Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc

Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves

Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates?

There is a significant amount of variation in DNA methylation characteristics across organisms. Likewise, the biological role of DNA methylation varies across taxonomic lineages. The complexity of DNA methylation patterns in invertebrates has only recently begun to be characterized in-depth. In some invertebrate species that have been examined to date, methylated DNA is found primarily within coding regions and patterning is closely associated with gene function. Here we provide a perspective on the potential role of DNA methylation in these invertebrates with a focus on how limited methylation may contribute to increased phenotypic plasticity in highly fluctuating environments. Specifically, limited methylation could facilitate a variety of transcriptional opportunities including access to alternative transcription start sites, increasing sequence mutations, exon skipping, and transient methylation

DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas)

<p>Abstract</p> <p>Background</p> <p>DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (<it>Crassostrea gigas</it>).</p> <p>Results</p> <p>Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in <it>C. gigas </it>genes and demonstrated that this species possesses intragenic methylation. <it>In silico </it>analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the <it>C. gigas </it>genome, and that specific functional categories of genes have significantly different levels of methylation.</p> <p>Conclusions</p> <p>The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in <it>Crassostrea gigas</it>, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.</p

Stress related epigenetic changes may explain opportunistic success in biological invasions in Antipode mussels

Different environmental factors could induce epigenetic changes, which are likely involved in the biological invasion process. Some of these factors are driven by humans as, for example, the pollution and deliberate or accidental introductions and others are due to natural conditions such as salinity. In this study, we have analysed the relationship between different stress factors: time in the new location, pollution and salinity with the methylation changes that could be involved in the invasive species tolerance to new environments. For this purpose, we have analysed two different mussels’ species, reciprocally introduced in antipode areas: the Mediterranean blue mussel Mytilus galloprovincialis and the New Zealand pygmy mussel Xenostrobus securis, widely recognized invaders outside their native distribution ranges. The demetylathion was higher in more stressed population, supporting the idea of epigenetic is involved in plasticity process. These results can open a new management protocols, using the epigenetic signals as potential pollution monitoring tool. We could use these epigenetic marks to recognise the invasive status in a population and determine potential biopollutants

Cross-Species Analysis of Genic GC(3) Content and DNA Methylation Patterns

The GC content in the third codon position (GC3) exhibits a unimodal distribution in many plant and animal genomes. Interestingly, grasses and homeotherm vertebrates exhibit a unique bimodal distribution. High GC3 was previously found to be associated with variable expression, higher frequency of upstream TATA boxes, and an increase of GC3 from 5′ to 3′. Moreover, GC3-rich genes are predominant in certain gene classes and are enriched in CpG dinucleotides that are potential targets for methylation. Based on the GC3 bimodal distribution we hypothesize that GC3 has a regulatory role involving methylation and gene expression. To test that hypothesis, we selected diverse taxa (rice, thale cress, bee, and human) that varied in the modality of their GC3 distribution and tested the association between GC3, DNA methylation, and gene expression. We examine the relationship between cytosine methylation levels and GC3, gene expression, genome signature, gene length, and other gene compositional features. We find a strong negative correlation (Pearson’s correlation coefficient r = −0.67, P value < 0.0001) between GC3 and genic CpG methylation. The comparison between 5′-3′ gradients of CG3-skew and genic methylation for the taxa in the study suggests interplay between gene-body methylation and transcription-coupled cytosine deamination effect. Compositional features are correlated with methylation levels of genes in rice, thale cress, human, bee, and fruit fly (which acts as an unmethylated control). These patterns allow us to generate evolutionary hypotheses about the relationships between GC3 and methylation and how these affect expression patterns. Specifically, we propose that the opposite effects of methylation and compositional gradients along coding regions of GC3-poor and GC3-rich genes are the products of several competing processes

A molecular framework to identify novel modes of action of endocrine disrupting compounds in shellfish

