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. 2025 May 15;152(10):dev204799.
doi: 10.1242/dev.204799. Epub 2025 May 23.

Chromatin profiling data indicate regulatory mechanisms for differentiation during development in the acoel Hofstenia miamia

Paul Bump  1 , Kaitlyn Loubet-Senear  2 , Sarah Arnold  1   3 , Mansi Srivastava  1
Affiliations

Chromatin profiling data indicate regulatory mechanisms for differentiation during development in the acoel Hofstenia miamia

Paul Bump et al. Development. .

Abstract

Chromatin profiling data can generate and corroborate hypotheses for regulatory events that underlie the control of gene expression in biological processes. Here, we have profiled chromatin accessibility to build a catalog of putative regulatory DNA during embryonic development in an acoel. Acoels represent an enigmatic phylum-level lineage of animals, the Xenacoelomorpha, which is placed either as a sister group to all other animals with bilateral symmetry or as an early diverging ambulacrarian, positioned equally well to inform the evolution of developmental mechanisms. We focused on the acoel Hofstenia miamia, a new research organism for studying whole-body regeneration that also enables investigations of development from zygote to hatching. We profiled chromatin landscapes encompassing major morphological events during development, and combined transcription factor-binding analyses with single-cell RNA-sequencing data to provide regulatory linkages in a hypothesized differentiation trajectory for epidermis, as well as a new gene regulatory network associated with the formation of muscle. This work enables comparisons of chromatin state during embryogenesis between acoels and other animals, as well as comparisons of embryogenesis to regeneration.

Keywords: Acoel; Chromatin; Embryonic development; Evolution; Gene regulation; Regeneration; Regulatory DNA; Transcription factor binding.

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Conflict of interest statement

Competing interests The authors declare no competing or financial interests.

References

    1. Andrikou, C., Pai, C.-Y., Su, Y.-H. and Arnone, M. I. (2015). Logics and properties of a genetic regulatory program that drives embryonic muscle development in an echinoderm. eLife 4, e07343. 10.7554/eLife.07343 - DOI - PMC - PubMed
    1. Arenas-Mena, C. and Akin, S. (2023). Widespread priming of transcriptional regulatory elements by incipient accessibility or RNA polymerase II pause in early embryos of the sea urchin Strongylocentrotus purpuratus. Genetics 225, iyad145. 10.1093/genetics/iyad145 - DOI - PMC - PubMed
    1. Bentsen, M., Goymann, P., Schultheis, H., Klee, K., Petrova, A., Wiegandt, R., Fust, A., Preussner, J., Kuenne, C., Braun, T.et al. (2020). ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat. Commun. 11, 4267. 10.1038/s41467-020-18035-1 - DOI - PMC - PubMed
    1. Blythe, S. A. and Wieschaus, E. F. (2016). Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis. eLife 5, e20148. 10.7554/eLife.20148 - DOI - PMC - PubMed
    1. Bolaños, D. M., Rock, A., Ros-Rocher, N., Sikes, J. and Srivastava, M. (2023). PCP components control anterior and posterior regeneration, with a Prickle homolog impacting muscle organization, in the acoel Hofstenia miamia. bioRxiv. 10.1101/2023.10.03.560791 - DOI

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