Gene body methylation patterns in Daphnia are associated with gene family size
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA258376 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1552830_1.fastq.gz | Fastqsanger.gz | |||
| SRR1552830_2.fastq.gz | Fastqsanger.gz | |||
| SRR1552831_1.fastq.gz | Fastqsanger.gz | |||
| SRR1552831_2.fastq.gz | Fastqsanger.gz | |||
| SRR1552832_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the characterized gene body methylation patterns in two Daphnia species.
2016-04-04 | GSE60475 | GEO
Project description:The relation between gene body methylation and gene function remains elusive. Yet, our understanding of this relationship can contribute significant knowledge on how and why organisms target specific gene bodies for methylation. Here, we studied gene body methylation patterns in two Daphnia species. We observed both highly methylated genes and genes devoid of methylation in a background of low global methylation levels. A small but highly significant number of genes was highly methylated in both species. Remarkably, functional analyses indicate that variation in methylation within and between Daphnia species is primarily targeted to small gene families whereas large gene families tend to lack variation. The degree of sequence similarity could not explain the observed pattern. Furthermore, a significant negative correlation between gene family size and the degree of methylation suggests that gene body methylation may help regulate gene family expansion and functional diversification of gene families leading to phenotypic variation.
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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
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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: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.
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Project description:Although cyanobacteria produce a wide range of natural toxins that impact aquatic organisms, food webs and water quality, the mechanisms of toxicity are still insufficiently understood. Here, we implemented a whole-genome expression microarray to identify pathways, gene networks and paralogous gene families responsive to Microcystis stress in Daphnia pulex. Therefore, neonates of a sensitive isolate were given a diet contaminated with Microcystis to contrast with those given a control diet for sixteen days. The microarray revealed 2247 differentially expressed (DE) genes (7.6% of the array) in response to Microcystis, of which 17% are lineage specific and 49% are gene duplicates (paralogs). We identified four pathways/gene networks and eight paralogous gene families affected by Microcystis. Differential regulation of the ribosome including 3 paralogous gene families encoding 40S, 60S and mitochondrial ribosomal proteins, suggests an impact of Microcystis on protein synthesis of Daphnia. In addition, differential regulation of the oxidative phosphorylation pathway, including the NADH ubquinone oxidoreductase gene family, and trypsin paralogous gene family, major component of the digestive system in Daphnia, could explain why fitness is reduced based on energy budget considerations. For others (.e.g Neurexin IV), a link with fitness remains to be established. RNA was isolated from three independent and concurrently replicated exposures of Daphnia to control and Microcystis conditions. RNA was hybridized to 4 microarrays using a standard, control vs. treated design that included dye swaps.
2012-07-26 | E-GEOD-36635 | biostudies-arrayexpress
Project description:Although cyanobacteria produce a wide range of natural toxins that impact aquatic organisms, food webs and water quality, the mechanisms of toxicity are still insufficiently understood. Here, we implemented a whole-genome expression microarray to identify pathways, gene networks and paralogous gene families responsive to Microcystis stress in Daphnia pulex. Therefore, neonates of a sensitive isolate were given a diet contaminated with Microcystis to contrast with those given a control diet for sixteen days. The microarray revealed 2247 differentially expressed (DE) genes (7.6% of the array) in response to Microcystis, of which 17% are lineage specific and 49% are gene duplicates (paralogs). We identified four pathways/gene networks and eight paralogous gene families affected by Microcystis. Differential regulation of the ribosome including 3 paralogous gene families encoding 40S, 60S and mitochondrial ribosomal proteins, suggests an impact of Microcystis on protein synthesis of Daphnia. In addition, differential regulation of the oxidative phosphorylation pathway, including the NADH ubquinone oxidoreductase gene family, and trypsin paralogous gene family, major component of the digestive system in Daphnia, could explain why fitness is reduced based on energy budget considerations. For others (.e.g Neurexin IV), a link with fitness remains to be established.
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