Biology subjects

Quiroga-Artigas, G.

Publications and source records attributed to Quiroga-Artigas, G..

7 recordsLinked to original sources

bioRxiv2026

Evolutionary landscapes of zygotic genome activation across animals

During early animal embryogenesis, gene expression control shifts from maternally deposited products to newly transcribed RNA through zygotic genome activation (ZGA). Although essential and universal, ZGA remains poorly understood outside a few model species. Here, we generated a transcriptomic atlas of early embryogenesis across 61 animal species from 13 phyla and used a unified computational framework to infer ZGA timing systematically. We find extensive variation in ZGA onset across animals, but show that the ratio between genome size and egg cytoplasmic volume, a proxy for the nuclear-to-cytoplasmic ratio, robustly predicts when genome activation begins. We also reveal that zygotic genes also differ from maternal transcripts in genomic architecture, function and evolutionary conservation, suggesting that ZGA follows a conserved molecular logic despite flexible transcriptomic outputs.

evolutionary biology↗

bioRxiv2025

Compromised DNA replication in gut cells underlies tardigrade sensitivity to genotoxic stress

Tardigrades withstand severe DNA insults, including extreme doses of ionizing radiation, through unique protective proteins and strong upregulation of canonical DNA repair pathways. Yet, these extremophile animals are not immortal, and the cellular and organismal processes that ultimately fail under sustained genotoxic stress have not been characterized. Here, we identify DNA replication as the key vulnerability in the tardigrade Hypsibius exemplaris. Using the radiomimetic drug zeocin to induce DNA breaks, we show that continuous exposure progressively kills tardigrades, accompanied by striking body shrinkage and lipid depletion. DNA synthesis labeling reveals that zeocin disrupts replication and triggers de novo reparative synthesis in select non-dividing tissues. Pulse-wash experiments demonstrate that even transient damage to dividing gut cells irreversibly exhausts their replicative capacity, leading to midgut failure and animal death, despite systemic induction of DNA repair genes. Germ cells and embryos, with their high proliferation rates, show heightened sensitivity. Cross-phyla survival assays in the eutelic nematode Caenorhabditis elegans and neoblast-rich planarian Schmidtea mediterranea further link proliferative activity to mortality kinetics under DNA damage. Collectively, our findings pinpoint DNA replication as an Achilles heel of organismal survival under genotoxic stress, even in animals renowned for their extraordinary DNA damage tolerance.

cell biology↗

bioRxiv2023

Storage cell proliferation during somatic growth establishes that tardigrades are not eutelic organisms

Tardigrades, microscopic ecdysozoans renowned for their resilience to extreme environments, have long been thought to maintain a constant cell number after completing embryonic development, a phenomenon known as eutely. However, sporadic reports of dividing cells have raised questions about this assumption. In this study, we investigated whether tardigrades truly exhibit a fixed cell number during somatic growth using the model species Hypsibius exemplaris. Comparing hatchlings to adults, we observed an overall increase in the number of storage cells, a tardigrade cell type involved in nutrient storage. To assess cell proliferation, we monitored DNA replication via the incorporation of the thymidine analog 5-ethynyl-2-deoxyuridine (EdU). A significantly higher number of storage cells incorporated EdU while animals were still growing. Starvation halted both animal growth and storage cell proliferation, linking the two processes. Additionally, we found that EdU incorporation in storage cells is associated with molting, a critical process in tardigrade post-embryonic development, since it involves cuticle renewal to enable further growth. Finally, we show that hydroxyurea, a drug that slows down DNA replication progression, strongly reduces the number of EdU+ cells and results in molting-related fatalities. Our data not only provide a comprehensive picture of replication events during tardigrade growth but also highlight the critical role of proper DNA replication in tardigrade molting and survival. This study definitively challenges the notion of eutely in tardigrades, offering promising avenues for exploring cell cycle, replication stress, and DNA damage management in these remarkable creatures as genetic manipulation techniques emerge within the tardigrade research field. SIGNIFICANCETardigrades, microscopic invertebrate animals renowned for their resilience in extreme conditions, have traditionally been considered eutelic, implying little to no somatic cell proliferation during their growth. However, a few isolated reports challenged this notion. In this study, using the emerging model Hypsibius exemplaris, we provide unequivocal molecular evidence of DNA replication and proliferation in a specific tardigrade cell type called storage cells, primarily involved in nutrient storage, throughout the animals growth. Furthermore, we demonstrate that this proliferation is associated with the timing of cuticle molting, and we highlight the critical role of proper DNA replication in tardigrade molting and survival. Our research definitively resolves the long-standing controversy surrounding tardigrade eutely, opening up uncharted territories in tardigrade research.

