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CRISPR with Transcriptional Readout reveals influenza transcription is modulated by NELF and can precipitate an interferon response

ABSTRACT: CRISPR with Transcriptional Readout reveals influenza transcription is modulated by NELF and can precipitate an interferon response

PROVIDER: PRJNA1185380 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31321355_1.fastq.gz	Fastqsanger.gz
	SRR31321355_2.fastq.gz	Fastqsanger.gz
	SRR31321356_1.fastq.gz	Fastqsanger.gz
	SRR31321356_2.fastq.gz	Fastqsanger.gz
	SRR31321357_1.fastq.gz	Fastqsanger.gz

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CRISPR with Transcriptional Readout reveals influenza transcription is modulated by NELF and can precipitate an interferon response

Project description:Transcription of interferons upon viral infection is critical for cell-intrinsic innate immunity. This process is influenced by many host and viral factors. To identify host factors that modulate interferon induction within cells infected by influenza A virus, we developed CRISPR with Transcriptional Readout (CRITR-seq). CRITR-seq is a method linking CRISPR guide sequence to activity at a promoter of interest. Employing this method, we find that depletion of the Negative Elongation Factor complex increases both flu transcription and interferon expression. We find that the process of flu transcription, both in the presence and absence of viral replication, is a key contributor to interferon induction. Taken together, our findings highlight innate immune ligand concentration as a limiting factor in triggering an interferon response, identify NELF as an important interface with the flu life cycle, and validate CRITR-seq as a tool for genome-wide screens for phenotypes of gene expression.

2024-11-14 | GSE281730 | GEO

NELF-A phosphorylation site identification

Project description:NELF-A phosphorylation by P-TEFb is a key event in the pausing release. We conduct IMAC-LC-MS-MS to identified NELF-A phosphorylation site by activation P-TEFb kinase.

2016-03-23 | PXD003433 | Pride

NELF-dependent transcription activation

Project description:Jurkat T-cells were latently infected with a defective HIV provirus carrying a GFP reporer gene. The cells were superinfected with a lentiviral vector expressing shRNA to NELF-E. The impact of NELF-depletion on RNAP II distribution on cellular genes and the HIV provirus was measured by ChIP-Seq. Data sets contained between 45 and 56 million mapped reads Four samples were compared: Control shRNA, NELF-E shRNA, Control shRNA plus TNF-a, NELF-E shRNA plus TNF-a.

2014-03-26 | E-GEOD-47481 | biostudies-arrayexpress

Heart tissue from Nelf-b CreER mice

Project description:Negative elongation factor (NELF) is known to enforce promoter-proximal pausing of RNA polymerase II (Pol II), a pervasive phenomenon observed across multicellular genomes. However, the physiological impact of NELF on tissue homeostasis remains unclear. Here we show for the first time that whole-body conditional deletion of the B subunit of NELF (NELF-B) in adult mice results in cardiomyopathy and impaired response to cardiac stress. Tissue-specific knockout of NELF-B confirms its cell-autonomous function in cardiomyocytes. NELF directly supports transcription of those genes encoding rate-limiting enzymes in fatty acid oxidation and the tricarboxylic acid (TCA) cycle. NELF also shares extensively transcriptional target genes with peroxisome proliferator-activated receptors alpha (PPARalpha), a master regulator of energy metabolism in myocardium. Mechanistically, NELF helps stablize the transcription initation complex at the metabolism-related genes. Our findings strongly indicate that NELF is part of the PPARalpha-mediated transcription regulatory network that maintains metabolic homeostasis in cardiomyocytes. 3 Nelf-b f/f and 3 Nelf-b f/f; CreER female mice were injected with Tamoxifen at 8 wk old. Heart tissue were harvested at 20 wks old and used for RNA preparation.

2014-03-01 | E-GEOD-54372 | biostudies-arrayexpress

Novel CRITR-seq approach reveals influenza transcription is modulated by NELF and is a key event precipitating an interferon response.

| S-EPMC11601499 | biostudies-literature

Heart tissue from Nelf-b CreER mice

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Chromatin immunoprecipitation of Drosophila Schneider 2 cells using NELF-E and NELF-B antibodies

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Translation initiation at a non-AUG start codon for mouse and human NELF-B

Project description:Negative elongation factor (NELF), a four-subunit protein complex in metazoan, plays an important role in regulating promoter-proximal pausing of RNA polymerase II (RNAPII). Genetic studies demonstrate that the B subunit of mouse NELF (NELF-B) is critical for embryonic development and homeostasis in adult tissue. We report here that both human and mouse NELF-B proteins are translated from a non-AUG codon upstream of the annotated AUG. This non-AUG codon sequence is conserved in mammalian NELF-B but not NELF-B orthologs of lower metazoan. The full-length and a truncated NELF-B that starts at the first AUG codon interact with the other three NELF subunits with comparable efficiency. Furthermore, these two forms of NELF-B have a similar impact on the transcriptomics and proliferation of mouse embryonic fibroblasts. These results strongly suggest that additional amino acid sequence upstream of the annotated AUG is dispensable for the essential function of NELF in supporting cell growth in vitro. While the majority of mouse adult tissues surveyed exclusively express the full-length NELF-B protein, mouse kidney only contains a truncated NELF-B protein with the same apparent size as the AUG-initiated version. This result raises the distinct possibility that translational initiation of mouse NELF-B is regulated in a tissue-dependent manner. triplicates for ATG-Nelf-B, triplicates for FL-Nelf-B

2014-10-11 | E-GEOD-62248 | biostudies-arrayexpress

NELF-dependent transcription activation

2014-03-26 | GSE47481 | GEO

Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF

Project description:UV-light-induced protein-RNA cross-linking followed by MS analysis was used to identify RNA-binding regions of enhancer RNAs (eRNAs) to the negative elongation factor (NELF) complex, and NELF as part of the paused elongation complex (PEC) of human RNA polymerase II.

2022-03-08 | PXD030569 | Pride

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