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Article
Interplay between chromatin marks in development and disease
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have important roles in transcriptional regulation. Although many reports have characterized the functions of such chromatin marks in...
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Protocol
Profiling Histone Methylation in Low Numbers of Cells
Chromatin immunoprecipitation (ChIP) enables the study of DNA–protein interactions. When coupled with high-throughput sequencing (ChIP-seq), this method allows the generation of genome-wide profiles of the dis...
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Article
Open AccessRepression of germline genes by PRC1.6 and SETDB1 in the early embryo precedes DNA methylation-mediated silencing
Silencing of a subset of germline genes is dependent upon DNA methylation (DNAme) post-implantation. However, these genes are generally hypomethylated in the blastocyst, implicating alternative repressive path...
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Article
NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing
De novo DNA methylation (DNAme) in mammalian germ cells is dependent on DNMT3A and DNMT3L. However, oocytes and spermatozoa show distinct patterns of DNAme. In mouse oocytes, de novo DNAme requires the lysine ...
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Article
Setting the chromatin stage in oocytes
Post-translational histone modifications are important regulators of nuclear reprogramming. A study now reveals that histone lysine demethylase KDM4A-mediated H3K9me3 demethylation in mammalian oocytes is esse...
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Article
Open AccessEvolution of imprinting via lineage-specific insertion of retroviral promoters
Imprinted genes are expressed from a single parental allele, with the other allele often silenced by DNA methylation (DNAme) established in the germline. While species-specific imprinted orthologues have been ...
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Article
Open AccessZFP57 regulation of transposable elements and gene expression within and beyond imprinted domains
KRAB zinc finger proteins (KZFPs) represent one of the largest families of DNA-binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retr...
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Article
SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development
The oocyte epigenome plays critical roles in mammalian gametogenesis and embryogenesis. Yet, how it is established remains elusive. Here, we report that histone-lysine N-methyltransferase SETD2, an H3K36me3 methy...
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Article
Open AccessLTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation
De novo DNA methylation (DNAme) during mouse oogenesis occurs within transcribed regions enriched for H3K36me3. As many oocyte transcripts originate in long terminal repeats (LTRs), which are heterogeneous eve...
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Article
Open AccessDevelopment and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)
Allele-specific transcriptional regulation, including of imprinted genes, is essential for normal mammalian development. While the regulatory regions controlling imprinted genes are associated with DNA methyla...
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Article
On the role of H3.3 in retroviral silencing
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Article
Epigenetic modifier drugs trigger widespread transcription of endogenous retroviruses
A study in this issue demonstrates that epigenome-modifying drugs used in cancer chemotherapy induce transcription from thousands of previously unannotated transcription start sites, most of which are derived ...
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Article
Open AccessVisRseq: R-based visual framework for analysis of sequencing data
Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computa...
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Article
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
Combined chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) has enabled genome-wide epigenetic profiling of numerous cell lines and tissue types. A major limitation of ChIP-seq, however, i...
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Article
Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
An extensive analysis of HERVH (a primate-specific endogenous retrovirus) expression in human pluripotent stem cells is presented, identifying a sub-population of cells within cultured human embryonic stem cel...
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Article
Correction: Corrigendum: Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
Nature 464, 927–931 (2010); doi:10.1038/nature08858 In Fig. 1a of this Letter, it has come to our attention that the lanes for the Dnmt3l+/+ and Dnmt3l−/− testes RNA samples were run on different gels (norther...
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Article
Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells
Vitamin C is a direct regulator of Tet enzyme activity and DNA methylation fidelity in mouse ES cells; addition of vitamin C promotes Tet activity, increases 5-hydroxymethlycytosine (5hmC) and DNA demethylatio...
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Article
Open AccessDistinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells
In mouse embryonic stem cells (mESCs), transcriptional silencing of numerous class I and II endogenous retroviruses (ERVs), including IAP, ETn and MMERVK10C, is dependent upon the H3K9 methyltransferase (KMTas...
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Article
Open AccessH3K9me3-binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral silencing
Endogenous retroviruses (ERVs) are parasitic sequences whose derepression is associated with cancer and genomic instability. Many ERV families are silenced in mouse embryonic stem cells (mESCs) via SETDB1-depo...
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Article
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
Endogenous retroviruses are widely dispersed in mammalian genomes, and are silenced in somatic cells by DNA methylation. Here, an endogenous retroviruses silencing pathway independent of DNA methylation is sho...
