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Genome-wide maps of chromatin state during the differentiation of hESC into hNECs

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE76084 | GEO | 2017/06/23

SECONDARY ACCESSION(S): PRJNA306169

REPOSITORIES: GEO

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Genome-wide maps of chromatin state during the differentiation of hESC into hNECs (MNase-Seq)

Project description:To study the epigenetic regulation during neuroectoderm specification process, we generated in-depth maps of nucleosome and histone modifications.We found that the depletion of nucleosome marked with H2A.Z in promoter regions contributes to the activation of key neuroectoderm related genes as providing open chromatin state for Pol II binding. Meanwhile, HMs undergo active remodeling with recruiting key transcription factors.So our study provided a full view on the transcriptional regulation of epigenome during neuroectoderm specification.

2017-06-23 | GSE76083 | GEO

Genome-wide maps of chromatin state during the differentiation of hESC into hNECs (ChIP-Seq)

2017-06-23 | GSE76082 | GEO

Genome-wide maps of chromatin state during the differentiation of hESC into hNECs

Project description:Genome-wide maps of chromatin state during the differentiation of hESC into hNECs

| PRJNA306169 | ENA

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

| S-EPMC2921165 | biostudies-literature

Genome-wide maps of chromatin state in renin cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-10-31 | GSE117725 | GEO

Genome-wide maps of chromatin state in HCT116 colorectal cancer cell

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-01-04 | GSE179545 | GEO

Genome-wide maps of chromatin state in human primary CAR-T cells

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2022-09-02 | GSE174282 | GEO

Transcriptomic data and Genome-wide maps of chromatin state in prostate cancer

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-08-01 | GSE131830 | GEO

Genome-wide maps of chromatin state in NCCIT cells

Project description:H2B mono-ubiquitylation is required for multiple methylations of both H3K4 and H3K79 and has been implicated in gene expression from yeast to human. However, molecular crosstalk between H2BUb1 and other modifications, especially H3K4 and H3K79 methylations, remains unclear in vertebrates. To understand the functional role of H2BUb1, genome-wide histone modification patterns were measured in human cells. This study proposes dual roles of H2BUb1 that are both H3 methylation dependent and independent. First, H2BUb1 is a 5'-enriched active transcription mark and is co-occupied with H3K79 methylations in actively transcribed regions. Importantly, this study found a unique role of H2BUb1 in chromatin architecture independent of histone H3 methylations. H2BUb1 is well positioned in exon-intron boundaries of highly expressed exons and is specifically enriched in 5'-biased exons. Furthermore, H2BUb1 demonstrates increased occupancy in skipped exons compared to flanking exons for the human and mouse genome. Our findings suggest that a potentiating mechanism links H2BUb1 to both H3K79 methylations in actively transcribed regions and the exon-intron structure of highly expressed exons through the regulation of nucleosome dynamics during transcription elongation. We generated high-throughput sequencing (ChIP-seq) data for genome-wide occupancy of H2BUb1, nucleosome, H3K4me3, H3K36me3, H379me1/2/3, H3Ac, and mRNA in human embryonic carcinoma cells. We performed ChIP-seq for seven different histone modifications, MNase-seq, mRNA-seq (two replications), and inputDNA-seq in NCCIT cell lines (human embryonic carcinoma cell lines). We also performed mRNA-seq for RNF20-siRNA transfected NCCIT cells, where H2BUb1 signals decreased.

2012-03-07 | E-GEOD-25882 | biostudies-arrayexpress

Genome-wide maps of chromatin state in rice endosperm

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone H3 trimethylation in rice endosperm. By obtaining about four hundred million bases of sequence from rice chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of rice endosperm. We find that the presence of H3K27me3 in either upstream or downstream of a gene is predominately associated with repression of the gene, while its absence is mainly associated with high gene expression. Examination of Histone H3 lysine 27 trimethylation in rice endosperm.

2011-12-06 | E-GEOD-27048 | biostudies-arrayexpress

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