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Strongylocentrotus purpuratus

ABSTRACT: Parental environments alter DNA methylation in offspring of the purple sea urchin, Strongylocentrotus purpuratus

PROVIDER: PRJNA525826 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8697520.fastq.gz	Fastqsanger.gz
	SRR8697530.fastq.gz	Fastqsanger.gz
	SRR8697540.fastq.gz	Fastqsanger.gz
	SRR8697511.fastq.gz	Fastqsanger.gz
	SRR8697521.fastq.gz	Fastqsanger.gz

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Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

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Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under three different seawater CO2 concentrations 400, 800, 1200 M-BM-5atm. The goal was to determine the effects of CO2, an important climate change variable, on global gene expression Larvae were cultured under three different seawater CO2 concentrations 400, 800, 1200 M-BM-5atm, each with four replicate cultures, and sampled at two developmental stages (gastrula and pluteus)

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Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under four different seawater conditions: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. The goal was to determine the effects of temperature and CO2, both important climate change variables, on gene expression

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Synergistic effects of temperature and pCO2 on growth, development and gene expression of Strongylocentrotus purpuratus larvae

Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under four different seawater conditions: (i)13M-BM-0C/400 M-BM-5atm pCO2, (ii)13M-BM-0C/1100 M-BM-5atm pCO2, (iii)18M-BM-0C/400 M-BM-5atm pCO2 (iv)18M-BM-0C/1100 M-BM-5atm pCO2. The goal was to determine the effects of temperature and CO2, both important climate change variables, on gene expression Larvae were cultured under four different seawater conditions (ii)13M-BM-0C/1100 M-BM-5atm pCO2, (iii)18M-BM-0C/400 M-BM-5atm pCO2 (iv)18M-BM-0C/1100 M-BM-5atm pCO2, (i)13M-BM-0C/400 M-BM-5atm each with three replicate cultures for each condition and sampled at pluteus stage

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Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes [Hi-C]

Project description:we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the bat sea star Patiria miniata and the purple sea urchin Strongylocentrotus purpuratus

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Nucleosome positioning and sensitivity suggest novel functional organization of the purple sea urchin (Strongylocentrotus purpuratus) genome

Project description:The eukaryotic nucleosome is the fundamental subunit of chromatin and plays functional roles in DNA templated processes including replication and transcription. In eukaryotic promoters, nucleosome organization is generally thought to be highly structured, with nucleosomes occupying canonical positions flanking the transcription start site (TSS), thereby regulating access of the transcriptional machinery to the underlying DNA. We sought to determine whether this canonical distribution is present in the purple sea urchin, Strongylocentrotus purpuratus, an important developmental model organism. We used titrations of micrococcal nuclease to produce high throughput maps of nucleosome distribution, sensitivity to digestion, and subnucleosomal footprints from female urchin gonad tissue. Unlike yeast, flies, zebrafish, maize, or humans, urchins lack a nucleosome depleted region over TSSs. Urchin promoters are dominated by strongly positioned and highly occupied +1 and +2 nucleosomes which are most prominent in highly expressed genes. Additionally, urchin promoters exhibit distinct patterns of sensitivity to nuclease digestion, with heightened sensitivity upstream of the TSS and limited resistance to nuclease digestion. Discretely positioned sensitive nucleosomes were enriched in promoters of highly expressed genes, suggesting a relationship between nucleosome sensitivity and transcriptional regulation. Moreover, urchin promoters were enriched for small fragment-protected footprints associated with known regulatory motifs. Collectively, we present a comprehensive overview of the unique interplay between nucleosome positioning, chromatin sensitivity, cis-regulatory interactions, and gene expression in sea urchins. Our study not only provides a reproducible methodology applicable to other organisms, but also advances our understanding of functional chromatin organization and gene regulation in urchins.

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