Summary Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome‐wide expression of duplicated genes remain largely unknown. Here, we useTragopogon(Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids.The naturally occurring allotetraploidTragopogon miscellusformed in the last 95–100 yr from parental diploidsTragopogon dubiusandT. pratensis. We profiled the DNA methylomes of these three species using whole‐genome bisulfite sequencing.Genome‐wide methylation levels inT. miscelluswere intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized.This study provides the first assessment of both overall and locus‐specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes.
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Maternal upbringing and selective breeding for voluntary exercise behavior modify patterns of DNA methylation and expression of genes in the mouse brain
Abstract Selective breeding has been utilized to study the genetic basis of exercise behavior, but research suggests that epigenetic mechanisms, such as DNA methylation, also contribute to this behavior. In a previous study, we demonstrated that the brains of mice from a genetically selected high runner (HR) line have sex‐specific changes in DNA methylation patterns in genes known to be genomically imprinted compared to those from a non‐selected control (C) line. Through cross‐fostering, we also found that maternal upbringing can modify the DNA methylation patterns of additional genes. Here, we identify an additional set of genes in which DNA methylation patterns and gene expression may be altered by selection for increased wheel‐running activity and maternal upbringing. We performed bisulfite sequencing and gene expression assays of 14 genes in the brain and found alterations in DNA methylation and gene expression forBdnf,Pde4dandGrin2b. Decreases inBdnfmethylation correlated with significant increases inBdnfgene expression in the hippocampus of HR compared to C mice. Cross‐fostering also influenced the DNA methylation patterns forPde4din the cortex andGrin2bin the hippocampus, with associated changes in gene expression. We also found that the DNA methylation patterns forAtrxandOxtrin the cortex andAtrxandBdnfin the hippocampus were further modified by sex. Together with our previous study, these results suggest that DNA methylation and the resulting change in gene expression may interact with early‐life influences to shape adult exercise behavior.
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- Award ID(s):
- 2038528
- PAR ID:
- 10508988
- Publisher / Repository:
- Genes, Brain and Behavior
- Date Published:
- Journal Name:
- Genes, Brain and Behavior
- Volume:
- 22
- Issue:
- 6
- ISSN:
- 1601-1848
- Subject(s) / Keyword(s):
- Bdnf bisulfite sequencing brain cross-fostering cyclic AMP response element-binding protein DNA methylation exercise genetic selection Grin2b Pde4d wheel-running
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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