DNA hydroxymethylation profiling of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using hMeDIP-seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Branchiostoma lanceolatum Danio rerio Strongylocentrotus purpuratus
PROVIDER: GSE188332 | GEO | 2021/11/08
REPOSITORIES: GEO
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Project description:DNA hydroxymethylation profiling of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using hMeDIP-seq
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Project description:Fasting has been shown to increase longevity and alter immune function in a variety of animals, but little is understood about how reduced caloric intake may impact regeneration and infections in animals that must regularly repair and regenerate tissue in marine environments that contain high levels of bacteria. We examined the possibility that fasting could enhance spine regeneration and reduce bacteremia in the purple sea urchin Strongylocentrotus purpuratus. A small number of spines were removed from urchins and rates of spine regrowth and levels of culturable bacteria from the coelomic fluid were measured for 21 days in fed and fasted urchins. Fasted urchins had higher rates of spine regrowth and lower levels of colony-forming units (CFU) per milliliter of coeolomic fluid. The predominant bacteria in the coelomic fluid was isolated and identified by DNA sequence-based methods as Vibrio cyclitrophicus. After 21 days, fasted and fed urchins were injected with V. cyclitrophicus. Two hours after injection, fed urchins had about 25% more culturable bacteria remaining in their coelomic fluid compared to fasted urchins. We found no evidence that fasting altered coelomic fluid cell number or righting response, indicators of physiologic and behavioral stress in urchins. Our results demonstrate that V. cyclitrophicus is present in purple urchin coelomic fluid, that fasting can increase spine regeneration and that fasted urchins have much lower levels of culturable bacteria in their coelomic fluid than fed urchins. Overall, our data suggests that fasting may ultimately reduce bacteremia and infection in injured or damaged urchins.
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Project description:Flexible resource investment is a risk sensitive reproductive strategy where individuals trade resources spent on reproduction for basic metabolic maintenance and survival. This study examined morphological variation in herbivorous sea urchin grazers across a mosaic landscape of macroalgae dominated habitats interspersed with patches of sea urchin barrens to determine whether sea urchins shift energy allocation in response to food limitation. Extensive underwater surveys of habitat attributes (e.g., sea urchin density, algae cover) were paired with detailed laboratory assays (e.g., sea urchin dissections) to determine how resource abundance affects energy allocation between reproductive capacity and body structure in the purple sea urchin, Strongylocentrotus purpuratus. We found that: (1) sea urchins had a more elongate jaw structure relative to body size in habitats void of macroalgae (i.e., barrens), (2) sea urchin reproductive capacity (i.e., gonad index) was lower in barrens and the barrens habitat was primarily comprised of encrusting algae, and (3) sea urchin jaw morphology (i.e., lantern index) and reproductive capacity (i.e., gonad index) were inversely related. These results suggest that sea urchins respond to macroalgae limited environments by shifting energy allocation between reproductive capacity and modifications of the foraging apparatus, which may explain the ability of sea urchins to acquire food in resource-limited environments.
| S-EPMC8086578 | biostudies-literature
Project description:We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
| S-EPMC3159423 | biostudies-literature
Project description:Codon usage bias has been documented in a wide diversity of species, but the relative contributions of mutational bias and various forms of natural selection remain unclear. Here, we describe for the first time genome-wide patterns of codon bias at 4623 genes in the purple sea urchin, Strongylocentrotus purpuratus. Preferred codons were identified at 18 amino acids that exclusively used G or C at third positions, which contrasted with the strong AT bias of the genome (overall GC content is 36.9%). The GC content of third positions and coding regions exhibited significant correlations with the magnitude of codon bias. In contrast, the GC content of introns and flanking regions was indistinguishable from the genome-wide background, which suggested a limited contribution of mutational bias to synonymous codon usage. Five distinct clusters of genes were identified that had significantly different synonymous codon usage patterns. A significant correlation was observed between codon bias and mRNA expression supporting translational selection, but this relationship was driven by only one highly biased cluster that represented only 8.6% of all genes. In all five clusters preferred codons were evolutionarily conserved to a similar degree despite differences in their synonymous codon usage distributions and magnitude of codon bias. The third positions of preferred codons in two codon usage groups also paired significantly more often in stems than in loops of mRNA secondary structure predictions, which suggested that codon bias might also affect mRNA stability. Our results suggest that mutational bias has played a minor role in determining codon bias in S. purpuratus and that preferred codon usage may be heterogeneous across different genes and subject to different forms of natural selection.
