Gene body methylation patterns in Daphnia are associated with gene family size
Ontology highlight
ABSTRACT:
ORGANISM(S): Daphnia pulex Daphnia magna
PROVIDER: GSE60475 | GEO | 2016/04/04
SECONDARY ACCESSION(S): PRJNA258376
REPOSITORIES: GEO
Similar Datasets
Project description:Gene body methylation patterns in Daphnia are associated with gene family size
| PRJNA258376 | ENA
Project description: Not available
| S-EPMC4860698 | biostudies-literature
Project description:To profile the Daphnia species methylome and to achieve a better understanding of the level of variations in the methylome of Daphnia species, we performed whole genome bisulfite sequencing (WGBSeq) of adult Daphnia magna Bham2 strain and Daphnia pulex Eloise Butler strain (EB45 and EB31 strains). We also analysed the correlation between gene expression and methylation in the two species, using data generated in this study and RNA-seq data from Orsini, et al. 2016. We found that methylation percentage across the genome of Daphnia spp. follows a bimodal distribution. Furthermore, CpG methylation in Daphnia predominantly occurs at coding regions. Although methylation levels significantly decrease towards the 3’ end of a gene with a significant drop in methylation levels from one exon to the neighbouring intron, there is a clear spike in relative methylation levels between exon and intron boundaries, which may be linked to regulation of splicing. We further demonstrate that DNA methylation in Daphnia is responsive to intrinsic and extrinsic factors. We also compared the methylation and gene expression correlations found in Daphnia to publicly available dataset from two other invertebrate species (Apis mellifera and Nasonia vitripennis) and two vertebrate species (Homo sapiens and Mus musculus). We observed that similar to other invertebrates, Daphnia’s genome is sparsely methylated at a lower level and the methylation is predominantly focused at gene body while in vertebrate species the genome is heavily methylated (global methylation). Although the level and distribution of methylation across CpG sites is different between vertebrates and invertebrates it is possible that methylation density at coding regions has the same function between vertebrates and invertebrates. We demonstrate evolutionary conservation of a positive correlation between high methylation density at coding regions and gene expression across vertebrates and invertebrates, leading to potentially ensuring continuous high expression of genes required throughout the life in both vertebrates and invertebrates.
2018-12-11 | GSE103939 | GEO
Project description:Daphnia (Daphnia pulex) is a small planktonic crustacean and a key constituent of aquatic ecosystems. It is commonly used as a model organism for studying environmental toxic challenges. In the past decade, a Daphnia genomic information and proteomic dataset has been developed. This dataset has expanded the opportunity to relate toxicological effects with “Daphnia proteomics” as it integrates proteomic knowledge in Daphnia, those approach will provide greater insights for toxicological research. In order to exploit Daphnia for ecotoxicological research, information on the post-translational modification (PTM) of proteins is necessary as this is a critical regulator of biological processes. Acetylation of lysine (Kac) is a reversible and highly regulated PTM that is associated with diverse biological functions. However, a comprehensive description of Kac in Daphnia is not yet available. Here, to understand the cellular distribution of lysine acetylation in Daphnia, we identified 98 acetylation sites in 65 proteins by immunoprecipitation using an anti-acetyllysine antibody and an liquid chromatography system supported by mass spectroscopy. We identified 28 acetylated sites connected with metabolic proteins and 6 acetylated enzymes associated with the TCA cycle in Daphnia. From GO and KEGG enrichment analyses, we showed that Kac in D. pulex is highly enriched in proteins associated with metabolic processes. Our data provide the first global analysis of lysine acetylation in D. pulex. The expanded proteomic dataset will be an important resource for the functional analysis of Kac in D. pulex and it will be nice to have a first step done using a promising future model organism.
