Ontology highlight
ABSTRACT:
PROVIDER: PRJNA505679 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8206030_1.fastq.gz | Fastqsanger.gz | |||
| SRR8206030_2.fastq.gz | Fastqsanger.gz | |||
| SRR8206040_1.fastq.gz | Fastqsanger.gz | |||
| SRR8206040_2.fastq.gz | Fastqsanger.gz | |||
| SRR8206050_1.fastq.gz | Fastqsanger.gz |
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Project description:We describe how the cancer-causing Epstein-Barr virus (EBV), a prototypic herpesvirus, alters proteome at viral replication forks prominently identifies chromatin modifying and transcriptional repression proteins. Specifically, to transition from transcription, the viral DNA polymerase processivity factor EA-D is SUMOylated by the transcriptional corepressor KAP1-TRIM28. KAP1 function is triggered by phosphorylation via the PI3K-related kinase ATM and the helicase RECQ5 at the transcription machinery. SUMO-EA-D recruits the histone loader CAF1 and the methyltransferase SETDB1 to silence the parental genome, prioritizing replication. Thus, DNA repair, epigenetic, and transcription-replication interference pathways orchestrate the handover from transcription to replication, a fundamental feature of DNA viruses
2023-02-27 | MSV000091375 | MassIVE
Project description:RNA polymerase (RNAP) is the key transcription machinery and its interaction with genomic DNA orchestrates gene expression in response to environmental cues. Dynamic interaction and localization between RNAP and nucleoid were observed before and after osmotic stress. Chromatin immunoprecipitation (ChIP) of RNAP β’ subunit together with chromatin profiling by ChIP-on-chip analysis demonstrated the dynamics of genome-wide RNAP-DNA interactions during osmotic stress.
2018-04-11 | GSE110831 | GEO
Project description:Human cells identify invading pathogens and activate immune signaling pathways through a wide array of pattern recognition receptors, such as DNA sensors. The interferon-inducible protein 16 (IFI16) is a nuclear DNA sensor that recognizes double-stranded DNA from a number of viral sources, including genomes of nuclear-replicating viruses such as the prevalent human pathogen, herpes simplex virus 1 (HSV-1). Upon binding to the DNA genome of HSV-1, IFI16 both induces antiviral cytokine expression and suppresses virus gene expression. Here, we use a multi-omics approach of DNA sequencing techniques paired with targeted mass spectrometry to obtain an extensive view of the interaction between IFI16 and the HSV-1 genome, and how this binding affects the viral DNA structure and protein expression. Through ChIP-seq, we find that IFI16 binds to the HSV-1 genome in a sequence-independent manner while simultaneously exhibiting broad enrichment at two loci: UL30, the viral DNA polymerase gene, and US1-US7. ATAC-seq analysis reveals that these two regions are among the most accessible stretches of DNA on the genome, thereby facilitating IFI16 binding. Accessibility of the entire HSV-1 genome is elevated upon IFI16-KO, indicating that expression of IFI16 globally induces chromatinization of viral DNA, regardless of IFI16 enrichment. Deletion of IFI16 also results in a global increase in the expression of HSV-1 proteins, as measured by parallel reaction monitoring-mass spectrometry. Altogether, we demonstrate that IFI16 interacts with the HSV-1 genome in a sequence-independent manner, and this interaction coordinates epigenetic silencing of the viral genome, resulting in decreased protein expression and virus replication.
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Project description:We report the application of high throughput sequencing technology for investigating the transcriptional regulatory network of the human innate immune response. With ChIP-seq, we generated genome-wide virus-activated transcription factor and transcription machinery maps of infected and uninfected human Namalwa B cells. Analysis of ChIP-seq data reveals extensive collaboration of IRF3 and NF-κB with Mediator throughout the human genome, and implicates additional transcription factor partners in antiviral responses. Moreover, analysis of Pol II occupancy and elongation status during virus infection indicates that IRF3 and NF-κB drive both de novo polymerase recruitment and mediate polymerase pause-release at their target sites, stimulating the expression of a variety of protein-coding, non-coding, and unannotated loci. Examination of 6 different proteins before and after virus infection in 1 cell type.
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Project description:Background: The intracellular pathogen Mycobacterium tuberculosis is known to encounter several stress conditions during infection, including low pH, hypoxia, starvation and oxidative and nitrosative stress. Mycobacterial adaptation to stress conditions is, in part, mediated by several nucleic acid-associated proteins. In this study, we sought to establish an affinity purification-mass spectrometry (AP-MS) approach that would enable the collective identification of nucleic acid-associated proteins in mycobacteria. We hypothesized that targeting the RNA polymerase complex through affinity purification would allow for the identification of RNA- and DNA-associated proteins that not only maintain the bacterial chromosome but also enable transcription and translation. Results: AP-MS analysis of the RNA polymerase β-subunit cross-linked to nucleic acids identified 275 putative nucleic acid-associated proteins in the model organism Mycobacterium smegmatis under standard culturing conditions. The AP-MS approach successfully identified proteins that are known to make up the RNA polymerase complex, as well as several other known RNA polymerase complex-associated proteins such as a DNA polymerase, sigma factors, transcriptional regulators, and helicases. Gene ontology enrichment analysis of the identified proteins revealed that this approach selected for proteins with GO terms associated with nucleic acids and cellular metabolism. Importantly, we identified several proteins of unknown function not previously known to be associated with nucleic acids. Validation of several candidate nucleic acid-associated proteins demonstrated for the first time DNA association of ectopically expressed MSMEG_1060, MSMEG_2695 and MSMEG_4306 through affinity purification. Conclusions: Effective identification of nucleic acid-associated proteins, which make up the RNA polymerase complex as well as other DNA- and RNA-associated proteins, was facilitated by affinity purification of the RNA polymerase β-subunit in M. smegmatis. The successful identification of several transcriptional regulators suggest that our approach could be sensitive enough to investigate the nucleic acid-associated proteins that maintain cellular functions and mediate transcriptional and translational change in response to environmental stress.
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2020-07-30 | MSV000085857 | MassIVE
Project description:Primary outcome(s): Development of Gene - Environmental interaction risk score methodology and Gene - Environmental Risk Score (GERS) of colorectal cancer;Development of high risk criteria that could be applied final GERS prediction model
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