Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
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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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Function and information content of DNA methylation
TL;DR: These observations indicate that the underlying DNA sequence largely accounts for local patterns of methylation, which is highly informative when studying gene regulation in normal and diseased cells, and it can potentially function as a biomarker.
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TL;DR: Mapping genome-wide chromatin interactions in human embryonic stem cells and four human ES-cell-derived lineages reveals extensive chromatin reorganization during lineage specification, providing a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.
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The diverse roles of DNA methylation in mammalian development and disease
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Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
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TL;DR: In this article, a single-cell bisulfite sequencing (scBS-seq) method was used to accurately measure DNA methylation at up to 48.4% of CpG sites.
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Impact of cytosine methylation on DNA binding specificities of human transcription factors.
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TL;DR: This work systematically analyzed binding specificities of full-length transcription factors and extended DNA binding domains to unmethylated and CpG-methylated DNA by using methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment).
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