A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state

A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state

The epithelial and interstitial stem cells of the freshwater polyp 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 d...

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Bibliographic Details
Published in:Genome research Vol. 33; no. 2; pp. 283 - 298
Main Authors: Cazet, Jack F, Siebert, Stefan, Little, Hannah Morris, Bertemes, Philip, Primack, Abby S, Ladurner, Peter, Achrainer, Matthias, Fredriksen, Mark T, Moreland, R Travis, Singh, Sumeeta, Zhang, Suiyuan, Wolfsberg, Tyra G, Schnitzler, Christine E, Baxevanis, Andreas D, Simakov, Oleg, Hobmayer, Bert, Juliano, Celina E
Format: Journal Article
Language:English
Published: United States Cold Spring Harbor Laboratory Press 01-02-2023
Subjects:
Animals
Cell Differentiation
Chromatin
Chromatin - metabolism
Chromosomes
Conserved sequence
Divergence
Ectoderm
Epigenesis, Genetic
Epigenetics
Gene mapping
Gene regulation
Genomes
Histones
Hydra - genetics
Hydra - metabolism
Nucleotide sequence
Polyps (organisms)
Resources
Stem cells
Transcription
Transcriptomics
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Summary:The epithelial and interstitial stem cells of the freshwater polyp 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 is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in , including new genome assemblies for and the AEP strain of , 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 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 and the jellyfish more than 400 million years ago.
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ISSN:1088-9051
1549-5469
1549-5469
DOI:10.1101/gr.277040.122