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Sebé-Pedrós A, Chomsky E, Pang K, Lara-Astiaso D, Gaiti F, Mukamel Z, Amit I, Hejnol A, Degnan BM, Tanay A. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat Ecol Evol 2018; 2:1176-1188. [PMID: 29942020 PMCID: PMC6040636 DOI: 10.1038/s41559-018-0575-6] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/09/2018] [Indexed: 12/11/2022]
Abstract
A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement cell type-specific functions. However, the evolution of metazoan cell types and their underlying gene regulatory programs remain largely uncharacterized. Here, we use whole-organism single-cell RNA-seq to map cell type-specific transcription in Porifera (sponges), Ctenophora (comb jellies) and Placozoa species. We describe the repertoires of cell types in these non-bilaterian animals, uncovering diverse instances of previously unknown molecular signatures, such as multiple types of peptidergic cells in Placozoa. Analysis of the regulatory programs of these cell types reveal variable levels of complexity. In placozoans and poriferans, sequence motifs in the promoters are predictive of cell type-specific programs. In contrast, the generation of a higher diversity of cell types in ctenophores is associated to lower specificity of promoter sequences and to the existence of distal regulatory elements. Our findings demonstrate that metazoan cell types can be defined by networks of TFs and proximal promoters, and indicate that further genome regulatory complexity may be required for more diverse cell type repertoires.
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Affiliation(s)
- Arnau Sebé-Pedrós
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
| | - Elad Chomsky
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Kevin Pang
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - David Lara-Astiaso
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia.,Department of Medicine, Weill Cornell Medicine and New York Genome Center, New York, NY, USA
| | - Zohar Mukamel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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Fritzsch B, Elliott KL. Gene, cell, and organ multiplication drives inner ear evolution. Dev Biol 2017; 431:3-15. [PMID: 28866362 DOI: 10.1016/j.ydbio.2017.08.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/27/2017] [Accepted: 08/25/2017] [Indexed: 12/14/2022]
Abstract
We review the development and evolution of the ear neurosensory cells, the aggregation of neurosensory cells into an otic placode, the evolution of novel neurosensory structures dedicated to hearing and the evolution of novel nuclei in the brain and their input dedicated to processing those novel auditory stimuli. The evolution of the apparently novel auditory system lies in duplication and diversification of cell fate transcription regulation that allows variation at the cellular level [transforming a single neurosensory cell into a sensory cell connected to its targets by a sensory neuron as well as diversifying hair cells], organ level [duplication of organ development followed by diversification and novel stimulus acquisition] and brain nuclear level [multiplication of transcription factors to regulate various neuron and neuron aggregate fate to transform the spinal cord into the unique hindbrain organization]. Tying cell fate changes driven by bHLH and other transcription factors into cell and organ changes is at the moment tentative as not all relevant factors are known and their gene regulatory network is only rudimentary understood. Future research can use the blueprint proposed here to provide both the deeper molecular evolutionary understanding as well as a more detailed appreciation of developmental networks. This understanding can reveal how an auditory system evolved through transformation of existing cell fate determining networks and thus how neurosensory evolution occurred through molecular changes affecting cell fate decision processes. Appreciating the evolutionary cascade of developmental program changes could allow identifying essential steps needed to restore cells and organs in the future.
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Affiliation(s)
- Bernd Fritzsch
- University of Iowa, Department of Biology, Iowa City, IA 52242, United States.
| | - Karen L Elliott
- University of Iowa, Department of Biology, Iowa City, IA 52242, United States
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