Project description:We report the proteomic characterization of gonads from wild P. lividus collected along coastal Sardinia, and describe the changes occurring in gonads according to sex and developmental stage. Gonads in the recovery, pre-mature, mature, and spent stages were analyzed using a shotgun proteomics approach based on filter-aided sample preparation followed by tandem mass spectrometry and label-free differential analysis. A detailed characterization of the proteome changes occurring in gonads of both sexes along maturation was achieved. Significant changes were seen in numerous proteins involved in nutrient accumulation and in gamete biology and maturation. Adding to an improved understanding of the P. lividus reproductive cycle in its natural environment, the results described in this work form the basis for defining novel protein markers and procedures for an easier sexing and staging, and for monitoring sea urchin gonad maturation in aquaculture plants.

2016-06-09 | PXD004200 | Pride

eeSphGran1

Project description:Sphaerechinus granularis, genomic assembly, eeSphGran1, alternate haplotype.

| PRJEB122436 | ENA

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.

2025-05-05 | GSE283453 | GEO

Project description:intestines and gonad of sea urchin transcriptome

| PRJNA603436 | ENA