Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide mapping of open chromatin in mouse embryonic stem cell

ABSTRACT: Micrococcal nuclease was used to digest mESC nuclei under a mild digestion condition to release the relatively open chromatin, and under an extensive digestion condition to release the genome chromatin. By comparing the genome distribution of mono-nucleasome under these two conditions, open chromatin regions were detected. One mild digestion and one extensive digestion was applied to the mESC cells, followed by sequencing.

ORGANISM(S): Mus musculus

SUBMITTER: Xia Li

PROVIDER: E-GEOD-50706 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin.

Chen Ping P Zhao Jicheng J Wang Yan Y Wang Min M Long Haizhen H Liang Dan D Huang Li L Wen Zengqi Z Li Wei W Li Xia X Feng Hongli H Zhao Haiyong H Zhu Ping P Li Ming M Wang Qian-fei QF Li Guohong G

Genes & development 20130924 19

The histone variants H3.3 and H2A.Z have recently emerged as two of the most important features in transcriptional regulation, the molecular mechanism of which still remains poorly understood. In this study, we investigated the regulation of H3.3 and H2A.Z on chromatin dynamics during transcriptional activation. Our in vitro biophysical and biochemical investigation showed that H2A.Z promoted chromatin compaction and repressed transcriptional activity. Surprisingly, with only four to five amino ...[more]

PMID: 24065740

Similar Datasets

Genome-wide mapping of open chromatin in mouse embryonic stem cell

Project description:Micrococcal nuclease was used to digest mESC nuclei under a mild digestion condition to release the relatively open chromatin, and under an extensive digestion condition to release the genome chromatin. By comparing the genome distribution of mono-nucleasome under these two conditions, open chromatin regions were detected.

2013-10-01 | GSE50706 | GEO

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (CLIP)

Project description:Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365 nm UV light. We found small differences in the accuracy of these methods in identifying binding sites of HuR, a protein that binds low-complexity sequences and Argonaute 2, which has a complex binding specificity. We show that crosslink-induced mutations lead to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect sufficiently their sites under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific ribonucleases strongly biases the set of recovered binding sites. We finally show that this bias can be substantially reduced by milder nuclease digestion conditions. We performed duplicate experiments for each variant of the CLIP protocol (CLIP, PAR-CLIP), each protein (HuR, Ago2), and enzymatic digestion (complete T1 digestion, mild MNase digestion). In addition, we performed a single PAR-CLIP experiment with mild T1 digestion.

2011-05-15 | E-GEOD-28859 | biostudies-arrayexpress

The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells

Project description:The RNA polymerase II (RNAPII) associated factor 1 complex (Paf1C) plays critical roles in modulating the release of paused RNAPII into productive elongation. However, regulation of Paf1C-mediated promoter-proximal pausing is complex and context dependent. In fact, in cancer cell lines opposing models of Paf1Cs’ role in RNAPII pause-release control have been proposed. Here we show that the Paf1C positively regulates RNAPII pause-release at both protein-coding genes and at enhancers in mouse embryonic stem cells (mESC). Our analyses reveal extensive Paf1C binding at mESC enhancers, in particular at super enhancers. Importantly, Paf1C occupancy correlates with the strength of enhancer activity. Depletion of Paf1C attenuates the expression of genes regulated by targeted enhancers and affects RNAPII Ser2 phosphorylation at the binding sites, suggesting that mESC self-renewal depends on Paf1C-mediated positive regulation of pluripotency enhancers.

2020-12-25 | GSE149999 | GEO

The landscape of accessible chromatin in mammalian pre-implantation embryos (RNA-Seq)

Project description:In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. RNA-seq was performed in these embryos at various stages in preimplantation development.

2016-06-15 | E-GEOD-66582 | biostudies-arrayexpress

FIREWACh: High-throughput Functional Detection of Transcriptional Regulatory Modules in Mammalian Cells

Project description:We report a new method called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), a high-throughput functional assay for directly identifying active promoter and enhancer elements. FIREWACh simultaneously assessed over 80,000 DNA fragments derived from M-bM-^@M-^\nucleosome-free regionsM-bM-^@M-^] within embryonic stem cell (ESC) chromatin to identify 6,364 new active regulatory elements. Many FIREWACh DNAs represent newly discovered ESC-specific enhancers and their analyses identified enriched binding site motifs for ESC transcription factors including SOX2, POU5f1 (OCT4), and KLF4. Thus FIREWACh identifies endogenous regulators of gene expression and can be used for the discovery of key cell-specific transcription factors. The application of FIREWACh to additional cultured cell types will facilitate functional annotation of the genome and expand our view of transcriptional network dynamics. Nucleosome free DNA (i.e. "open chromatin") is isolated enzymatically from cross-linked nuclei of cells (e.g. mouse embryonic stem cells, mESC) and cloned upstream of a minimal promoter driving GFP within a lentivral reporter construct. Virus is made from a pooled library of these plasmids, and used to transfect the target cell (mESC). GFP positive cells contain active NFRs and can be sorted by FACS. The loci of the NFR is determined using high throughput sequencing and mapping.

2014-03-22 | E-GEOD-54863 | biostudies-arrayexpress

The landscape of accessible chromatin in mammalian pre-implantation embryos (ChIP -Seq)

Project description:In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Mouse 2-cell embryos were obtained from crosses of C57BL/6N x PWK for ChIP-seq samples.

2016-06-15 | E-GEOD-79935 | biostudies-arrayexpress

The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq)

Project description:In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. ATAC-seq was performed in these embryos at various stages in preimplantation development.

2016-06-15 | E-GEOD-66581 | biostudies-arrayexpress

ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs

Project description:Here, we report a new strategy that combines in situ nuclear proximity ligation and transposase digestion, called ChIATAC, for highly efficient mapping of chromatin interactions between open chromatin loci simultaneously from lower input cells.

2022-12-23 | GSE194036 | GEO

Effects of MBD3 depletion on nucleosome occupancy in MCF-7 cells

Project description:We and others have identified that MBD3/NuRD localizes at active promoters and enhancers, suggesting an active role of NuRD at open chromatin region. Because NuRD includes nucleosome remodelers, CHD3 and CHD4, we hypothesized that NuRD regulates nucleosome organization at open chromatin region. To test this idea, we performed micrococcal nuclease digestion followed by massively parallel sequencing (MNase-seq) in MBD3 knockdowned MCF-7 cells. We observed the decrease of nucleosome occupancy at promoters and enhancers in MBD3 knockdowned cells. Our results suggest a regulatory role of MBD3/NuRD at open chromatin region. Mapped nucleosome positioning in control (shLuc) and MBD3 knockdowned MCF-7 cells, in duplicate.

2013-10-31 | E-GEOD-51097 | biostudies-arrayexpress

In vivo nucleosome occupancy in yeast (MNase-seq)

Project description:Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. Regulatory DNA elements are made accessible by nucleosome-depeleted states. Thus, nucleosome remodelling and modification should be intimately coupled with open chromatin formation and regulation. However, our knowledge of nucleosome regulation is largely limited to promoter regions, which comprise only a subset of all regulatory loci in the genome. In order to examine nucleosome patterns in open chromatin regions, we performed micrococcal nuclease (MNase) sequencing for a laboratory strain of yeast. Nucleosome occupancy profiled by Micrococcal nuclease (MNase) digestion

2013-01-06 | E-GEOD-34923 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data