Impact of circadian time, feeding-fasting rhythm and the autonomous clock on the transcriptome

Using an "omics"-based approach, we investigated the interaction between the autonomous liver clock and feeding-fasting rhythm. Transcriptomic analysis and subsequent quantification of exonic and intronic reads revealed that transcriptional mechanisms mediate, at least in part, the integration of feeding signals by the liver clock to drive mRNA oscillations. Therefore, we performed ATAC-seq to probe the state of chromatin accessibility genome-wide. While most open chromatin regions are unchanged across genotype, time and feeding status, transcription factor (TFs) footprints showed altered activity of certain TFs in Liver-RE AL vs NF. For example, CEBPB activity is altered in Liver-RE AL and restored in NF, an observation accompanied by restored CEBPB and BMAL1 common target gene oscillations. Finally, metabolomics analysis illustrated the partial rescue of hepatic metabolism in Liver-RE NF compared to AL (extensive carbohydrate pathway oscillations), and made clear that extra-hepatic clocks contribute significantly to metabolic oscillations in the liver, particularly for pathways involving lipids. Please see the associated reference for full results. Overall design: 8-12 week old male wild type (WT), Bmal1-KO (Bmal1 stop-Fl; KO) and Bmal1 Liver-reconstituted (Bmal1 stop-Fl, AlfP cre +/-; Liver-RE) mice were subjected to ad libitum feeding (AL) or feeding restricted to the nighttime (NF, ZT12-24) of normal chow for 2 weeks under a standard 12 hr light - 12 hr dark cycle. Livers were collected at ZT0, 4, 8, 12, 16 and 20 and prepared for RNA-sequencing.