A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet1,
- Stefan Siebert1,2,
- Hannah Morris Little1,
- Philip Bertemes3,
- Abby S. Primack1,
- Peter Ladurner3,
- Matthias Achrainer3,
- Mark T. Fredriksen4,
- R. Travis Moreland4,
- Sumeeta Singh4,
- Suiyuan Zhang4,
- Tyra G. Wolfsberg4,
- Christine E. Schnitzler5,
- Andreas D. Baxevanis4,
- Oleg Simakov6,
- Bert Hobmayer3 and
- Celina E. Juliano1
- 1Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA;
- 2Lyell Immunopharma, South San Francisco, California 94080, USA;
- 3Institute of Zoology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria;
- 4Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
- 5Whitney Laboratory for Marine Bioscience and Department of Biology, University of Florida, St. Augustine, Florida 32080, USA;
- 6Department of Molecular Evolution and Development, University of Vienna, 1010 Vienna, Austria
Abstract
The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best-characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained and how they give rise to their diverse differentiated progeny. To address such questions, a thorough understanding of transcriptional regulation in Hydra is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in Hydra, including new genome assemblies for Hydra oligactis and the AEP strain of Hydra vulgaris, an updated whole-animal single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, chromatin accessibility, sequence conservation, and histone modifications. These data revealed the existence of large kilobase-scale chromatin interaction domains in the Hydra genome that contain transcriptionally coregulated genes. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types: isorhiza-type nematocytes and somatic gonad ectoderm. Finally, we identified novel candidate regulators of cell type–specific transcription, several of which have likely been conserved at least since the divergence of Hydra and the jellyfish Clytia hemisphaerica more than 400 million years ago.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277040.122.
- Received June 28, 2022.
- Accepted January 10, 2023.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