Concern over human and wildlife health has brought increased attention to a group of emerging environmental contaminants referred to as endocrine disrupting compounds (EDCs). While progress has been made in describing the effects of these compounds, there are still gaps in our understanding of alternative modes of action and physiological effects outside of the reproductive axis, particularly in invertebrates. One way that EDCs may elicit these changes is through disruptions to normal epigenetic mechanisms. Epigenetics refers to heritable processes that alter gene activity without manipulating the underlying DNA sequence. Epigenetic marks, such as DNA methylation, are important regulators of gene expression in both plants and animals. This research aims to characterize alternative modes of action of endocrine disrupting compounds by utilizing molecular tools to examine epigenetic and physiological changes in Pacific oysters (Crassostrea gigas) exposed to the synthetic estrogen, 17α-ethinyl estradiol (EE2). In this experiment, juvenile oysters were exposed to EE2 during gonad maturation. Sex-ratio and size were evaluated after two months of exposure. Results of this exposure include a trend toward more females in the EE2 exposed. In addition, the EE2 exposed females were significantly larger than unexposed females. To investigate the molecular underpinnings of this phenotype, DNA methylation profiles of control and EE2 exposed females were directly compared using a DNA tiling microarray (MBD-ChIP) in order to test the hypothesis that invertebrate DNA methylation patterns will be altered upon exposure to EDCs. This analysis revealed a suite of genes that were differentially methylated in response to EE2. Functional annotations of these genes indicate that a number of biological pathways outside of the reproductive axis are being affected by exposure to EE2

Epigenetic DNA Methylation Mediating Octopus vulgaris Early Development: Effect of Essential Fatty Acids Enriched Diet

The common octopus, Octopus vulgaris, is a good candidate for aquaculture but a sustainable production is still unviable due to an almost total mortality during the paralarvae stage. DNA methylation regulates gene expression in the eukaryotic genome, and has been shown to exhibit plasticity throughout O. vulgaris life cycle, changing profiles from paralarvae to adult stages. This pattern of methylation could be sensitive to small alterations in nutritional and environmental conditions during the species early development, thus impacting on its health, growth and survival. In this sense, a full understanding of the epigenetic mechanisms operating during O. vulgaris development would contribute to optimizing the culture conditions for this species. Paralarvae of O. vulgaris were cultured over 28 days post-hatching (dph) using two different Artemia sp. based diets: control and a long chain polyunsaturated fatty acids (LC-PUFA) enriched diet. The effect of the diets on the paralarvae DNA global methylation was analyzed by Methyl-Sensitive Amplification Polymorphism (MSAP) and global 5-methylcytosine enzyme-linked immunosorbent assay (ELISA) approaches. The analysis of different methylation states over the time revealed a global demethylation phenomena occurring along O. vulgaris early development being directly driven by the age of the paralarvae. A gradual decline in methylated loci (hemimethylated, internal cytosine methylated, and hypermethylated) parallel to a progressive gain in non-methylated (NMT) loci toward the later sampling points was verified regardless of the diet provided and demonstrate a pre-established and well-defined demethylation program during its early development, involving a 20% of the MSAP loci. In addition, a differential behavior between diets was also observed at 20 dph, with a LC-PUFA supplementation effect over the methylation profiles. The present results show significant differences on the paralarvae methylation profiles during its development and a diet effect on these changes. It is characterized by a process of demethylation of the genome at the paralarvae stage and the influence of diet to favor this methylation loss.En prens

Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high‐quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole‐genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome‐wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance

Epigenomic and transcriptomic regulation of environmental responses in the Pacific oyster, Crassostrea gigas

Thesis (Ph.D.)--University of Washington, 2014Intertidal invertebrates such as bivalve molluscs live in constantly changing and frequently stressful environments and must be equipped to both detect and quickly respond to environmental changes. Our understanding of the molecular and cellular response systems in these organisms are an important part of species conservation and well as our ability to predict their response and limits to environmental stress. This dissertation explores environmental responses in oysters using transcriptomic and epigenomic approaches. The first chapter examines the transcriptomic responses of oysters from two locations with varying anthropogenic input using ultra short high-throughput sequencing reads. The work presented in Chapter 2 provides the first evidence that DNA methylation is present in the genome of a bivalve mollusc and suggests a regulatory role in these species. Chapter 3 provides the first whole methylome analysis of a locotrophozoan and identifies relationships between DNA methylation and gene expression. Finally, Chapter 4 presents a review of the current DNA methylation data available for bivalves and proposes new hypotheses for how DNA methylation may be regulating the genome in oysters. By combining transcriptional and epigenetic datasets, this work provides the most complete picture of epigenomic regulation for any molluscan species and paves the way into future investigations of the role of epigenetics in environmental regulation and local adaptation and evolution in marine invertebrates