Function and Evolution of DNA Methylation in Nasonia vitripennis

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dc.citation.issue10
dc.citation.volume9
dc.contributor.authorWang JH
dc.contributor.authorWheeler D
dc.contributor.authorAvery A
dc.contributor.authorRago A
dc.contributor.authorChoi J-H
dc.contributor.authorColbourne JK
dc.contributor.authorClark AG
dc.contributor.authorWarren JH
dc.coverage.spatialUnited States
dc.date.available2013
dc.date.available2013-08-27
dc.date.issued2013
dc.description.abstractThe parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5′ regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5′ and 3′ UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression patterns. We speculate that loss of methylation may result in increased developmental specialization in evolution and acquisition of methylation may lead to broader constitutive expression.
dc.description.publication-statusPublished
dc.format.extente1003872 - ?
dc.identifierhttps://www.ncbi.nlm.nih.gov/pubmed/24130511
dc.identifierPGENETICS-D-13-01303
dc.identifier.citationPLoS Genet, 2013, 9 (10), pp. e1003872 - ?
dc.identifier.doi10.1371/journal.pgen.1003872
dc.identifier.eissn1553-7404
dc.identifier.elements-id196650
dc.identifier.harvestedMassey_Dark
dc.identifier.urihttps://hdl.handle.net/10179/7494
dc.languageeng
dc.publisherPublic Library of Science
dc.relation.isPartOfPLoS Genet
dc.subjectAlternative Splicing
dc.subjectAnimals
dc.subjectConserved Sequence
dc.subjectCpG Islands
dc.subjectDNA Methylation
dc.subjectEvolution, Molecular
dc.subjectExons
dc.subjectGenome
dc.subjectHymenoptera
dc.subjectIntrons
dc.subjectPhylogeny
dc.subjectRNA Splicing
dc.subject.anzsrc0604 Genetics
dc.titleFunction and Evolution of DNA Methylation in Nasonia vitripennis
dc.typeJournal article
pubs.notesNot known
pubs.organisational-group/Massey University
pubs.organisational-group/Massey University/College of Sciences
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