ArticleBMC genomics2013
Phylogenetic and DNA methylation analysis reveal novel regions of variable methylation in the mouse IAP class of transposons.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates.Genome research · 2023Article
- Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates.bioRxiv : the preprint server for biology · 2023Article
- Roles of transposable elements in the regulation of mammalian transcription.Nature reviews. Molecular cell biology · 2022Review
- Article
- The role of environmental exposures and the epigenome in health and disease.Environmental and molecular mutagenesis · 2020Review
- Perinatal exposures to phthalates and phthalate mixtures result in sex-specific effects on body weight, organ weights and intracisternal A-particle (IAP) DNA methylation in weanling mice.Journal of developmental origins of health and disease · 2019Article
- The developmental-genetics of canalization.Seminars in cell & developmental biology · 2019Review
- Mild inborn errors of metabolism in commonly used inbred mouse strains.Molecular genetics and metabolism · 2019Article
- Article
- Article
- Sexually Dimorphic Effects of Early-Life Exposures to Endocrine Disruptors: Sex-Specific Epigenetic Reprogramming as a Potential Mechanism.Current environmental health reports · 2017Review
- Perinatal lead (Pb) exposure results in sex and tissue-dependent adult DNA methylation alterations in murine IAP transposons.Environmental and molecular mutagenesis · 2017Article
- Environmentally induced epigenetic toxicity: potential public health concerns.Critical reviews in toxicology · 2016Review
- Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A.Epigenetics · 2016Article
- Prenatal maternal immune activation causes epigenetic differences in adolescent mouse brain.Translational psychiatry · 2014Article
- Longitudinal epigenetic drift in mice perinatally exposed to lead.Epigenetics · 2014Article
- The use of epigenetic phenomena for the improvement of sheep and cattle.Frontiers in genetics · 2014Review
- Early-life lead exposure results in dose- and sex-specific effects on weight and epigenetic gene regulation in weanling mice.Epigenomics · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundSelect retrotransposons in the long terminal repeat (LTR) class exhibit interindividual variation in DNA methylation that is altered by developmental environmental exposures. Yet, neither the full extent of variability at these "metastable epialleles," nor the phylogenetic relationship underlying variable elements is well understood. The murine metastable epialleles, Avy and CabpIAP, result from independent insertions of an intracisternal A particle (IAP) mobile element, and exhibit remarkably similar sequence identity (98.5%).
resultsUtilizing the C57BL/6 genome we identified 10802 IAP LTRs overall and a subset of 1388 in a family that includes Avy and CabpIAP. Phylogenetic analysis revealed two duplication and divergence events subdividing this family into three clades. To characterize interindividual variation across clades, liver DNA from 17 isogenic mice was subjected to combined bisulfite and restriction analysis (CoBRA) for 21 separate LTR transposons (7 per clade). The lowest and highest mean methylation values were 59% and 88% respectively, while methylation levels at individual LTRs varied widely, ranging from 9% to 34%. The clade with the most conserved elements had significantly higher mean methylation across LTRs than either of the two diverged clades (p = 0.040 and p = 0.017). Within each mouse, average methylation across all LTRs was not significantly different (71%-74%, p > 0.99).
conclusionsCombined phylogenetic and DNA methylation analysis allows for the identification of novel regions of variable methylation. This approach increases the number of known metastable epialleles in the mouse, which can serve as biomarkers for environmental modifications to the epigenome.
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