and abolishing rhythmic (24-h) oscillation of the clock TF, Bmal1.  In addition, various TTFL genes and CCGs exhibited altered circadian expression profiles, consistent with the advanced daily behaviour under 12hr light- 12hr dark conditions. Taken together, these findings reveal the extensive genome-wide regulation conferred by ZFHX3 in the central clock that orchestrates daily timekeeping in mammals. Overall design: Gene expression profiling analysis of RNA-seq data in the SCN at six distinct time-points , ZT2,6,10,14,18,22 from control (Creneg), tamoxifen control (Pre-tam) and ZFHX3-KO (Post-tam) conditions. Each time-point had 2-4 biological replicates. Each biological replicate constituted 3-4 individual SCN samples.