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A New Model Organism to Investigate Extraocular Photoreception: Opsin and Retinal Gene Expression in the Sea Urchin Paracentrotus lividus

ABSTRACT: Sea urchins lack proper eye organs but are photosensitive. In this study, we investigate an extraocular photoreceptor cell (PRC) system in developmental stages of the sea urchin Paracentrotus lividus.

ORGANISM(S): Paracentrotus lividus

PROVIDER: GSE211842 | GEO | 2022/09/20

REPOSITORIES: GEO

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Comparative genomics of the sea urchin P. lividus highlights contrasting trends of genome and regulatory evolution in deuterostomes

Project description:Sea urchins are emblematic marine animals with a rich fossil record and represent instrumental models for developmental biology. As echinoderms, sea urchins display several characteristics that set them apart from other deuterostomes such as their highly regulative embryonic development and their unique pentaradial adult body plan. To determine whether these characteristics are linked to particular genomic rearrangement or gene regulatory rewiring, we introduce a chromosome-scale genome assembly for sea urchin Paracentrotus lividus as well as extensive transcriptomic and epigenetic profiling during its embryonic development. We found that sea urchins show opposite modalities of genome evolution as compared to those of vertebrates: they retained ancestral chromosomal linkages that otherwise underwent mixing in vertebrates, while their intrachromosomal gene order has evolved much faster between sea urchin species that split 60 Myr ago than it did in vertebrates. We further assessed the conservation of the cis-regulatory program between sea urchins and chordates and identified conserved modules despite the developmental and body plan differences. We documented regulatory events underlying processes like zygotic genome activation and transition to larval stage in sea urchins. We also identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes are involved in organismal novelties, such as Aristotle's lantern, tube feet, or in the specification of lineages through for instance the pmar1 and pop genes. Altogether, our results suggest that gene regulatory networks controlling development can be conserved despite extensive gene order rearrangement.

2023-02-09 | GSE202034 | GEO

A molecular model of sea urchin reversible adhesion based on quantitative proteomics

Project description:Marine bioadhesives have unmatched performances especially in wet environments, being valuable sources of inspiration for industrial and biomedical applications. In sea urchins specialized adhesive organs, called tube feet, mediate adhesion. These are composed by a disc, which produces adhesive and de-adhesive secretions for strong reversible attachment, and a motile stem. After detachment, the secreted adhesive remains bound to the substratum as a footprint. Previous studies showed that sea urchin adhesive is composed of proteins and sugars, but so far only one protein, Nectin, was shown to be over-expressed as a transcript in tube feet discs, suggesting its involvement in sea urchin adhesion. Here we use high-resolution quantitative mass-spectrometry technologies to profile Paracentrotus lividus tube feet differential proteome, comparing protein expression levels in its adhesive part (disc) versus the non-adhesive part (stem). This allowed us to identify 163 highly over-expressed disc proteins and propose the first molecular model of sea urchin reversible adhesion. The secreted adhesive proteome was also analyzed, whereby we found that 70% of its components fall within five protein groups, involved in adhesive exocytosis and protection against microbes. Our data also provides evidence that Nectin is not only highly expressed in tube feet discs but is a component of the adhesive itself, thus constituting the first report of a sea urchin tube foot adhesive protein. These results give us an unprecedented insight on the molecular mechanics underlying sea urchins reversible adhesion, opening new doors to develop new, wet-reliable, reversible, efficient, ecological biomimetic adhesives.

2016-03-21 | PXD003122 | Pride

Molecular characterization of the sea urchin larva photosensory system: Insights into the evolution of a Go-Opsin positive neuronal population

Project description:Sea urchin larvae possess a group of photoreceptor cells (PRCs) deploying a Go-Opsin (Opsin3.2). In this study, we investigate investigate the molecular signature of the Sp-Opsin3.2 cells using single cell transcriptomics.

2023-09-13 | GSE240882 | GEO

Ethanol-treated Lytechinus variegatus (sea urchin) embryos

Project description:The effects of ethanol on developmental gene expression in sea urchins is compared to controls at three time points during gastrulation.

2022-06-28 | GSE207100 | GEO

Base-resolution DNA methylation maps of purple sea urchin (Strongylocentrotus purpuratus)

Project description:Using MethylC-seq we investigated single-base resolution methylomes of sea urchin during development.

2021-11-08 | GSE188333 | GEO

Elements of divergence in germline determination in closely related sea urchin species

Project description:Evolutionary transitions enable the wide diversity in life histories of plants and animals. This is particularly germane in the development of the germline in which fitness is a direct readout of evolutionary change. Here, we focused on two distinct sea urchin species who shared a common ancestor 50 million years ago. Even though they both rely on inherited mechanisms to specify their germ line, the integration of stage-matched scRNA seq datasets from these two sea urchins revealed, amongst others, a broader expression of Nanos2 in Lytechinus variegatus (Lv) compared to Strongylocentrotus purpuratus (Sp). In Sp, Nanos2 mRNA expression is highly restricted to the PGCs by a lability element in its 3’UTR. This element is lacking in Lv Nanos2, explaining how this mRNA more broadly accumulates in the Lv embryos. We discovered that the Lv Nanos2 3’UTR instead leads to a germline specific translation of the protein. The results emphasize that regulatory mechanisms resulting in germline diversity rely less on transcriptional regulation and more on post-transcriptional and post-translational restrictions of key gene products, such as Nanos2.

2023-01-19 | GSE208709 | GEO

Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization

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

Gene expression alterations in SoxC knockdown sea urchin embryos

Project description:Transcription factor SoxC is required for all neural development in purple sea urchin S. purpuratus embryos. To begin to develop a gene regulatory network for neural development, we used RNA-Seq to compare transcript populations in SoxC knockdown and control embryos.

2015-12-16 | GSE76067 | GEO

The sea urchin larval response to immune challenge with Vibrio diazotrophicus

Project description:Seawater exposure to the gram negative marine bacterium Vibrio diazotrophicus induces a robust cellular response in sea urchin larvae that includes the migration of pigment cells to the gut epithelium, changes in cell behavior and altered gut morphology (Ho et al., 2016; PMID 27192936). To investigate the transcriptional underpinnings of this response, whole transcriptome sequencing was performed on mRNA isolated from larval samples collected at 0, 6, 12 and 24 hr of exposure to V. diazotrophicus. The morphological simplicity of the sea urchin larva provides a systems-level model for identifying biologically relevant transcriptional state changes in response to dysbiosis in the gut lumen.

2017-03-24 | GSE96940 | GEO

DNA hydroxymethylation profiling of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using hMeDIP-seq

Project description:Using hMeDIP-seq we validated the single-base resolution hydroxymethylomes (ACE-seq) of sea urchin, lancelet and zebrafish embryos.

2021-11-08 | GSE188332 | GEO

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