A collagenous extracellular matrix regulates germline gene expression in the sea star embryo
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1244632 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32938478_1.fastq.gz | Fastqsanger.gz | |||
| SRR32938478_2.fastq.gz | Fastqsanger.gz | |||
| SRR32938479_1.fastq.gz | Fastqsanger.gz | |||
| SRR32938479_2.fastq.gz | Fastqsanger.gz | |||
| SRR32938480_1.fastq.gz | Fastqsanger.gz |
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Project description:The sea star Patiria miniata uses cell-cell signaling mechanisms in the inductive process of germline formation and here we test if these cells require the extracellular matrix (ECM) in this process. The ECM is a network of proteins and long-chain sugar polymers necessary for structural support, cell signaling, and migration. Collagen is a fundamental component of the ECM network that provides tensile strength and structural integrity, in addition to interacting with other proteins such as laminin and integrins. Here we used b-aminopropionitrile (BAPN), a well-known inhibitor of lysyl oxidase (LOX), an enzyme important for cross-linking mature collagen, a morpholino antisense oligonucleotide to LOX2A, and Col003, an inhibitor of collagen processing to test for a role of the ECM with cells that form the germ line. A DEG-RNA-seq approach was used to broadly test for genes responsive to the ECM at different times in development. A qPCR-based analysis of these resultant candidates show that some ECM responsive genes markedly increase gene expression, including eIF5A1, LvN1.2, ATF3, and the newly described BAPN-Associated Target with Malformed Archenteron (BATMAN), identified here. Furthermore, genes involved in germline formation in this embryo differentially respond to the ECM, including Nanos3, Vasa, PIWI, and the signaling factors BMP2/4, Nodal, and Wnt8. Our results show that disruption of the ECM dysregulates germline gene expression and normal gut morphogenesis during specific development stages. This paradigm adds to a growing list of mechanisms in how primordial germ cells use the ECM in an inductive mode
2025-06-01 | GSE293441 | GEO
Project description:Marine organisms represent a rich source for discovering natural products and materials that could inspire the development of novel molecules or materials for a high variety of industrial applications. Among them are sea stars, emblematic animals of the seashore. These organisms rely on epidermal secretions to cope with their benthic life. Their integument produces a mucus, which represents the first barrier against invaders; and their tube feet produce adhesive secretions to pry open mussels and attach strongly but temporarily to rocks. In this study, we investigate for the first time the protein content of mucous and adhesive secretions from the sea star Asterias rubens. These secretomes were analysed using tandem mass spectrometry and resulting MS/MS data were searched against in silico translated tube foot transcriptome. Tube foot transcripts coding for proteins identified in the two secretions were then functionally annotated by similarity searches against NCBI nr database.
2015-07-20 | PXD001607 | Pride
Project description:We identified cis-regulatory elements based on their dynamic chromatin accessibility during the gastrula-larva stages of sea urchin and sea star and studied their evolution in these echinoderm species
2021-10-24 | GSE186363 | GEO
Project description:‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming
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Project description:Regeneration is pervasive among the metazoa, but to vastly varying degrees. Platyhelminthes, Cnidaria, and Echinodermata are examples of phyla whose members are capable of whole-body regeneration (WBR). While planaria and hydra have been exemplary models of this phenomenon, the molecular details of echinoderm WBR are less established. It remains unclear to what degree such a dramatic regenerative capacity is due to the operation of conserved mechanisms and, in particular, whether any of these are involved in a regenerating Deuterostome. We characterize regeneration in the larval sea star (Patiria miniata) via transcriptome assessment. Transcriptome profiling highlight functions common to regeneration, such as wound healing, axis patterning and proliferation. This dataset was used as a basis for comparison to published Platyhelminth and Cnidarian regeneration datasets. These analyses show that sea star larvae undergo regeneration through a trajectory including wound response, axis respecification, and blastemal proliferation. Commonalities between this Deuterostome model and other WBR models suggest a deep conservation of whole-body regeneration among the metazoa.
2018-11-21 | GSE97230 | GEO
Project description:Skeletal elements from the feather star Anneissia japonica were isolated and stripped of organic material. The skeleton was then demineralized and the occluded proteins isolated. The proteins were separated by SDS-PAGE and fractions were analyzed by LC-MS/MS. The results were compared to predicted proteins encoded by the genome. The proteins found in the organic matrix of the skeleton were compared to those found in other skeletons both within Echinodermata and to other taxa.
2021-09-09 | PXD019526 | Pride
Project description:In most species, early germline development occurs in the absence of transcription with germline determinants subject to complex translational and post-translational regulations. Here, we report for the first time that early germline development is influenced by dynamic regulation of the proteasome system, previously thought to be ubiquitously expressed and to serve ‘housekeeping’ roles in controlling protein homeostasis. We show that proteasomes are present in a gradient with highest levels in the animal hemisphere but extending into the vegetal hemisphere of Xenopus oocytes. This distribution changes dramatically during the oocyte-to-embryo transition, with proteasomes becoming enriched in and restricted to the animal hemisphere and therefore separated from vegetally localized germline determinants. We identify Dead-end1 (Dnd1), a master regulator of vertebrate germline development, as a novel substrate of the ubiquitin-independent proteasomes. In the oocyte, ubiquitin-independent proteasomal degradation acts together with translational repression to prevent premature accumulation of Dnd1 protein. In the embryo, artificially increasing ubiquitin-independent proteasomal degradation in the vegetal pole interferes with germline development. Our work thus reveals novel inhibitory functions and spatial regulation of the ubiquitin-independent proteasome during vertebrate germline development.
