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Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development

Author

Listed:
  • Shalu Jhanwar

    (University of Basel
    University of Basel)

  • Jonas Malkmus

    (University of Basel)

  • Jens Stolte

    (University of Basel
    EPFL Innovation Park)

  • Olga Romashkina

    (University of Basel)

  • Aimée Zuniga

    (University of Basel)

  • Rolf Zeller

    (University of Basel)

Abstract

Chromatin remodeling and genomic alterations impact spatio-temporal regulation of gene expression, which is central to embryonic development. The analysis of mouse and chicken limb development provides important insights into the morphoregulatory mechanisms, however little is known about the regulatory differences underlying their morphological divergence. Here, we identify the underlying shared and species-specific epigenomic and genomic variations. In mouse forelimb buds, we observe striking synchrony between the temporal dynamics of chromatin accessibility and gene expression, while their divergence in chicken wing buds uncovers species-specific regulatory heterochrony. In silico mapping of transcription factor binding sites and computational footprinting establishes the developmental time-restricted transcription factor-DNA interactions. Finally, the construction of target gene networks for HAND2 and GLI3 transcriptional regulators reveals both conserved and species-specific interactions. Our analysis reveals the impact of genome evolution on the regulatory interactions orchestrating vertebrate limb bud morphogenesis and provides a molecular framework for comparative Evo-Devo studies.

Suggested Citation

  • Shalu Jhanwar & Jonas Malkmus & Jens Stolte & Olga Romashkina & Aimée Zuniga & Rolf Zeller, 2021. "Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25935-3
    DOI: 10.1038/s41467-021-25935-3
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    Cited by:

    1. Fabrice Darbellay & Anna Ramisch & Lucille Lopez-Delisle & Michael Kosicki & Antonella Rauseo & Zahra Jouini & Axel Visel & Guillaume Andrey, 2024. "Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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