Cell-Autonomous and Systemic Circadian Regulation of Gene Expression in Adipocytes

Circadian clocks strongly influence adipocyte biology. Studying adipocyte circadian regulation in the absence of organismal cues isolates cell-autonomous clock control, providing insight into mechanisms relevant to metabolic disease. To resolve circadian core biological programs, we deeply sequenced bulk RNA from inguinal-derived, in vitro-differentiated adipocytes (IVDAs) over 2.5 days and compared clock-controlled genes (CCGs) with existing mouse supraclavicular brown (BAT) and epididymal white (eWAT) adipose tissue circadian time-course datasets. Using Phase Set Enrichment Analysis (PSEA), we report 21% of the protein-coding transcriptome is rhythmic in IVDAs. Intrinsic circadian regulation governs key processes in energy metabolism, molecular transport and transcription. Integration with in vivo datasets reveals that BAT and IVDAs exhibit more cohesive rhythmic pathways than does eWAT, clustering around the late-night early-morning transition. To explore how these pathways may be regulated, we reexamined a recent interscapular BAT cistrome dataset. Using IVDA transcription factors that were phase-aligned (≤4hr) with in vivo as input, motif enrichment analysis revealed two temporally distinct regulatory programs; an early E-box activator ARNT-family/bHLH-PAS program was enriched for transcriptional regulation, RNA metabolism, and signaling pathways, and a late nuclear receptor-associated program enriched for energy metabolism, phospholipid biosynthesis, mitochondrial function, ECM organization, and nuclear receptor signaling. Overall, we identify novel rhythmic transcripts and define cell-autonomous circadian programs in adipocytes whose timing is further sculpted by systemic cues in vivo. Because obesity is associated with adipocyte hypertrophy and hyperplasia, processes likely influenced by circadian regulation, these findings advance our understanding of clock-controlled adipocyte metabolism and its contribution to metabolic dysfunction.