Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
TLDR
By mapping base-resolution methylomes in adult mouse tissues at shallow coverage, this work identifies 302,864 tissue-specific differentially methylated regions (tsDMRs) and estimates that >6.7% of the mouse genome is variably methylated, and suggests that epigenetic memory of embryonic development may be retained in adult tissues.Abstract:
Mammalian development requires cytosine methylation, a heritable epigenetic mark of cellular memory believed to maintain a cell's unique gene expression pattern. However, it remains unclear how dynamic DNA methylation relates to cell type-specific gene expression and animal development. Here, by mapping base-resolution methylomes in 17 adult mouse tissues at shallow coverage, we identify 302,864 tissue-specific differentially methylated regions (tsDMRs) and estimate that >6.7% of the mouse genome is variably methylated. Supporting a prominent role for DNA methylation in gene regulation, most tsDMRs occur at distal cis-regulatory elements. Unexpectedly, some tsDMRs mark enhancers that are dormant in adult tissues but active in embryonic development. These 'vestigial' enhancers are hypomethylated and lack active histone modifications in adult tissues but nevertheless exhibit activity during embryonic development. Our results provide new insights into the role of DNA methylation at tissue-specific enhancers and suggest that epigenetic memory of embryonic development may be retained in adult tissues.read more
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Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns
Yang Zhou,Shuli Liu,Shuli Liu,Yan Hu,Lingzhao Fang,Yahui Gao,Han Xia,Steven G. Schroeder,Benjamin D. Rosen,Erin E. Connor,Congjun Li,Ransom L. Baldwin,John B. Cole,Curtis P. Van Tassell,Liguo Yang,Li Ma,George E. Liu +16 more
TL;DR: This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.
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Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues
Jingyao Zeng,Shoucheng Liu,Yuhui Zhao,Xinyu Tan,Hasan Awad Aljohi,Wanfei Liu,Wanfei Liu,Songnian Hu +7 more
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An epigenetic signature for within-generational plasticity of a reef fish to ocean warming
Taewoo Ryu,Taewoo Ryu,Heather D. Veilleux,Heather D. Veilleux,Philip L. Munday,Imgook Jung,Jennifer M. Donelson,Timothy Ravasi +7 more
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Detection of differentially methylated regions in whole genome bisulfite sequencing data using local Getis-Ord statistics
TL;DR: This work uses beta-binomial regression to model the whole-genome bisulfite sequencing data and provides statistical inference for direct DMR detection, and demonstrates that GetisDMR achieves better sensitivities, positive predictive values, more exact locations and better agreement of DMRs with current biological knowledge.
Journal ArticleDOI
Polycomb in Transcriptional Phase Transition of Developmental Genes
TL;DR: The mechanisms of transition between transcriptional status of developmental regulators are summarized, including complex processes for enhancer activation and promoter-enhancer association, and testable models in which Polycomb group factors contribute to promoter- enhancer associations and thus proper gene expression are proposed.
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