bims-ciryme Biomed News
on Circadian rhythms and metabolism
Issue of 2026–01–18
two papers selected by
Gabriela Da Silva Xavier, University of Birmingham
  1. A mouse circadian proteome atlas.
  2. Temporal constraints on enhancer usage shape the regulation of limb gene transcription.
  1. Mol Cell. 2026 Jan 09. pii: S1097-2765(25)01019-6. [Epub ahead of print]
    A mouse circadian proteome atlas.
    Yuta Otobe, Norie Deki-Arima, Shao Xinyan, Kazuma Itabashi, Nobuhiro Kurabayashi, Utaro Nakamura, Anna Uchida, Ryutaro Shimazaki, Kaneyoshi Yamamoto, Takeshi Sakurai, Ying-Hui Fu, Louis J Ptáček, Arisa Hirano, Masao Doi, Hikari Yoshitane.
      The circadian clock drives daily rhythms of gene expression and physiology. Advances in next-generation DNA sequencing have provided extensive insights into RNA expression, but more functional information at the protein level with sufficient depth has been limited by technical challenges. In this study, we generated a comprehensive mouse circadian proteome atlas (https://chronoproteinology.org/circadian_atlas) by analyzing 32 tissues, including the suprachiasmatic nucleus (SCN), using the next-generation mass spectrometer Orbitrap Astral. Data-independent acquisition of 584 samples, including developmental samples, revealed the spatiotemporal profiles of about 19,000 proteins. Proteome and phospho-proteome analyses of whole-cell and nuclear proteins in the liver revealed circadian changes in protein quantity and quality, as well as global changes in hPER2-S662G mutant mice, a genetic model of human familial advanced sleep phase (FASP). This multi-tissue circadian proteome atlas provides a fundamental resource for understanding when, where, and which proteins are expressed and function.
    Keywords:  circadian clock; circadian rhythm; mass spectrometry; nuclear localization; phosphorylation; proteome analysis
    DOI:  https://doi.org/10.1016/j.molcel.2025.12.020
  2. Nat Commun. 2026 Jan 12. 17(1): 5
    Temporal constraints on enhancer usage shape the regulation of limb gene transcription.
    Raquel Rouco, Antonella Rauseo, Fabrice Darbellay, Guillaume Sapin, Olimpia Bompadre, Lucille Lopez-Delisle, Guillaume Andrey.
      Enhancer repertoires orchestrate gene expression during embryonic development, shaping organ structure and function. Individual enhancers can act in overlapping or distinct spatial domains, but their temporal specificity and coordinated action over time remain poorly understood. Here, we identify temporally restricted enhancer repertoires at multiple loci involved in mouse limb development. To capture their dynamic roles, we introduce the regulatory trajectory framework comprising initiation, maintenance, and decommissioning of gene expression. Using a transgenic recorder at the Shox2 locus, we demonstrate that early enhancers initiate transcription, while late enhancers maintain it. Additionally, we found that changes in 3D topology associate with enhancer activities and that loss of enhancer-promoter contacts occurs during decommissioning. Finally, we show that Shox2 regulatory decommissioning can be driven by Hoxd13, a known antagonist of Shox2 expression. Overall, our work uncovers how temporally restricted enhancers generate complex expression patterns and sheds light on the dynamics of enhancer-promoter interactions.
    DOI:  https://doi.org/10.1038/s41467-025-66055-6
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