Similar Datasets
Project description:Generic and context-dependent gene modulations during Hydra whole body regeneration
| PRJNA437305 | ENA
Project description:The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. The canonical Wnt pathway plays a central role in head organizer function during regeneration and during bud formation, which is the asexual mode of reproduction in Hydra. However, it is unclear how shared the developmental programs of head organizer genesis are in budding and regeneration. Time-series analysis of gene expression changes during head regeneration and budding revealed a set of 298 differentially expressed genes during the 48-h head regeneration and 72-h budding time courses. In order to understand the regulatory elements controlling Hydra head regeneration, we first identified 27,137 open-chromatin elements that are open in one or more sections of the organism body or regenerating tissue. We used histone modification ChIP-seq to identify 9,998 candidate proximal promoter and 3,018 candidate enhancer-like regions respectively. We show that a subset of these regulatory elements is dynamically remodeled during head regeneration and identify a set of transcription factor motifs that are enriched in the enhancer regions activated during head regeneration. Our results show that Hydra displays complex gene regulatory structures of developmentally dynamic enhancers, which suggests that the evolution of complex developmental enhancers predates the split of cnidarians and bilaterians.
| S-EPMC8651858 | biostudies-literature
Project description:Whole-genome duplication (WGD) generates polyploid cells possessing more than two copies of the genome and is among the most common genetic abnormalities in cancer. The frequency of WGD increases in advanced and metastatic tumors, and WGD is associated with poor prognosis in diverse tumor types, suggesting a functional role for polyploidy in tumor progression. Experimental evidence suggests that polyploidy has both tumor-promoting and suppressing effects, but how polyploidy regulates tumor progression remains unclear. Using a genetically engineered mouse model of Her2-driven breast cancer, we explored the prevalence and consequences of whole-genome duplication during tumor growth and recurrence. While primary tumors in this model are invariably diploid, nearly 40% of recurrent tumors undergo WGD. WGD in recurrent tumors was associated with increased chromosomal instability, decreased proliferation and increased survival in stress conditions. The effects of WGD on tumor growth were dependent on tumor stage. Surprisingly, in recurrent tumor cells WGD slowed tumor formation, growth rate and opposed the process of recurrence, while WGD promoted the growth of primary tumors. These findings highlight the importance of identifying conditions that promote the growth of polyploid tumors, including the cooperating genetic mutations that allow cells to overcome the barriers to WGD tumor cell growth and proliferation.
| S-EPMC8298634 | biostudies-literature
Project description:The neural code relates the activity of the nervous system to the activity of the muscles to the generation of behavior. To decipher it, it would be ideal to comprehensively measure the activity of the entire nervous system and musculature in a behaving animal. As a step in this direction, we used the cnidarian Hydra vulgaris to explore how physiological and environmental conditions alter simple contractile behavior and its accompanying neural and muscle activity. We used whole-body calcium imaging of neurons and muscle cells and studied the effect of temperature, media osmolarity, nutritional state, and body size on contractile behavior. In mounted Hydra preparations, changes in temperature, nutrition state, or body size did not have a major effect on neural or muscle activity, or on contractile behavior. But changes in media osmolarity systematically altered contractile behavior and foot detachments, increasing their frequency in hypo-osmolar media solutions and decreasing it in hyperosmolar media. Similar effects were seen in ectodermal, but not in endodermal muscle. Osmolarity also bidirectionally changed the activity of contraction burst (CB) neurons, but did not affect the network of rhythmic potential (RP) neurons in the ectoderm. These findings show osmolarity-dependent changes in the activity of CB neurons and ectodermal muscle, consistent with the hypothesis that CB neurons respond to media hypo-osmolarity, activating ectodermal muscle to generate CBs. This dedicated reflex could serve as an excretory system to prevent osmotic injury. This work demonstrates the feasibility of studying an entire neuronal and muscle activity in a behaving animal.
| S-EPMC7452734 | biostudies-literature
Project description:Positional RNA-sequencing of isolated Hydra body pieces and RNA-sequencing of fully regenerated Hydra animal was combined with RNA-sequencing of actively regenerating spheroids (see submission E-MTAB-9672) in order to elucidate the role of tissue stretching on regeneration and body pattern formation.
