Protect-seq: Genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin
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ABSTRACT:
PROVIDER: PRJNA559362 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9931530_1.fastq.gz | Fastqsanger.gz | |||
| SRR9931530_2.fastq.gz | Fastqsanger.gz | |||
| SRR9931540.fastq.gz | Fastqsanger.gz | |||
| SRR9931550_1.fastq.gz | Fastqsanger.gz | |||
| SRR9931550_2.fastq.gz | Fastqsanger.gz |
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Project description:In metazoan cell nuclei, heterochromatin constitutes large chromatin domains that are in close contact with the nuclear lamina. These heterochromatin/lamina-associated domains (LADs) domains are difficult to profile and warrants a simpler and direct method. Here we report a new method, Protect-seq, aimed at identifying regions of heterochromatin via resistance to nuclease degradation followed by next-generation sequencing (NGS). We performed Protect-seq on the human colon cancer cell line HCT-116 and observed overlap with previously curated LADs. We provide evidence that these protected regions are enriched for and can distinguish between the repressive histone modification H3K9me3, H3K9me2 and H3K27me3. Moreover, in human cells the loss of H3K9me3 leads to an increase in chromatin accessibility and loss of Protect-seq signal. For further validation, we performed Protect-seq in the fibrosarcoma cell line HT1080 and found a similar correlation with previously curated LADs and repressive histone modifications. In sum, Protect-seq is an efficient technique that allows rapid identification of nuclease resistant chromatin, which correlate with heterochromatin and radial positioning.
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Project description:Metazoan chromosomes in interphase nucleus are partitioned into discrete three dimensional physical domains which confine epigenetically modified chromatin and are relative stable across different cell types even species1-4. Physical domains are segregated preferentially at DNase I hypersensitive sequences of high density of active gene and insulator proteins which are hypothesized contributing together to domain border formation3,4. However, whether physical domain structure can be maintained without insulator proteins and transcription is unknown5-8. Transcription of most genes and the insulator proteins binding can be severely impaired in heat shocked (HS) fruit fly nuclei9. Here we show that chromatin contact frequency increases within and decreases beyond ~100kb after HS respectively accompanied by repartitioning of the Drosophila chromosomes into a different array of physical domain. Prominently, domains tend to merge because borders disappeared are more than borders newly emerged which are located more frequently in repressive chromatin. In contrast to previous hypothesis1,3,4, changes in insulator proteins enrichment and RNAPII show no noticeable difference at lost or emerged borders. Our results show a metazoan genome can be quickly reconfigured as cells undergo brief physiological stress. In addition to insulator proteins and transcription, we speculate that extra trans-factors binding and various biological activities are required for the establishment and maintenance of physical domains. Moreover, we found long-range chromatin interaction network is reshaped after HS implying long-range chromatin interactions can be formed due to domain level reorganization of chromosomes despite functional relevance. We anticipate our analysis to be a starting point for more intensive experimental investigation into the elusive mechanisms behind the physical domain partition and dynamic reconfiguration of metazoan genomes.
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Project description:Activation of the innate immune system via pattern recognition receptors (PRRs) is key to generate lasting adaptive immunity. PRRs detect unique chemical patterns associated with invading microorganism, but if and how the physical properties of PRR ligands influence development of the immune response remains unknown. Through the study of fungal mannans we show that the physical form of PRR ligands dictates the immune response. Soluble mannans are immunosilent in the periphery but elicit a potent pro-inflammatory response in the draining lymph node (dLN). By modulating the physical form of mannans, we developed a formulation that targets both the periphery and dLN. When combined with viral glycoprotein antigens, this mannan formulation broadens epitope recognition, elicits potent antigen-specific neutralizing antibodies, and confers protection against viral infections of the lung. Thus, the physical properties of microbial ligands determine the outcome of the immune response and can be harnessed for vaccine development.
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Project description:The purpose of the research is to assess the impact of Protect Your Colon, a colorectal cancer (CRC) screening decision aid, on patients’ CRC screening behaviors. The Investigators hypothesize that Protect Your Colon, through optimizing shared decision making, will lead to selection of a test that accurately matches patients’ values and increase CRC screening uptake. To test this hypothesis, the investigators will conduct a pilot randomized controlled trial (RCT) to assess if provision of Protect Your Colon improves communication on CRC screening, intent to complete screening, and ultimately uptake of screening vs. usual care.
| 65332 | ecrin-mdr-crc
Project description:Background: Regulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes has described accessible chromatin regions, but little work has been done in filamentous fungi. Results: Here we present a genome-scale characterization of accessible chromatin regions in Neurospora crassa, which revealed characteristic molecular features of accessible and inaccessible chromatin. We present experimental evidence of inaccessibility within heterochromatin regions in Neurospora, and we examine features of both accessible and inaccessible chromatin, including the presence of histone modifications, types of transcription, transcription factor binding, and relative nucleosome turnover rates. Chromatin accessibility is not strictly correlated with expression level. Accessible chromatin regions in the model filamentous fungus Neurospora are characterized the presence of H3K27 acetylation and commonly associated with pervasive non-coding transcription. Conversely, methylation of H3 lysine-36 catalyzed by ASH1 is correlated with inaccessible chromatin within promoter regions. Conclusions: In N. crassa, H3K27 acetylation is the most predictive histone modification for open chromatin. Conversely, our data show that H3K36 methylation is a key marker of inaccessible chromatin in gene-rich regions of the genome. Our data are consistent with an expanded role for H3K36 methylation in intergenic regions of filamentous fungi compared to the model yeasts, S. cerevisiae and S. pombe, which lack homologs of the ASH1 methyltransferase. of accessible chromatin in Neurospora
2020-11-12 | GSE154497 | GEO
Project description:We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80mM or 150mM NaCl after digestion contain predominantly mononucleosomes and represent calssical 'active' chromatin. Profiles of these low-salt-soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of RNA polymerase II. Nearly quantitative recovery of chromatin is obtained with 600mM NaCl, however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics. Keywords: Chromatin affinity-purification on microarray For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf All experiments were done using two channels per chip, comparing DNAs extracted from either salt-extracted or insoluble chromatin to whole nuclear chromatin, whole nuclear chromatin to randomly fragmented genomic DNA, streptavidin-bound biotin-tagged histone-variant-containing chromatin to salt-extracted chromatin, gel-purified mononucleosomes to whole EDTA-extracted soluble chromatin, streptavidin-bound biotin-tagged histone-variant-containing chromatin to whole EDTA-extracted soluble chromatin, or oligo(dT)-primed cDNA to randomly fragmented genomic DNA from S2 cell nuclei.
2008-12-11 | E-GEOD-13217 | biostudies-arrayexpress
Project description:We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80mM or 150mM NaCl after digestion contain predominantly mononucleosomes and represent calssical 'active' chromatin. Profiles of these low-salt-soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of RNA polymerase II. Nearly quantitative recovery of chromatin is obtained with 600mM NaCl, however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics. Keywords: Chromatin affinity-purification on microarray For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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