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Integrative analysis of 111 reference human epigenomes
TLDR
It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Expand
Chromatin architecture reorganization during stem cell differentiation
TLDR
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. Expand
Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution.
TLDR
Genome-wide analysis of two key histone modifications indicated that iPS cells are highly similar to ES cells, and data show that transcription factor-induced reprogramming leads to the global reversion of the somatic epigenome into an ES-like state. Expand
Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures.
TLDR
Genome-wide data and high-resolution array profiling demonstrated that there is no common specific subkaryotypic alteration that is required for reprograming and that reprogramming does not lead to genomic instability, and suggest that iPSCs should be considered a unique subtype of pluripotent cell. Expand
Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells
TLDR
It is found that promoters that are active in early developmental stages tend to be CG rich and mainly engage H3K27me3 upon silencing in nonexpressing lineages, while promoters for genes expressed preferentially at later stages are often CG poor and primarily employ DNA methylation upon repression. Expand
Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes
TLDR
Genome-wide analysis of postnatal NSCs indicates that Dnmt3a occupies and methylates intergenic regions and gene bodies flanking proximal promoters of a large cohort of transcriptionally permissive genes, many of which encode regulators of neurogenesis and may be used for maintaining active chromatin states of genes critical for development. Expand
The landscape of accessible chromatin in mammalian preimplantation embryos
TLDR
A genome-wide map of accessible chromatin in mouse preimplantation embryos is reported using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion, which reveals a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Expand
Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
TLDR
A panoramic view of the landscape of H3K4me3, a histone hallmark for transcription initiation, from developing gametes to post-implantation embryos is provided by developing a highly sensitive approach, STAR ChIP–seq, to unveil inheritance and highly dynamic reprogramming of the epigenome in early mammalian development. Expand
Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome
TLDR
A base-resolution, allele-specific DNA methylation map in the mouse genome is generated, finding parent-of-origin dependent (imprinted) ASM at 1,952 CG dinucleotides and a surprising presence of non-CG methylation in the adult mouse brain, with some showing evidence of imprinting. Expand
Allelic reprogramming of 3D chromatin architecture during early mammalian development
TLDR
The data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development, as characterized by slow consolidation of TADs and segregation of chromatin compartments in preimplantation development. Expand
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