2022-10-13 | E-MTAB-9676 | biostudies-arrayexpress
Project description:Recent body of evidence demonstrates that extracellular vesicles (EVs) represent the first language of cell-cell communication emerged during evolution. In aquatic environments, transferring signals between cells by EVs offer protection against degradation, allowing delivering of chemical information in high local concentrations to the target cells. The packaging of multiple signals, including those of hydrophobic nature, ensures target cells to receive the same EV-conveyed messages, and the coordination of a variety of physiological processes across cells of a single organisms, or at the population level, i.e. mediating the population´s response to changing environmental conditions. Here, we purified EVs from the medium of the freshwater invertebrate Hydra vulgaris, and the molecular profiling by proteomic and transcriptomic analyses revealed multiple markers of the exosome EV subtype. Moreover, positive and negative regulators of the Wnt/β-catenin signaling pathway, the major developmental pathway acting in body axial patterning, were identified. Functional analysis on amputated polyps revealed EV ability to interfere with both head and foot regeneration, suggesting an active role in setting up tissue gradients and oro-aboral polarity through delivery of short and long-distance signals. Our results open the path to unravel EV biogenesis and function in all cnidarian species, tracing back the origin of the cell-cell, cross-species or cross-kingdom communication in aquatic ecosystems
2021-07-30 | GSE180886 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-03-09 | GSE205918 | GEO
Project description:BackgroundThe restoration of adults from fragments of blood vessels in botryllid ascidians (termed whole body regeneration [WBR]) represents an inimitable event in the chordates, which is poorly understood on the mechanistic level.ResultsTo elucidate mechanisms underlying this phenomenon, a subtracted EST library for early WBR stages was previously assembled, revealing 76 putative genes belonging to major signaling pathways, including Notch/Delta, JAK/STAT, protein kinases, nuclear receptors, Ras oncogene family members, G-Protein coupled receptor (GPCR) and transforming growth factor beta (TGF-beta) signaling. RT-PCR on selected transcripts documented specific up-regulation in only regenerating fragments, pointing to a broad activation of these signaling pathways at onset of WBR. The followed-up expression pattern of seven representative transcripts from JAK/STAT signaling (Bl-STAT), the Ras oncogene family (Bl-Rap1A, Bl-Rab-33), the protein kinase family (Bl-Mnk), Bl-Cnot, Bl-Slit and Bl-Bax inhibitor, revealed systemic and site specific activations during WBR in a sub-population of circulatory cells.ConclusionWBR in the non-vertebrate chordate Botrylloides leachi is a multifaceted phenomenon, presided by a complex array of cell signaling and transcription factors. Above results, provide a first insight into the whole genome molecular machinery of this unique regeneration process, and reveal the broad participation of cell signaling and transcription factors in the process. While regeneration involves the participation of specific cell populations, WBR signals are systemically expressed at the organism level.
| S-EPMC2576188 | biostudies-literature
Project description:Hydra has long been studied for its remarkable ability to regenerate its head. Previous studies focusing on molecular mechanisms of axial patterning and head regeneration using a candidate gene approach have revealed a central role for the canonical Wnt pathway. We performed a global gene expression analysis during Hydra magnipapillata head regeneration using RNA-seq to identify additional genes that are transcriptionally regulated during the regeneration of the head organizer in hydra. Differential expression analysis revealed a set of 4,978 genes with significant changes during a 48-hour head regeneration time-course that includes many key genes in the Wnt, TGF-M-NM-2/BMP and MAP kinase pathways. We observed the differential regulation of several genes that are part of the epithelial-to-mesenchymal transition in bilaterians such as Snail. We assembled 806 novel putative lincRNAs with 176 of these are differentially expressed during the time course. We observed the coordinated transcriptional regulation of several factors that regulate the effective pool of free M-NM-2-catenin that together synergize to increase the amount of M-NM-2-catenin available for transcriptional regulation of downstream genes. The differential expression of Snail and some of its interacting regulators and downstream targets suggests that a partial-EMT-like response is involved in hydra head regeneration. This time-course is a valuable resource for the study of the transcriptional dynamics of head regeneration in hydra. mRNA profiling of regenerating head from 6 time points post bisection of Hydra head (H. magnipapillata), generated by deep sequencing, in duplicates, using Illumina HiSeq2500.
2014-12-13 | E-GEOD-64127 | biostudies-arrayexpress
Project description:The lymphatic vasculature mediates essential physiological functions including fluid homeostasis, lipid and hormone transport, and immune cell trafficking. Recent studies have suggested that promoting lymphangiogenesis enhances cardiac repair following injury, but it is unknown whether lymphangiogenesis is required for cardiac regeneration. Here, we describe the anatomical distribution, regulation, and function of the cardiac lymphatic network in a highly regenerative zebrafish model system using transgenic reporter lines and loss-of-function approaches. We show that zebrafish lacking functional vegfc and vegfd signaling are devoid of a cardiac lymphatic network and display cardiac hypertrophy in the absence of injury, suggesting a role for these vessels in cardiac tissue homeostasis. Using two different cardiac injury models, we report a robust lymphangiogenic response following cryoinjury, but not following apical resection injury. Although the majority of mutants lacking functional vegfc and vegfd signaling were able to mount a full regenerative response even in the complete absence of a cardiac lymphatic vasculature, cardiac regeneration was severely impaired in a subset of mutants, which was associated with heightened pro-inflammatory cytokine signaling. These findings reveal a context-dependent requirement for the lymphatic vasculature during cardiac growth and regeneration.
| S-EPMC6706389 | biostudies-literature