developmental biology↗

bioRxiv2023

The genome of the colonial hydroid Hydractinia reveals their stem cells use a toolkit of genes shared with all animals

Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinias i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinias stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.

genomics↗

bioRxiv2022

GNL3 is an evolutionarily-conserved stem cell gene influencing cell proliferation, animal growth, and regeneration in the hydrozoan Hydractinia

Nucleostemin (NS) is a vertebrate gene preferentially expressed in stem and cancer cells, which acts to regulate cell cycle progression, genome stability, and ribosome biogenesis. NS and its paralogous gene, GNL3-like (GNL3L), arose in the vertebrate clade after a duplication event from their orthologous gene, G protein Nucleolar 3 (GNL3). Research on invertebrate GNL3, however, has been limited. To gain a greater understanding of the evolution and functions of the GNL3 gene, we have performed studies in the hydrozoan cnidarian Hydractinia symbiolongicarpus, a colonial hydroid that continuously generates pluripotent stem cells throughout its life cycle and presents impressive regenerative abilities. We show that Hydractinia GNL3 is expressed in stem and germline cells. The knockdown of GNL3 reduces the number of mitotic and S-phase cells in Hydractinia larvae of different ages. Genome editing of Hydractinia GNL3 via CRISPR/Cas9 resulted in colonies with reduced growth rates, polyps with impaired regeneration capabilities, gonadal morphological defects, and low sperm motility. Collectively, our study shows that GNL3 is an evolutionarily-conserved stem cell and germline marker involved in cell proliferation, animal growth, regeneration, and sexual reproduction in Hydractinia, and sheds new light into the evolution of GNL3 and of stem cell systems.

evolutionary biology↗

bioRxiv2020

Gene knockdown via electroporation of short hairpin RNAs in embryos of the marine hydroid Hydractinia symbiolongicarpus

Performing gene function analyses in a broad range of research organisms is crucial for understanding the biological functions of genes and their evolution. Recent studies have shown that short hairpin RNAs (shRNAs) can induce gene-specific knockdowns in two cnidarian species. We have developed a detailed, straightforward, and scalable method to deliver shRNAs into fertilized eggs of the hydrozoan cnidarian Hydractinia symbiolongicarpus via electroporation, yielding gene-targeted knockdowns that can be assessed throughout embryogenesis, larval settlement, and metamorphosis. Our electroporation protocol allows for the transfection of shRNAs into hundreds of fertilized H.symbiolongicarpus eggs simultaneously with minimal embryo death and no long-term harmful consequences on the developing animals. We show RT-qPCR and detailed phenotypic evidence of our method successfully inducing significant knockdowns of an exogenous gene (eGFP) and an endogenous gene (Nanos2). We also provide visual confirmation of successful shRNA transfection inside embryos through electroporation. This is the first time that electroporation as a delivery system has been developed for Hydractinia. Our detailed protocol for electroporation of shRNAs in H. symbiolongicarpus embryos constitutes an important experimental resource for the hydrozoan community while also serving as a successful model for the development of similar methods for interrogating gene function in other marine invertebrates.

developmental biology↗

bioRxiv2018

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

Jellyfish (medusae) are a distinctive life-cycle stage of medusozoan cnidarians. They are major marine predators, with integrated neurosensory, muscular and organ systems. The genetic foundations of this complex form are largely unknown. We report the draft genome of the hydrozoan jellyfish Clytia hemisphaerica and use multiple transcriptomes to determine gene use across life-cycle stages. Medusa, planula larva and polyp are each characterised by distinct transcriptome signatures reflecting abrupt life cycle transitions, and all deploy a mixture of phylogenetically old and new genes. Medusa specific transcription factors, including many with bilaterian orthologs, associate with diverse neurosensory structures. Compared to Clytia, the polyp-only hydrozoan Hydra has lost many of the medusa-expressed transcription factors, despite similar overall rates of gene content and sequence evolution. Absence of expression and gene loss among Clytia orthologs of genes patterning the anthozoan aboral pole, secondary axis and endomesoderm support simplification of planulae and polyps in Hydrozoa, including loss of bilateral symmetry. Consequently, although the polyp and planula are generally considered the ancestral cnidarian forms, in Clytia the medusa maximally deploys ancestral cnidarian-bilaterian transcription factor gene complexity.

evolutionary biology↗