2019-04-10 | PXD013446 | Pride
Project description:Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star and sea urchin orthologs. We sought to identify targets of sea urchin and sea star orthologs of Tbr. Because less is known about the function of Tbr during sea star development, we used RNA-seq in conjuction with ChIP-seq studies (GEO:xxxx) to determine the targets of sea star Tbr in early development. Methods: Sea star (Patiria miniata) embryos were injected with translation-blocking morpholino antisense oligonucleotides to knock-down PmTbr expression, as described previously. Control morpholinos were injected into sibling embryos. Embryos were allowed to develop until hatching (30-36 hpf) at which point injected embryos were collected and RNA was extracted. RNA-seq libraries were prepared, sequenced, and analyzed using standard protocols. Results: There are 2,562 genes that are significantly differentially expressed relative to control morpholino inected embryos (FDR < 0.05). There are roughly equivalent numbers of genes down-regulated (1,041) and up-regulated (1,521) by Pm-tbr knockdown, suggesting that PmTbr may act as both a transcriptional activator and repressor. 1,165 differentially expressed genes are located within 75 kb of a PmTbr binding site determined using ChIP-seq, and this set is used as a basis for comparison between sea star and sea urchin binding sites. Conclusions: 1,165 targets of the PmTbr transcription factor were identified based on differential expression following knockdown and the presence of transcription factor binding sites proximal to differentially expressed genes. There are an equal number of up- and down-regulated targets, suggesting Tbr may function as a transcriptional activator and repressor, depending on context and target gene. There was no clear association of motif utilization with either the direction of differential expression or ontological category of the target gene. There are only a small fraction of target genes (approximately 10%) that are in common between the sea star and sea urchin sets.
2016-12-01 | GSE89863 | GEO
Project description:Alternative RNA splicing can generate distinct protein isoforms to allow for the differential control of cell processes across cell types. The chromosome segregation and cell division programs associated with somatic mitosis and germline meiosis display dramatic differences such as kinetochore orientation, cohesin removal, or the presence of a gap phase. These changes in chromosome segregation require alterations to the established cell division machinery. However, it remains unclear what aspects of kinetochore function and its regulatory control differ between the mitotic and meiotic cell divisions to rewire these core processes. Additionally, the alternative splice isoforms that differentially modulate distinct cell division programs have remained elusive. Here, we demonstrate that mammalian germ cells express an alternative mRNA splice isoform for the kinetochore component, DSN1, a subunit of the MIS12 complex that links the centromeres to spindle microtubules during chromosome segregation. This germline DSN1 isoform bypasses the requirement for Aurora kinase phosphorylation for its centromere localization due to the absence of a key regulatory region allowing DSN1 to display persistent centromere localization. Expression of the germline DSN1 isoform in somatic cells results in constitutive kinetochore localization, chromosome segregation errors, and growth defects, providing an explanation for its tight cell type-specific expression. Reciprocally, precisely eliminating expression of the germline-specific DSN1 splice isoform in mouse models disrupts oocyte maturation and early embryonic divisions coupled with a reduction in fertility. Together, this work identifies a germline-specific splice isoform for a chromosome segregation component and implicates its role in mammalian fertility.
2025-02-07 | MSV000097075 | MassIVE
Project description:Collagenous connective tissue is responsible for body integrity in all multicellular organisms and has many biomedical applications within a multibillion-dollar industry. An inspiration for a new generation of collagen-based biomaterials with a wide range of applications may come from echinoderms, a group of marine invertebrates that includes sea stars, sea cucumbers, brittle stars, sea urchins, and sea lilies. Echinoderms are capable of reversibly controlling the pliability of certain connective tissue components (i.e., tendons and ligaments) that are composed of mutable collagenous tissue (MCT). The MCTs variable tensility allows echinoderms to perform unique functions, including energy-saving posture maintenance, autotomy, and asexual reproduction. It is known that neurosecretory juxtaligamental cells in the nervous system control the MCT. These cells release substances that either soften or stiffen the MCT. So far, only a few of these substances have been purified and characterized, and the genomics behind MCT biology are still mostly unknown. Therefore, we propose to identify the putative MCT-related genes in echinoderms and better understand the biology of the juxtaligamental cells. Our research improves our knowledge about the MCT molecular control mechanism, with the ultimate goal of unlocking new biomaterial applications. In this project, we utilize RNA-Seq to identify and annotate differentially expressed genes in the MCT structures of the brittle star Ophiomastix wendtii
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