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Project description:BackgroundRecent analysis of immune-related genes within the sea urchin genome revealed a number of large gene families with vertebrate homologues, such as the Toll-like and NOD/NALP-like receptor families and C-type lectins in addition to a rudimentary complement system. Therefore, the immune response of the purple sea urchin appears to be more complex than previously believed. Another component of the sea urchin immune response is an unusual family of mRNAs, known as 185/333, which is strongly upregulated in response to pathogen challenge. The work presented here indicates that this family of transcripts is derived from an unexpectedly diverse gene family.ResultsThe 185/333 genes are small (< 2 kb) with only two exons. Their extraordinary diversity was exemplified by 121 unique sequences identified from 171 cloned genes. Sequences from the second exons were aligned optimally by introducing large gaps, which defined blocks of sequence known as elements. Genes were defined by the presence or absence of elements. Phylogenetic analysis defined five intron types which, when combined with the exon element patterns resulted in 31 gene patterns, 14 of which were not described previously. Sequence diversity was present in all elements, and was higher in the intron than the exons. Repeats within the sequence facilitated multiple alignments, of which two were analyzed in detail. Although the two alignments differed in length, number of elements, and number of patterns, both were about equally accurate at describing the 185/333 sequences. The genes were closely linked and flanked by short repeats. The repeats within and between the genes may promote their diversification through gene conversion, recombination, and meiotic mispairing.ConclusionThe diversity of the 185/333 gene family represents an intriguing addition to what is known about the S. purpuratus immune response, and provides further evidence that invertebrate immune systems are neither simple nor static.
| S-EPMC1988830 | biostudies-literature
Project description:Development depends on the precise control of gene expression in time and space. A critical step towards understanding the global gene regulatory networks underlying development is to obtain comprehensive information on gene expression. In this study, we measured expression profiles for the entire expressed gene set during sea urchin embryonic development. We confirmed the reliability of these profiles by comparison with NanoString measurements for a subset of genes and with literature values. The data show that ~16,500 genes have been activated by the end of embryogenesis, and for half of them the transcript abundance changes more than 10-fold during development. From this genome scale expression survey, we show that complex patterns of expression by many genes underlie embryonic development, particularly during the early stages before gastrulation. An intuitive web application for data query and visualization is presented to facilitate use of this large dataset.
| S-EPMC3898891 | biostudies-literature
Project description:BackgroundThe organic matrix of biominerals plays an important role in biomineral formation and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin, which is an important model organism for developmental biology and biomineralization, only few matrix components have been identified and characterized at the protein level. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of possible matrix proteins at the gene level, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy, proteomic analysis.ResultsWe identified 110 proteins as components of sea urchin test and spine organic matrix. Fourty of these proteins occurred in both compartments while others were unique to their respective compartment. More than 95% of the proteins were detected in sea urchin skeletal matrices for the first time. The most abundant protein in both matrices was the previously characterized spicule matrix protein SM50, but at least eight other members of this group, many of them only known as conceptual translation products previously, were identified by mass spectrometric sequence analysis of peptides derived from in vitro matrix degradation. The matrices also contained proteins implicated in biomineralization processes previously by inhibition studies using antibodies or specific enzyme inhibitors, such as matrix metalloproteases and members of the mesenchyme-specific MSP130 family. Other components were carbonic anhydrase, collagens, echinonectin, a alpha2-macroglobulin-like protein and several proteins containing scavenger receptor cysteine-rich domains. A few possible signal transduction pathway components, such as GTP-binding proteins, a semaphorin and a possible tyrosine kinase were also identified.ConclusionThis report presents the most comprehensive list of sea urchin skeletal matrix proteins available at present. The complex mixture of proteins identified in matrices of the sea urchin skeleton may reflect many different aspects of the mineralization process. Because LC-MS/MS-based methods directly measures peptides our results validate many predicted genes and confirm the existence of the corresponding proteins. Considering the many newly identified matrix proteins, this proteomic study may serve as a road map for the further exploration of biomineralization processes in an important model organism.
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