Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.
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ABSTRACT:
SUBMITTER: Schmitz RJ
PROVIDER: S-EPMC3787263 | biostudies-literature | 2013 Oct
REPOSITORIES: biostudies-literature
Publications
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.
Schmitz Robert J RJ He Yupeng Y Valdés-López Oswaldo O Khan Saad M SM Joshi Trupti T Urich Mark A MA Nery Joseph R JR Diers Brian B Xu Dong D Stacey Gary G Ecker Joseph R JR
Genome research 20130605 10
Cytosine DNA methylation is one avenue for passing information through cell divisions. Here, we present epigenomic analyses of soybean recombinant inbred lines (RILs) and their parents. Identification of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 ...[more]
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Project description:Epigenetic regulation of gene expression has been shown to change over time and may be associated with environmental exposures in common complex traits. Age-related hearing impairment is a complex disorder, known to be heritable, with heritability estimates of 57-70%. Epigenetic regulation might explain the observed difference in age of onset and magnitude of hearing impairment with age. Epigenetic epidemiology studies using unrelated samples can be limited in their ability to detect small effects, and recent epigenetic findings in twins underscore the power of this well matched study design. We investigated the association between venous blood DNA methylation epigenome-wide and hearing ability. Pure-tone audiometry (PTA) and Illumina HumanMethylation array data were obtained from female twin volunteers enrolled in the TwinsUK register. Two study groups were explored: first, an epigenome-wide association scan (EWAS) was performed in a discovery sample (n=115 subjects, age range: 47-83 years, Illumina 27 k array), then replication of the top ten associated probes from the discovery EWAS was attempted in a second unrelated sample (n=203, age range: 41-86 years, Illumina 450 k array). Finally, a set of monozygotic (MZ) twin pairs (n = 21 pairs) within the discovery sample (Illumina 27 k array) was investigated in more detail in an MZ discordance analysis. Hearing ability was strongly associated with DNA methylation levels in the promoter regions of several genes, including TCF25 (cg01161216, p = 6.6 × 10(-6)), FGFR1 (cg15791248, p = 5.7 × 10(-5) and POLE (cg18877514, p= 6.3 × 10(-5)). Replication of these results in a second sample confirmed the presence of differential methylation at TCF25 (p(replication)=6 × 10(-5)) and POLE (p(replication)?=0.016). In the MZ discordance analysis, twins' intrapair difference in hearing ability correlated with DNA methylation differences at ACP6 (cg01377755, r=?-0.75, p=1.2 × 10(-4)) and MEF2D (cg08156349, r=?-0.75, p=1.4 × 10(-4)). Examination of gene expression in skin, suggests an influence of differential methylation on expression, which may account for the variation in hearing ability with age.
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Project description:The epigenomics approaches presented here provide the first comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations paving the way for understanding how methylation variants contribute to phenotypic variation.
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