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Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis

ABSTRACT: ChIP-seq provides a genome-wide view of the binding sites of Alx1, a pivotal transcription factor in a gene regulatory network that controls skeletogenesis in sea urchins and other echinoderms.

ORGANISM(S): Strongylocentrotus purpuratus

PROVIDER: GSE131370 | GEO | 2019/07/10

REPOSITORIES: GEO

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Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis

Project description:Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis

| PRJNA543356 | ENA

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

The brittle star genome illuminates the genetic basis of animal appendage regeneration

Project description:Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited available genomic resources. Here, we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star displays the most rearranged genome amongst echinoderms sequenced to date, featuring a reorganised Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression throughout brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, notably during the proliferative phase of regeneration. Our findings emphasise the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.

2024-05-07 | GSE246675 | GEO

Genome-wide detection of Tbrain binding sites during early development in both sea urchin (S. purpuratus) and sea star (P. miniata)

Project description:Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). While cis regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low affinity, secondary binding motif, although the primary, high affinity motif is conserved. To date, however, no genome-wide comparisons have been performed in order to provide an unbiased assessment of the evolution of GRNs between these taxa; and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology. The study here measures genome-wide binding of Tbrain orthologs using ChIP-seq, and associates these with putative target genes to assess global function. Targets of both factors are enriched for other regulatory genes, although non-overlapping sets of functional enrichments in the two datasets suggest a much diverged function. The number of low affinity binding motifs are significantly depressed in sea urchins compared to sea star, but both motifs types are associated with genes from a range of functional categories. Only a small fraction (~10%) of genes are predicted to be orthologous targets. Collectively these data indicate that Tbr has evolved significantly different developmental roles in these echinoderms, and that the maintained and unique targets, and their associated binding motifs are dispersed throughout the hierarchy of the GRN, rather than being biased towards terminal process or discrete functional blocks suggesting extensive evolutionary tinkering.

2016-12-01 | GSE89862 | GEO

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

Project description: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.

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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

Genetic risk of osteoarthritis operates during human skeletogenesis

Project description:Osteoarthritis (OA) is a polygenic disease of older people resulting in the breakdown of cartilage within articular joints. Although a leading cause of disability, there are no disease-modifying therapies. Evidence is emerging to support the origins of OA in skeletogenesis. Whilst methylation QTLs (mQTLs) co-localizing with OA GWAS signals have been identified in aged human cartilage and used to identify effector genes and variants, such analyses have never been conducted during human development. Here, for the first time, we have investigated the developmental origins of OA genetic risk at seven well-characterized OA risk loci, comprising 39 OA-mQTL CpGs, in human fetal limb (FL) and cartilage (FC) tissues using a range of molecular genetic techniques. We compared our results to aged cartilage samples (AC) and identified significant OA-mQTLs at 14 CpGs and 29 CpGs in FL and FC tissues, respectively. Differential methylation was observed at 26 sites between fetal and aged cartilage, with the majority becoming actively hypermethylated in old age. Notably, 6/9 OA effector genes showed allelic expression imbalances during fetal development. Finally, we conducted ATAC-sequencing in cartilage from the developing and aged hip and knee to identify accessible chromatin regions, and found enrichment for transcription factor-binding motifs including SOX9 and FOS/JUN. For the first time, we have demonstrated the activity of OA-mQTLs and expression imbalance of OA effector genes during skeletogenesis. We show striking differences in the spatiotemporal function of these loci, contributing to our understanding of OA aetiology, with implications for the timing and strategy of pharmacological interventions.

2022-10-26 | GSE214394 | GEO

ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation

Project description:ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation

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ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation [ATAC-seq]

Project description:ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation [ATAC-seq]

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ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation [ChIP-seq]

Project description:ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation [ChIP-seq]

| PRJNA678324 | ENA