Table 1.
A Summary of Circadian-Regulated Metabolically Relevant Processes in Rodent Liver
| Under investigation | Method/Approach | Observation | Reference |
|---|---|---|---|
| Key intermediates of carbohydrate metabolism and redox balance | Enzymatic assays of steady-state metabolite levels | Diurnal variation in metabolic pathways for example, glycolysis, purine, metabolism, Krebs cycle, NADP+:NADPH ratio | (59) |
| “Clock gene” expression | Northern and western blot, bioluminescence | Circadian regulation of promoter activity, mRNA level, protein level, and localization | (7, 79, 140) |
| mRNA levels | Microarray | ∼10% transcriptome is rhythmically expressed | (1, 101) |
| Cytosolic protein levels | 2D-DIGE and mass spectrometry | ∼20% abundant soluble liver proteins are rhythmically expressed, approximately half exhibit rhythmic mRNA | (108) |
| Glucose metabolism | Pharmacological and conditional genetic manipulation | Glucose uptake/export, anabolism/catabolism, storage and intracellular insulin/glucagon signaling are clock-controlled and required for 24-h glucose homeostasis | (71, 74–76, 144) |
| Post-transcriptional regulation of gene expression | Various | Much of rhythmic protein expression is regulated at the level of mRNA stability, translation, and global ribosomal biogenesis | (54, 69) |
| Unfolded protein response | Northern and western blot, RT-PCR | A circadian-regulated 12 h rhythm in the ER IRE1α pathway that is required for normal lipid metabolism | (18) |
| SIRT1 activity/NAD+-salvage pathway | Various | NAD+ levels are a circadian output leading to rhythmic regulation of SIRT1 deacetylase activity (rhythmic input) | (3, 94, 106) |
| Autophagy | Various | C/EBPβ is rhythmically expressed in the liver and drives rhythmic autophagy | (84) |
| Steady state metabolite levels | Global metabolomics | ∼20% of detected metabolites exhibit diurnal rhythms. Most nucleotide biosynthesis is also circadian | (30, 37) |
| ROS production | Various | Rhythmic PRX over-oxidation, cytochrome P450 activity and lipid peroxidation | (31, 36, 118) |
| Epigenetic regulation of gene expression | ChIP-seq, nascent seq, RNA-seq | Circadian modulation of RNA polymerase II recruitment and chromatin remodeling occur on a genome-wide scale. Many loci exhibit rhythmic histone marks and circadian binding of transcription factors | (54, 68, 69, 77, 90, 131) |
| Protein acetylation | Quantitative mass spectrometry | Many cytosolic and mitochondrial enzymes are rhythmically acetylated | (89) |
ChIP-seq, chromatin immunoprecipitation sequencing; DIGE, difference in-gel electrophoresis; ER, endoplasmic reticulum; PRX, peroxiredoxin; ROS, reactive oxygen species; RT-PCR, reverse transcription polymerase chain reaction; SIRT1, SIRTUIN 1.