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6. CREB-binding protein (CBP) gene family regulates planarian survival and stem cell differentiation

Author

Fraguas, Susanna, Cárcel, Sheila, Vivancos, Coral, Molina, Ma Dolores, Ginés, Jordi, Mazariegos, Judith, Sekaran, Thileepan, Bartscherer, Kerstin, Romero, Rafael, Cebrià, Francesc, Fraguas, Susanna, Cárcel, Sheila, Vivancos, Coral, Molina, Ma Dolores, Ginés, Jordi, Mazariegos, Judith, Sekaran, Thileepan, Bartscherer, Kerstin, Romero, Rafael, and Cebrià, Francesc

Abstract

In developmental biology, the regulation of stem cell plasticity and differentiation remains an open question. CBP(CREB-binding protein)/p300 is a conserved gene family that functions as a transcriptional co-activator and plays important roles in a wide range of cellular processes, including cell death, the DNA damage response, and tumorigenesis. The acetyl transferase activity of CBPs is particularly important, as histone and non-histone acetylation results in changes in chromatin architecture and protein activity that affect gene expression. Many studies have described the conserved functions of CBP/p300 in stem cell proliferation and differentiation. The planarian Schmidtea mediterranea is an excellent model for the in vivo study of the molecular mechanisms underlying stem cell differentiation during regeneration. However, how this process is regulated genetically and epigenetically is not well-understood yet. We identified 5 distinct Smed-cbp genes in S. mediterranea that show different expression patterns. Functional analyses revealed that Smed-cbp-2 appears to be essential for stem cell maintenance. On the other hand, the silencing of Smed-cbp-3 resulted in the growth of blastemas that were apparently normal, but remained largely unpigmented and undifferentiated. Smed-cbp-3 silencing also affected the differentiation of several cell lineages including neural, epidermal, digestive, and excretory cell types. Finally, we analysed the predicted interactomes of CBP-2 and CBP-3 as an initial step to better understand their functions in planarian stem cell biology. Our results indicate that planarian cbp genes play key roles in stem cell maintenance and differentiation.

Published
2021

9. Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Author

Fraguas Susanna, Horn Thomas, Rodríguez-Esteban Gustavo, Cebrià Francesc, Abril Josep F, Calvo Beatriz, Bartscherer Kerstin, and Saló Emili

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

Published
2010
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16. Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Author

Abril Ferrando, Josep Francesc, 1970, Cebrià Sánchez, Francesc, Rodríguez-Esteban, Gustavo, Horn, Thomas, Fraguas, Susanna, Calvo, Beatriz, Bartscherer, Kerstin, Saló i Boix, Emili, and Universitat de Barcelona

Subjects
lcsh:QH426-470, DNA Repair, lcsh:Biotechnology, Receptors, Cell Surface, Eye, Genètica molecular, lcsh:TP248.13-248.65, Consensus Sequence, Databases, Genetic, Genetics, Planària, Animals, Molecular genetics, Homeodomain Proteins, Base Composition, Internet, Neurotransmitter Agents, Genome, Base Sequence, Reverse Transcriptase Polymerase Chain Reaction, Regeneració (Biologia), Gene Expression Profiling, Cell Cycle, Membrane Proteins, Reproducibility of Results, Molecular Sequence Annotation, Planaria, Planarians, Sequence Analysis, DNA, lcsh:Genetics, Regeneration (Biology), RNA Splice Sites, Cell Division, Biotechnology, Research Article, DNA Damage
Abstract

Background Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

18. Advances in Aquatic Invertebrate Stem Cell Research: From Basic Research to Innovative Applications

Author

/Ballarin, Loriano, Rinkevich, Baruch, Hobmayer, Bert, /Ballarin, Loriano, Rinkevich, Baruch, and Hobmayer, Bert

Subjects
Aquatic invertebrates--Cytology, Stem cells--Research
Abstract

This publication is based upon work from COST Action'16203 MARISTEM Stem cells of marine/aquatic invertebrates: from basic research to innovative applications', supported by COST (European Cooperation in Science and Technology).COST (European Cooperation in Science and Technology) is a funding agency for research and innovation networks. Our Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation.www.cost.eu Aquatic invertebrates represent the largest biodiversity and the widest phylogenetic radiation on Earth, with more than 2 million known species. Up until a few years ago, their use as model organisms in biological research was limited by the paucity of omics data. Recently, the situation has rapidly changed and is still changing. Today, the genomes and various transcriptomes of many aquatic invertebrate species, as well as many recombinant proteins of invertebrate origin, are available. New technologies have revolutionized the available toolbox of research methodologies. This explains the rising interest of researchers in the use of aquatic invertebrates as reliable model organisms.In contrast to the prevalence of diverse oligopotent and unipotent stem cells in vertebrates, aquatic invertebrates (especially non-ecdysozoan invertebrates) exhibit multiple adult cell types with stem cellattributes characterized by multipotency and pluripotency; furthermore, these give rise to cell lineages characteristic of more than a single germ layer, sometimes with somatic and germ line potentials. In addition, unlike vertebrates, aquatic invertebrate adult stem cells are disseminated and widespread inside the animal body, are not associated with a regulatory microenvironment (niche) and do participate in aging and regeneration phenomena. These properties can help us to better understand the processes and phenomena in mammalian stem cell biology, such as natural chimerism and cancer, aging and senescence, immunity and autoimmune responses, which are all difficult to explain or understand in the human context.The COST Action 16203 MARISTEM'Stem cells of marine/aquatic invertebrates: from basic research to innovative applications'started in 2017 with the aim to foster the knowledge of the biology of aquatic invertebrates stem cells and strengthen the European community of researchers on aquatic invertebrate stem cells in order to build innovative ideas relevant to various biomedical disciplines. This book represents one of the deliverables of the Action and collects part of the materials produced during the past 3 years within the network as a tool to disseminate and render available what has been achieved up to now. We hope that this book will be useful to scientists interested in stem cells of non-model organisms, with particular reference to aquatic invertebrates.

Published
2022

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