2016-01-05 | PXD002441 | Pride
Project description:Examination the DNA methylation statues of the main subpopulation of Chinese Mongolian sheep. A high quality methylome of Chinese Mongolian sheep was obtained, and established a list of DMRs potentially association with sheep body size
2016-09-28 | GSE62345 | GEO
Project description:Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes, but remains poorly understood. The A. thaliana strain Cvi has depleted methylation in gene bodies relative to the common reference strains Col and Ler. This naturally occurring hypomethylated strain offers the opportunity to improve understanding of the function and heritablity of genic CG methylation. We bisulfite-sequenced 10 recombinant inbred lines derived from a cross between Col and Cvi, as well as both parent lines, and examined the transmission of the different Col- and Cvi-derived gene body methylation states in these lines. We found that the majority of CG methylation polymorphisms were faithfully transmitted over nine generations according to the parental genotype in the RILs, with only 1-4% of CGs failing to maintain the parental methylation state. We found no evidence to suggest that these differences in gene body methylation led to changes in gene expression. However, we found that sites that fail to maintain the parental methylation state are nonrandom and are associated with intermediate levels of CG methylation and high methylation variability across many A. thaliana strains. These results provide new insights into the features determining the inheritance of gene body methylation and demonstrate that two different methylation equilibria can be maintained within single individuals.
2017-03-29 | GSE93968 | GEO
Project description:Purpose: To justify whether sex is strictly binary or variable along a spectrum, exhaustive investigation into intersexuality is necessary. In this study, by mutating the sex determining locus Doublesex1, we generated two Daphnia magna strains from which two different forms of feminized males could be obtained. mRNA sequencing of these intersex males was carried out to explore the transcritomic shift responsible for the changes in sexual phenotype. Methods: Two Doublesex1 mutants, namely Line A and Line B, were generated by microinection of designed TALENs into Daphnia magna eggs. Line A males showed severe, while Line B males showed minor bodywide feminization. Whole body mRNA profiles of 40 hour post oviposition embryos were generated for wildtype female, Line A male, Line B male and wildtype male using Illumina sequencing (mRNA sequencing service provided by Novogene). Data analysis was done using CLC Genomics Workbench software. Results: Among 731 sex-biased genes identified in this dataset, more than half (449 genes) showed non-binary expression profile in which their expression in the mutant males was at an intermediate level between wildtype female and wildtype male. Conclusions: Downstream genes of Doublesex1 cascade may fluctuate in activity and give rise to a spectrum of sexual phenotypes in Daphnia magna.
2020-05-20 | GSE150820 | GEO
Project description:In the past years, the research focus on the effects of microplastics (MP) on aquatic organisms extended from marine systems towards freshwater systems. An important freshwater model organism in the MP field is the cladoceran Daphnia, which plays a central role in lacustrine ecosystems and has been established as a test organism in ecotoxicology. To investigate the effects of MP on Daphnia magna, we performed a chronic exposure experiment with polystyrene MP under strictly standardized conditions. Chronic exposure of D. magna to PS microparticles led to a significant reduction in body length and number of offspring. To shed light on underlying molecular mechanisms induced by microplastic ingestion in D. magna, we assessed the effects of PS-MP at the proteomic level.
2021-07-07 | PXD025108 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE29854: Daphnia magna exposed to narcotics and polar narcotics - aniline GSE29856: Daphnia magna exposed to narcotics and polar narcotics - 4-chloroaniline GSE29857: Daphnia magna exposed to narcotics and polar narcotics - 3,5-dichloroaniline GSE29858: Daphnia magna exposed to narcotics and polar narcotics - 2,3,4-trichloroaniline GSE29862: Daphnia magna exposed to narcotics and polar narcotics - ethanol GSE29864: Daphnia magna exposed to narcotics and polar narcotics - isopropanol GSE29867: Daphnia magna exposed to narcotics and polar narcotics - methanol Refer to individual Series
2012-02-01 | E-GEOD-29993 | biostudies-arrayexpress
Project description: Not available
| S-EPMC5589248 | biostudies-literature