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Functional conservation of DNA methylation in the pea aphid and the honeybee.

Hunt BG, Brisson JA, Yi SV, Goodisman MA - Genome Biol Evol (2010)

Bottom Line: 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.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 regulation expression.

View Article: PubMed Central - PubMed

Affiliation: School of Biology, Georgia Institute of Technology, GA, USA.

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 regulation expression. Overall, our analyses support a conserved role for DNA methylation in insects with comparable methylation systems.

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Pan-genomic high CpGO/E status is less conserved than low CpGO/E status. Analysis of orthologs in Acyrthosiphon pisum and Apis mellifera show that a higher proportion of (A) low CpGO/E genes are conserved with respect to normalized CpG content than (B) high CpGO/E genes. Each circle represents the number of genes from one species belonging to the designated CpGO/E class; overlap designates the number of orthologs with agreement in CpGO/E classification in both species.
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fig2: Pan-genomic high CpGO/E status is less conserved than low CpGO/E status. Analysis of orthologs in Acyrthosiphon pisum and Apis mellifera show that a higher proportion of (A) low CpGO/E genes are conserved with respect to normalized CpG content than (B) high CpGO/E genes. Each circle represents the number of genes from one species belonging to the designated CpGO/E class; overlap designates the number of orthologs with agreement in CpGO/E classification in both species.

Mentions: To gain insight into the evolutionary maintenance of genes with different levels of methylation, we first investigated whether genes belonging to distinct CpGO/E classes showed differences in their conservation of CpGO/E status over evolutionary time. A total of 2,339 three-way orthologs were identified with nonzero CpGO/E values in A. pisum, Ap. mellifera, and D. melanogaster. By comparing the CpGO/E classification of orthologs in A. pisum and Ap. mellifera from this data, we found that genes with high CpGO/E exhibited considerably less conservation of CpGO/E status than genes with low CpGO/E (fig. 2, table 1; Pearson's Chi-squared test with Yates' continuity correction P = 0.0075). Thus, patterns of dense DNA methylation have been more conserved over evolutionary time than patterns of sparse DNA methylation in A. pisum and Ap. mellifera.


Functional conservation of DNA methylation in the pea aphid and the honeybee.

Hunt BG, Brisson JA, Yi SV, Goodisman MA - Genome Biol Evol (2010)

Pan-genomic high CpGO/E status is less conserved than low CpGO/E status. Analysis of orthologs in Acyrthosiphon pisum and Apis mellifera show that a higher proportion of (A) low CpGO/E genes are conserved with respect to normalized CpG content than (B) high CpGO/E genes. Each circle represents the number of genes from one species belonging to the designated CpGO/E class; overlap designates the number of orthologs with agreement in CpGO/E classification in both species.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2962555&req=5

fig2: Pan-genomic high CpGO/E status is less conserved than low CpGO/E status. Analysis of orthologs in Acyrthosiphon pisum and Apis mellifera show that a higher proportion of (A) low CpGO/E genes are conserved with respect to normalized CpG content than (B) high CpGO/E genes. Each circle represents the number of genes from one species belonging to the designated CpGO/E class; overlap designates the number of orthologs with agreement in CpGO/E classification in both species.
Mentions: To gain insight into the evolutionary maintenance of genes with different levels of methylation, we first investigated whether genes belonging to distinct CpGO/E classes showed differences in their conservation of CpGO/E status over evolutionary time. A total of 2,339 three-way orthologs were identified with nonzero CpGO/E values in A. pisum, Ap. mellifera, and D. melanogaster. By comparing the CpGO/E classification of orthologs in A. pisum and Ap. mellifera from this data, we found that genes with high CpGO/E exhibited considerably less conservation of CpGO/E status than genes with low CpGO/E (fig. 2, table 1; Pearson's Chi-squared test with Yates' continuity correction P = 0.0075). Thus, patterns of dense DNA methylation have been more conserved over evolutionary time than patterns of sparse DNA methylation in A. pisum and Ap. mellifera.

Bottom Line: 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.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 regulation expression.

View Article: PubMed Central - PubMed

Affiliation: School of Biology, Georgia Institute of Technology, GA, USA.

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 regulation expression. Overall, our analyses support a conserved role for DNA methylation in insects with comparable methylation systems.

Show MeSH