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

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

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

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

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

PAG XXI, 2013 - DNA methylation as a source of epigenetic regulation in the Pacific oysters

<p>Presented at the Aquaculture Workshop at PAG XXI, San Deigo CA 2013.</p> <p>This material is based upon work supported by the National Science Foundation under Grant Number 1158119.</p> <p>Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.</p

Facilitating analysis of genomic variation in Olympia oysters

<p>This dataset includes genomic intervals (BED format) to facilitate RADSeq design and functional annotation of SNPs in Olympia oysters (<em>Ostrea lurida</em>). </p> <p>The files include a transcriptome (FASTA format) and the following 8 genomic interval files (BED format):</p> <p><strong>Oly_snps_bed:</strong> location of SNPs with variant annotated in the name column<br><strong>Oly_geneID_bed:</strong> these intervals cover the entire length of the transcript and are annoated with the SwissProt ID in the name column<br><strong>Oly_regionofblasthits_bed:</strong> these intervals cover only the region of homology between the subject and query for the blastx output<br><strong>Oly_inducible_bed:</strong> these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: <em>cell-cell signaling, signal transduction, cell adhesion, development, stress response</em><br><strong>Oly_housekeeping_bed:</strong> these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: <em>DNA metabolism, RNA metabolism, protein metabolism</em><br><strong>Oly_EcoRIsites_bed:</strong> location of EcoRI restriction sites<br><strong>Oly_NotIsites_bed:</strong> location of NotI restriction sites<br><strong>Oly_SbfI_bed:</strong> location of SbfI restriction sites</p> <p>This dataset was generated as part of the requirements for FISH 546: Bioinformatics for Environmental Science.  The slides for the final presentation are included (FISH546.pdf)</p> <p>The original data for the transcriptome, blastx annotations and SNP tables can be found here:<br>Transcriptome characterization of the Olympia oyster and pinto abalone. Steven Roberts, Emma Timmins-Schiffman. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.156431. Retrieved 18:14, Mar 18, 2013 (GMT)</p> <p> </p

Qualifying Exam

<p>This dataset is the product of my qualifying exams.</p> <p>The questions cover a range of topics including epigenetics and the host pathogen relationship, reproductive biology of oysters, estrogen signalling and understanding effects of various enviromental stresses on shellfish.  </p> <p>This document was prepared over (a nervewracking) 5 days, includes personal opinions, and is unedited - so pardon the typos.</p

Epigenetic considerations in aquaculture

Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture

Crassostrea gigas high-throughput bisulfite sequencing (gill tissue)

<p>This fileset contains genomic feature tracks from methylation-enriched high-throughput bisulfite sequencing and RNA-seq analysis for Pacific oyster (<em>Crassostrea gigas</em>) gill tissue. Feature tracks were developed to be viewed with Integrative Genomics Viewer (http://www.broadinstitute.org/igv/) in conjunction with the <em>C. gigas</em> genome (Fang et al. 2012). All data and instructions are also available at http://oystergen.es/bigill.</p> <p>File descriptions:</p> <p><em>BiGill_CpG_methylation.igv</em> - Location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage.</p> <p><em>BiGill_exon_clc_rpkm.igv</em> - Exon-specific gene expression values (RPKM) from RNA-seq analysis.</p> <p><em>BiGill_igv_charlie.xml</em> - A session file, which loads methylation and RNA-seq feature tracks as well as the location of C.gigas genome features.</p> <p><em>Query to derive_CG_AllData_IGV.txt</em> - Query (SQLShare) used to derive the methylation feature track from the original methratio output (http://goo.gl/5LGq9Q)</p> <p>Reference:</p> <p>Fang X, Li L, Luo R, Xu F, Wang X, Zhu Y, Yang L, Huang Z. 2012. Genomic data from the Pacific oyster (<em>Crassostrea gigas</em>). GigaScience. http://dx.doi.org/10.5524/100030.</p