Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

  1. Nikolai Hecker
  2. Niklas Kempynck
  3. David Mauduit
  4. Darina Abaffyová
  5. Roel Vandepoel
  6. Sam Dieltiens
  7. Lars Borm
  8. Ioannis Sarropoulos
  9. Carmen Bravo González-Blas
  10. Julie De Man
  11. Kristofer Davie
  12. Elke Leysen
  13. Jeroen Vandensteen
  14. Rani Moors
  15. Gert Hulselmans
  16. Lynette Lim
  17. Joris De Wit
  18. Valerie Christiaens
  19. Suresh Poovathingal
  20. Stein Aerts

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Combinations of transcription factors govern the identity of cell types, which is reflected by genomic enhancer codes. We used deep learning to characterize these enhancer codes and devised three metrics to compare cell types in the telencephalon across amniotes. To this end, we generated single-cell multiome and spatially resolved transcriptomics data of the chicken telencephalon. Enhancer codes of orthologous nonneuronal and γ-aminobutyric acid–mediated (GABAergic) cell types show a high degree of similarity across amniotes, whereas excitatory neurons of the mammalian neocortex and avian pallium exhibit varying degrees of similarity. Enhancer codes of avian mesopallial neurons are most similar to those of mammalian deep-layer neurons. With this study, we present generally applicable deep learning approaches to characterize and compare cell types on the basis of genomic regulatory sequences.

Article activity feed

  1. Mentioned by @shihcheng.bsky.social on Bluesky

    Enhancer codes reveal similarities in mammalian and bird pallium! Deep learning & metrics show high parallels in chicken telencephalon. #Genomics PMID:39946451, Science 2025, @ScienceMagazine https://doi.org/10.1126/science.adp3957 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

  2. Mentioned by @vibai.bsky.social on Bluesky

    In a new study, Nikolai Hecker, Niklas Kempynck et al. in the team of @steinaerts.bsky.social explore 300 million years of brain evolution through the lens of enhancer codes. www.science.org/doi/10.1126/...

  3. Version published to 10.1126/science.adp3957
  4. Mentioned by @sciences.skyfleet.blue on Bluesky

    Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium | Science

  5. Mentioned by @ethan-armand.bsky.social on Bluesky

    refs: doi.org/10.1038/s415... doi.org/10.1038/s415... www.biorxiv.org/content/10.1...

  7. Mentioned by @biorxiv-genomic.bsky.social on Bluesky

    Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium https://www.biorxiv.org/content/10.1101/2024.04.17.589795v1

  8. Mentioned by @biorxivpreprint.bsky.social on Bluesky

    Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium https://www.biorxiv.org/content/10.1101/2024.04.17.589795v1

  9. Version published to 10.1101/2024.04.17.589795v1 on bioRxiv