In this episode of the Epigenetics Podcast, we talked with Arnau Sebé-Pedrós from the Center for Genomic Regulation in Barcelona about his work on chromatin evolution.

The Interview starts by examining specific research findings, including his seminal 2018 paper demonstrating whole-organism single-cell transcriptomics to map larval and adult cell types in the model organism Nematostella vectensis. Dr. Sebe-Pedros recounted the challenges and triumphs faced when delving into single-cell studies of non-model organisms, revealing the innovative strategies employed in the lab to overcome these hurdles.

Shifting gears, we touched upon his work comparing cell types and molecular pathways in reef-building corals through single-cell RNA sequencing, contributing to our understanding of evolutionary conservation and divergence within the cnidarian lineage. We discussed how this comparative approach not only adds to knowledge about coral biology but also enhances methodological frameworks in ecological studies.

In addition, Dr. Sebe-Pedros shared insights into ongoing efforts to reconstruct eukaryotic chromatin evolution using comparative proteomics and genomics analysis, as well as the mechanisms of genomic regulation in various species. His reflections on the sharing of experimental insights across research groups illustrated the collaborative spirit prevalent in the scientific community, particularly regarding endeavors like the Biodiversity Cell Atlas consortium aimed at expanding single-cell efforts across the tree of life.

The episode culminated with Dr. Sebe-Pedros’s thoughts on the revolutionary impact of functional genomic technologies and the vast potential they hold for answering longstanding questions in evolutionary biology. With an emphasis on epigenetics, he defined this field as encompassing any information not encoded directly in the DNA, especially in its role in establishing cell identity and differentiation.

https://www.biodiversitycellatlas.org

Sebé-Pedrós, A., Saudemont, B., Chomsky, E., Plessier, F., Mailhé, M. P., Renno, J., Loe-Mie, Y., Lifshitz, A., Mukamel, Z., Schmutz, S., Novault, S., Steinmetz, P. R. H., Spitz, F., Tanay, A., & Marlow, H. (2018). Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq. Cell, 173(6), 1520–1534.e20. https://doi.org/10.1016/j.cell.2018.05.019

Sebé-Pedrós, A., Chomsky, E., Pang, K., Lara-Astiaso, D., Gaiti, F., Mukamel, Z., Amit, I., Hejnol, A., Degnan, B. M., & Tanay, A. (2018). Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nature ecology & evolution, 2(7), 1176–1188. https://doi.org/10.1038/s41559-018-0575-6

Kim, I.V., Navarrete, C., Grau-Bové, X. et al. Chromatin loops are an ancestral hallmark of the animal regulatory genome. Nature 642, 1097–1105 (2025). https://doi.org/10.1038/s41586-025-08960-w

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