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IRX3 controls a SUMOylation-dependent differentiation switch in adipocyte precursor cells

Author

Listed:
  • Jan-Inge Bjune

    (University of Bergen
    University of Bergen
    Haukeland University Hospital)

  • Samantha Laber

    (Harwell Campus)

  • Laurence Lawrence-Archer

    (University of Bergen
    Haukeland University Hospital)

  • Patrizia M. C. Nothnagel

    (University of Oslo)

  • Shuntaro Yamada

    (University of Bergen)

  • Xu Zhao

    (University of Oslo)

  • Pouda Panahandeh Strømland

    (Haukeland University Hospital)

  • Niyaz Al-Sharabi

    (University of Bergen)

  • Kamal Mustafa

    (University of Bergen)

  • Pål R. Njølstad

    (University of Bergen
    Haukeland University Hospital)

  • Melina Claussnitzer

    (University of Bergen
    Broad Institute of MIT and Harvard
    Massachusetts General Hospital
    Harvard Medical School)

  • Roger D. Cox

    (Harwell Campus)

  • Pierre Chymkowitch

    (University of Oslo)

  • Gunnar Mellgren

    (University of Bergen
    University of Bergen
    Haukeland University Hospital)

  • Simon N. Dankel

    (University of Bergen
    University of Bergen
    Haukeland University Hospital)

Abstract

IRX3 is linked to predisposition to obesity through the FTO locus and is upregulated during early adipogenesis in risk-allele carriers, shifting adipocyte fate toward fat storage. However, how this elevated IRX3 expression influences later developmental stages remains unclear. Here we show that IRX3 regulates adipocyte fate by modulating epigenetic reprogramming. ChIP-sequencing in preadipocytes identifies over 300 IRX3 binding sites, predominantly at promoters of genes involved in SUMOylation and chromatin remodeling. IRX3 knockout alters expression of SUMO pathway genes, increases global SUMOylation, and inhibits PPARγ activity and adipogenesis. Pharmacological SUMOylation inhibition rescues these effects. IRX3 KO also reduces SUMO occupancy at Wnt-related genes, enhancing Wnt signaling and promoting osteogenic fate in 3D cultures. This fate switch is partially reversible by SUMOylation inhibition. We identify IRX3 as a key transcriptional regulator of epigenetic programs, acting upstream of SUMOylation to maintain mesenchymal identity and support adipogenesis while suppressing osteogenesis in mouse embryonic fibroblasts.

Suggested Citation

  • Jan-Inge Bjune & Samantha Laber & Laurence Lawrence-Archer & Patrizia M. C. Nothnagel & Shuntaro Yamada & Xu Zhao & Pouda Panahandeh Strømland & Niyaz Al-Sharabi & Kamal Mustafa & Pål R. Njølstad & Me, 2025. "IRX3 controls a SUMOylation-dependent differentiation switch in adipocyte precursor cells," Nature Communications, Nature, vol. 16(1), pages 1-25, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62361-1
    DOI: 10.1038/s41467-025-62361-1
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    References listed on IDEAS

    as
    1. Lena Ho & Gerald R. Crabtree, 2010. "Chromatin remodelling during development," Nature, Nature, vol. 463(7280), pages 474-484, January.
    2. Michael Lawrence & Wolfgang Huber & Hervé Pagès & Patrick Aboyoun & Marc Carlson & Robert Gentleman & Martin T Morgan & Vincent J Carey, 2013. "Software for Computing and Annotating Genomic Ranges," PLOS Computational Biology, Public Library of Science, vol. 9(8), pages 1-10, August.
    3. Laura C. Hinte & Daniel Castellano-Castillo & Adhideb Ghosh & Kate Melrose & Emanuel Gasser & Falko Noé & Lucas Massier & Hua Dong & Wenfei Sun & Anne Hoffmann & Christian Wolfrum & Mikael Rydén & Nik, 2024. "Adipose tissue retains an epigenetic memory of obesity after weight loss," Nature, Nature, vol. 636(8042), pages 457-465, December.
    4. Wim de Lau & Nick Barker & Teck Y. Low & Bon-Kyoung Koo & Vivian S. W. Li & Hans Teunissen & Pekka Kujala & Andrea Haegebarth & Peter J. Peters & Marc van de Wetering & D. E. Stange & J. van Es & Dani, 2011. "Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling," Nature, Nature, vol. 476(7360), pages 293-297, August.
    5. Scott Smemo & Juan J. Tena & Kyoung-Han Kim & Eric R. Gamazon & Noboru J. Sakabe & Carlos Gómez-Marín & Ivy Aneas & Flavia L. Credidio & Débora R. Sobreira & Nora F. Wasserman & Ju Hee Lee & Vijitha P, 2014. "Obesity-associated variants within FTO form long-range functional connections with IRX3," Nature, Nature, vol. 507(7492), pages 371-375, March.
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