DHS study in grass
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32944 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3385710.fastq.gz | Fastqsanger.gz | |||
| ERR3385720.fastq.gz | Fastqsanger.gz | |||
| ERR3385730.fastq.gz | Fastqsanger.gz | |||
| ERR3385800.fastq.gz | Fastqsanger.gz | |||
| ERR3385810.fastq.gz | Fastqsanger.gz |
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Project description:Analysis of Dnase Hypersensitive Site (DHS) of P5424 mouse cell line using High-throughput reporter assay
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Project description:Upon fertilization, parental chromatin undergoes extensive reprogramming to generate the highly dynamic chromatin of the inner cell mass (ICM) cells from which an organism is derived. How the chromatin regulatory landscape is established during this process has remained a mystery due to the technical difficulties in chromatin analysis using limited cell numbers. Using a low-input DNase I sequencing (liDNase-seq) method, we generated DNase I-hypersensitive site (DHS) maps of mouse preimplantation embryos. We found that the DHSs are progressively established during development, with Oct4 contributing to a drastic gain of DHSs at the 8-cell stage. In addition, single nucleotide polymorphism analysis revealed that imprinted gene promoters harbor allele-specific DHSs before the onset of allelic gene expression. Furthermore, Nfya is required for 2-cell promoter DHS formation and zygotic genome activation. Thus, our study not only reveals chromatin regulatory landscapes, but also identifies key transcription factors important for DHS establishment in mammalian embryos.
2016-06-03 | GSE76642 | GEO
Project description:Here we performed DNAse-seq experiments on samples of adherent cultures of mouse neural stem cells (NS5 cell line) under normal growth conditions and upon differentiation by expression of an inducible version of the proneural factor Mash1/Ascl1 (Ascl1-ERT2). This resulted in the generation of genome-wide maps of regions of chromatin accessibility in both conditions.
2014-10-02 | E-MTAB-2270 | biostudies-arrayexpress
Project description:The epithelium lining the epididymis has a pivotal role in ensuring a luminal environment that can support normal sperm maturation. Many of the individual genes that encode proteins involved in establishing the epididymal luminal fluid are well characterized. They include ion channels, ion exchangers, transporters and solute carriers. However, the molecular mechanisms that coordinate expression of these genes and modulate their activities in response to biological stimuli are less well understood. To identify cis-regulatory elements for genes expressed in human epididymis epithelial cells we generated genome-wide maps of open chromatin by DNase-seq. This analysis identified 33,542 epididymis-selective DNase I hypersensitive sites (DHS), which were not evident in five cell types of different lineages. Identification of genes with epididymis-selective DHS at their promoters revealed gene pathways that are active in immature epididymis epithelial cells. These include processes correlating with epithelial function and also others with specific roles in the epididymis including retinol metabolism and ascorbate and aldarate metabolism. Peaks of epididymis-selective chromatin were seen in the androgen receptor gene and the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which has a critical role in regulating ion transport across the epididymis epithelium. In silico prediction of transcription factor binding sites that were over-represented in epididymis-selective DHS identified epithelial transcription factors including ELF5 and ELF3, the androgen receptor, Pax2 and Sox9, as components of epididymis transcriptional networks. Active genes, which are targets of each transcription factor, reveal important biological processes in the epididymis epithelium. To identify cis-regulatory elements for genes expressed in human epididymis epithelial cells we generated genome-wide maps of open chromatin by DNase-seq.
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Project description:Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100-500bp. Therefore, we have modified the double-hit method and use short DNA fragments to generate DNA libraries for next generation sequencing. We call this method Short DHS Assay (Short DNAse I Hypersensitive Site assay). The short segments are 100-300bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by the Short DHS assay are consistent with those identified by longer fragments in previous studies.
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Project description:Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The initial step of hypusination, the formation of deoxyhypusine, is catalyzed by deoxyhypusine synthase (DHS), however, the molecular details of the DHS-mediated reaction remained elusive. Recently, patient-derived variants of DHS and eIF5A have been linked to rare neurodevelopmental disorders. Here, we present the cryo-EM structure of the human eIF5A-DHS complex at 2.8Å resolution and a crystal structure of DHS trapped in the key reaction transition state. Furthermore, we show that disease-associated DHS variants influence the complex formation and hypusination efficiency. Hence, our work dissects the molecular details of the deoxyhypusine synthesis reaction and reveals how clinically-relevant mutations affect this crucial cellular process.
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Project description:Deep sequencing of size-selected DNaseI-treated chromatin (DNase-seq) allows high resolution measurement of chromatin accessibility to DNaseI cleavage, permitting identification of de novo active cis regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1 arrest larvae to generate high-resolution maps of TF binding. Over half of embryonic DNaseI hypersensitive sites (DHS) were annotated in noncoding sequences, with 23% in intergenic, 11% promoter regions and 21% in introns, with similar statistics in data collected from L1 arrest larvae. Noncoding DHS exhibit high evolutionary sequence conservation and are enriched in marks of enhancer activity and transcription. We validated noncoding DHS against a previously investigated set of enhancers from myo-2, myo-3, hlh-1, elt-2 and lin-26/lir-1 gene loci and recapitulated 15 of 17 known enhancers in these loci. We then mined the DNase-seq data to identify putative active CRMs and TF footprints. Our DNase-seq data could also be used to improve predictions of tissue-specific expression compared to motifs alone. In a pilot functional test, 10 of 15 DHS from pha-4, icl-1 and ceh-13 drove reporter gene expression in transgenic C. elegans. Overall, we provide experimental annotation of 26,644 putative CRMs in the embryo containing 55,890 TF footprints, and 15,841 putative CRMs in the L1 arrest larvae containing 32,685 TF footprints.
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Project description:Sequencing files provided here are mouse liver DNase-seq to identify DNase hypersensitive sites (DHS) in livers from intact and hypox female, hypox male, and hypox male mice given a single injection of GH and then euthanized 30, 90, or 240 minutes later. This is part of a larger study that includes DNase-seq in mouse liver from intact males determined to be STAT5-high or STAT5-low based on an endogenous pulse of GH/STAT5. This allows us to identify GH pulse-responsive DHS and better understand male-biased DHS regulation of sex-biased genes. Overall, our findings establish that pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is a novel mechanism for establishing widespread sex differences in chromatin accessibility and transcription factor binding, which are closely linked to sex-biased gene expression and the sexual dimorphism of liver function.
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Project description:Mouse liver DNase-seq identification of DNase hypersensitive sites (DHS) in male and female mouse liver for two mouse strains: C57BL/6J and CAST/EiJ.
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