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
Citations
More filters
Journal ArticleDOI
Supporting data for characterization of non-coding RNAs associated with the Neuronal growth regulator 1 (NEGR1) adhesion protein.
Prameet Kaur,Jun Rong Tan,Dwi Setyowati Karolina,Sugunavathi Sepramaniam,Arunmozhiarasi Armugam,Tsun-Hon Peter Wong,Kandiah Jeyaseelan,Kandiah Jeyaseelan +7 more
TL;DR: Detailed bioinformatics analysis of genetic signatures at the Negr1 gene locus retrieved from the UCSC genome browser could be adopted to identify putative regulatory non-coding RNAs in other tissues and diseases.
Journal ArticleDOI
MicroRNA Let-7f Mediates Mitochondrial Respiratory Deficit Induced by Repeated Ethanol Exposure and Withdrawal in HT22 Cells
TL;DR: It is suggested that repeated-ethanol/withdrawal provokes the dysregulation of let-7f, thereby damaging brain mitochondria and Mitochondria-associated microRNA may be a potential research and drug target to manage alcoholism.
Posted ContentDOI
Identification of methylation and hydroxymethylation haplotype blocks as distal regulatory elements aids in deconvolution of heterogeneous brain tissues
TL;DR: It is found that MHBs significantly overlapped with hMHBs in gene body regions which further supported that oxidized 5mC to 5hmC co-ordinately in a subset of cells within heterogeneous brain tissues.
Journal ArticleDOI
The Distinct Role of the HDL Receptor SR-BI in Cholesterol Homeostasis of Human Placental Arterial and Venous Endothelial Cells
TL;DR: In this article , the major HDL receptor, scavenger receptor class B type I (SR-BI), contributes to local cholesterol homeostasis in ECA and venous endothelial cells (ECV).
Journal ArticleDOI
Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats.
Laure Denoyelle,Laure Denoyelle,Pierre de Villemereuil,Frédéric Boyer,Meidhi Khelifi,Clément Gaffet,Florian J. Alberto,Badr Benjelloun,Badr Benjelloun,François Pompanon +9 more
TL;DR: In this paper, the authors characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco.
References
More filters
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz,Christopher Benner,Nathanael J. Spann,Eric Bertolino,Yin C. Lin,Peter Laslo,Jason X. Cheng,Cornelis Murre,Harinder Singh,Harinder Singh,Christopher K. Glass +10 more
TL;DR: It is demonstrated in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions.
Journal ArticleDOI
DNA methylation patterns and epigenetic memory
TL;DR: The heritability of methylation states and the secondary nature of the decision to invite or exclude methylation support the idea that DNA methylation is adapted for a specific cellular memory function in development.
Journal ArticleDOI
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon,Siddarth Selvaraj,Siddarth Selvaraj,Feng Yue,Audrey Kim,Yan-Yan Li,Yin-Zhong Shen,Ming Hu,Jun Liu,Bing Ren,Bing Ren +10 more
TL;DR: It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
Related Papers (5)
Human DNA methylomes at base resolution show widespread epigenomic differences
Ryan Lister,Mattia Pelizzola,Robert H. Dowen,R. David Hawkins,Gary C. Hon,Julian Tonti-Filippini,Joseph R. Nery,Leonard Lee,Zhen Ye,Que Minh Ngo,Lee Edsall,Jessica Antosiewicz-Bourget,Jessica Antosiewicz-Bourget,Ron Stewart,Ron Stewart,Victor Ruotti,Victor Ruotti,A. Harvey Millar,James A. Thomson,Bing Ren,Bing Ren,Joseph R. Ecker +21 more