DNA methylation is a common feature of eukaryotic genomes and is especially common in noncoding regions of plants. Protein coding regions of plants are often methylated also, but the extent, function, and evolutionary consequences of gene body methylation remain unclear. Here we investigate gene body methylation using an explicit comparative evolutionary approach. We generated bisulfite sequencing data from two tissues of Brachypodium distachyon and compared genic methylation patterns to those of rice (Oryza sativa ssp. japonica). Gene body methylation was strongly conserved between orthologs of the two species and affected a biased subset of long, slowly evolving genes. Because gene body methylation is conserved over evolutionary time, it shapes important features of plant genome evolution, such as the bimodality of G+C content among grass genes. Our results superficially contradict previous observations of high cytosine methylation polymorphism within Arabidopsis thaliana genes, but reanalyses of these data are consistent with conservation of methylation within gene regions. Overall, our results indicate that the methylation level is a long-term property of individual genes and therefore of evolutionary consequence.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays
Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana
Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates
Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression
Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids
Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes
Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach
Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
Gene flow and natural selection shape spatial patterns of genes in tree populations: implications for evolutionary processes and applications
MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild-growing species
Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes
Identification and characterization of paternal-preferentially expressed gene NF-YC8 in maize endosperm
Transposable elements, mRNA expression level and strand-specificity of small RNAs are associated with non-additive inheritance of gene expression in hybrid plants
Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in angiosperms
Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization
Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon
Body-hypomethylated human genes harbor extensive intragenic transcriptional activity and are prone to cancer-associated dysregulation
The Evolutionary Dynamics of Orthologs That Shift in Gene Body Methylation between Arabidopsis Species
Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization
Epigenetic Changes in the Regulation of Nicotiana tabacum Response to Cucumber Mosaic Virus Infection and Symptom Recovery through Single-Base Resolution Methylomes
DNA methylome analysis provides evidence that the expansion of the tea genome is linked to TE bursts
Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?
Epigenetic variation, inheritance, and parent-of-origin effects of cytosine methylation in maize (Zea mays)
Phylogenetic shifts in gene body methylation correlate with gene expression and reflect trait conservation
Identification of DNA methyltransferases and demethylases in Solanum melongena L., and their transcription dynamics during fruit development and after salt and drought stresses
Epigenetic Patterns and Geographical Parthenogenesis in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae).
------Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods.
A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response
The association of changes in DNA methylation with temperature-dependent sex determination in cucumber
Genome-wide comparative analysis of DNA methylation between soybean cytoplasmic male-sterile line NJCMS5A and its maintainer NJCMS5B
Changes in the epigenome and transcriptome of the poplar shoot apical meristem in response to water availability affect preferentially hormone pathways
DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development
Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity
Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L
Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon.
The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth
DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts
Analysis of γ-Tocopherol methyl transferase3 promoter activity and study of methylation patterns of the promoter and its gene body
Genome-Wide DNA Methylation Analysis of Soybean Curled-Cotyledons Mutant and Functional Evaluation of a Homeodomain-Leucine Zipper (HD-Zip) I Gene GmHDZ20.
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Alzheimer's Disease: MS4A
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Genetic Screens in iPSC-derived Brain Cells
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Chronic Fatigue Syndrome
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Pharmacology of Proteinopathies
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Alignment-free Sequence Analysis Tools
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