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Brain histone beta-hydroxybutyrylation couples metabolism with gene expression

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Abstract

Little is known about the impact of metabolic stimuli on brain tissue at a molecular level. The ketone body beta-hydroxybutyrate (BHB) can be a signaling molecule regulating gene transcription. Thus, we assessed lysine beta-hydroxybutyrylation (K-bhb) levels in proteins extracted from the cerebral cortex of mice undergoing a ketogenic metabolic challenge (48 h fasting). We found that fasting enhanced K-bhb in a variety of proteins including histone H3. ChIP-seq experiments showed that K9 beta-hydroxybutyrylation of H3 (H3K9-bhb) was significantly enriched by fasting on more than 8000 DNA loci. Transcriptomic analysis showed that H3K9-bhb on enhancers and promoters correlated with active gene expression. One of the most enriched functional annotations both at the epigenetic and transcriptional level was “circadian rhythms''. Indeed, we found that the diurnal oscillation of specific transcripts was modulated by fasting at distinct zeitgeber times both in the cortex and suprachiasmatic nucleus. Moreover, specific changes in locomotor activity daily features were observed during re-feeding after 48-h fasting. Thus, our results suggest that fasting remarkably impinges on the cerebral cortex transcriptional and epigenetic landscape, and BHB acts as a powerful epigenetic molecule in the brain through direct and specific histone marks remodeling in neural tissue cells.

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Data availability

RNA-seq and ChIP-seq datasets generated and analyzed during this study are available on the GEO database: accession number GSE168725.

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Acknowledgements

We thank Manuel Tongiani, Andrea Tognozzi, Matteo Alberti and Maria Grazia Giuliano for their help with the experiments. Special thanks to Vania Liverani and Antonella Calvello (Scuola Normale Superiore) for technical assistance in the lab. We thank Prof. Concetta Morrone and Prof. Paola Binda (University of Pisa) for their insightful comments.

Funding

This research was supported by H2020-MSCA-IF-2016 749697 GaMePLAY, University of Pisa PRA-2020, Italian Ministry of University and Research PNRR Tuscany Health Ecosystem Milestone 8.9.1 and PNRR young MSCA_0000081 iNsPIReD to PT, and funded in part by EFSD-Lilly 2019 to AG and PT. The work of SCh, MS, CM, and PB was in part supported by NIH Grant GM123558 to PB. RM was supported by Fondazione Umberto Veronesi.

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Author notes

  1. Sara Cornuti, Siwei Chen have contributed equally to this work.

Authors and Affiliations

  1. Bio@SNS Lab, Scuola Normale Superiore, Pisa, Italy

    Sara Cornuti, Leonardo Lupori, Francesca Damiani, Francesco Raimondi & Paola Tognini

  2. Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA

    Siwei Chen, Muntaha Samad, Christophe Magnan & Pierre Baldi

  3. Institute of Clinical Physiology, National Research Council, Pisa, Italy

    Francesco Finamore, Fabrizia Carli, Simona Fenizia, Silvia Rocchiccioli & Amalia Gastaldelli

  4. Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy

    Matteo Caldarelli & Paola Tognini

  5. Institute of Neuroscience, National Research Council, Pisa, Italy

    Raffaele Mazziotti

  6. Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy

    Raffaele Mazziotti

Authors
  1. Sara Cornuti
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Contributions

SC performed the experiments, analyzed the data, and prepared the figures. SCh performed the ChIP-seq and RNA-seq analysis. LL performed the daily activity analysis. FF and SR performed the Beta-hydroxybutyrilome analysis. FC, SF and AG performed the LC–MS-QTOF experiments and analysis. MS performed the RNA seq analysis. MC and FD helped with tissue harvesting and performed qPCR. FR helped with GO analysis. RM helped with correlations between ChIP-seq and RNA-seq. CM helped with ChIP-seq data alignment and analysis. PB supervised the RNA-seq and ChiP-seq data analysis. PT conceived and supervised the project, performed the experiments, and wrote the manuscript.

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Correspondence to Paola Tognini.

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All experiments were carried out in accordance with the European Directives (2010/63/EU) and were approved by the Italian Ministry of Health (authorization number 354/2020-PR).

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Cornuti, S., Chen, S., Lupori, L. et al. Brain histone beta-hydroxybutyrylation couples metabolism with gene expression. Cell. Mol. Life Sci. 80, 28 (2023). https://doi.org/10.1007/s00018-022-04673-9

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