Functional Conservation of DNA Methylation in the Pea Aphid and the Honeybee
Open Access
- 1 January 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Genome Biology and Evolution
- Vol. 2, 719-728
- https://doi.org/10.1093/gbe/evq057
Abstract
DNA methylation is a fundamental epigenetic mark known to have wide-ranging effects on gene regulation in a variety of animal taxa. Comparative genomic analyses can help elucidate the function of DNA methylation by identifying conserved features of methylated genes and other genomic regions. In this study, we used computational approaches to distinguish genes marked by heavy methylation from those marked by little or no methylation in the pea aphid, Acyrthosiphon pisum. We investigated if these two classes had distinct evolutionary histories and functional roles by conducting comparative analysis with the honeybee, Apis (Ap.) mellifera. We found that highly methylated orthologs in A. pisum and Ap. mellifera exhibited greater conservation of methylation status, suggesting that highly methylated genes in ancestral species may remain highly methylated over time. We also found that methylated genes tended to show different rates of evolution than unmethylated genes. In addition, genes targeted by methylation were enriched for particular biological processes that differed from those in relatively unmethylated genes. Finally, methylated genes were preferentially ubiquitously expressed among alternate phenotypes in both species, whereas genes lacking signatures of methylation were preferentially associated with condition-specific gene expression. Overall, our analyses support a conserved role for DNA methylation in insects with comparable methylation systems.Keywords
This publication has 54 references indexed in Scilit:
- Conserved role of intragenic DNA methylation in regulating alternative promotersNature, 2010
- Single base–resolution methylome of the silkworm reveals a sparse epigenomic mapNature Biotechnology, 2010
- DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis melliferaProceedings of the National Academy of Sciences, 2009
- Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence LevelMolecular Biology and Evolution, 2009
- PAML 4: Phylogenetic Analysis by Maximum LikelihoodMolecular Biology and Evolution, 2007
- Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genomeNature Genetics, 2007
- Insights into social insects from the genome of the honeybee Apis melliferaNature, 2006
- PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignmentsNucleic Acids Research, 2006
- A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promotersProceedings of the National Academy of Sciences, 2006
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994