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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 a 2.5-day circadian time-course and compared clock-controlled genes (CCGs) with existing mouse supraclavicular brown adipose tissue (BAT) and epididymal white adipose tissue (eWAT) circadian time-course datasets. Using Phase Set Enrichment Analysis (PSEA), we report that 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 reexamine a recent interscapular BAT cistrome dataset. Using in vitro-differentiated adipocyte (IVDA) transcription factors that are phase-aligned (\u22644\u2009h) with in vivo as input, motif enrichment analysis reveals 2 temporally distinct regulatory programs: an early E-box activator ARNT-family\/bHLH-PAS program is enriched for transcriptional regulation, RNA metabolism, and signaling pathways, and a late nuclear receptor-associated program is enriched for energy metabolism, phospholipid biosynthesis, mitochondrial function, extracellular matrix (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.<\/jats:p>","DOI":"10.1177\/07487304261480978","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T04:06:47Z","timestamp":1789531607000},"update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["Cell-Autonomous and Systemic Circadian Regulation of Gene Expression in Adipocytes"],"prefix":"10.1177","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-3863-6217","authenticated-orcid":false,"given":"Jennifer M.","family":"Worthen","sequence":"first","affiliation":[{"name":"Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Armina-Lyn M.","family":"Frederick","sequence":"additional","affiliation":[{"name":"Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5843-2864","authenticated-orcid":false,"given":"Phillip A.","family":"Dumesic","sequence":"additional","affiliation":[{"name":"Diabetes Center, University of California, San Francisco, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer J.","family":"Loros","sequence":"additional","affiliation":[{"name":"Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1577-0457","authenticated-orcid":false,"given":"Jay C.","family":"Dunlap","sequence":"additional","affiliation":[{"name":"Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"key":"e_1_3_3_2_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abk0297"},{"key":"e_1_3_3_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2024.114523"},{"key":"e_1_3_3_4_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra1802337"},{"key":"e_1_3_3_5_1","doi-asserted-by":"publisher","DOI":"10.1210\/en.2005-0771"},{"key":"e_1_3_3_6_1","doi-asserted-by":"publisher","DOI":"10.1210\/clinem\/dgaa492"},{"key":"e_1_3_3_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/75556"},{"key":"e_1_3_3_8_1","first-page":"1032","article-title":"Diabetes-specific regulation of adipocyte metabolism by the adipose tissue extracellular matrix","volume":"102","author":"Baker NA","year":"2017","unstructured":"Baker NA, Muir LA, Washabaugh AR, Neeley CK, Chen SY, Flesher CG, Vorwald J, Finks JF, Ghaferi AA, Mulholland MW, et al. 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