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Ribosome profiling of A549 cells depleted of RPLP1 and RPLP2 and infected with DENV.

ABSTRACT: Ribosome profiling of A549 cells depleted of RPLP1 and RPLP2 and infected with DENV.

PROVIDER: PRJNA549955 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9332880.fastq.gz	Fastqsanger.gz
	SRR9332881.fastq.gz	Fastqsanger.gz
	SRR9332882.fastq.gz	Fastqsanger.gz
	SRR9332883.fastq.gz	Fastqsanger.gz
	SRR9332884.fastq.gz	Fastqsanger.gz

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Ribosome profiling of A549 cells depleted of RPLP1 and RPLP2 and infected with DENV.

Project description:We used ribosome profiling to evaluate viral and cellular translation in RPLP1/2-depleted cells. This revealed that ribosomes pause in the sequence coding for the N-terminus of the envelope protein, immediately downstream of sequences encoding two adjacent transmembrane domains (TMDs). RPLP1/2 function to enhance ribosome elongation at this position and increase viral protein stability, possibly by improving co-translational folding of DENV proteins. We also analyzed the effects of RPLP1/2 depletion on cellular translation. We find that RPLP1/2 moderately affects ribosome density for a small subset of cellular mRNAs. However, meta-analysis of ribosome positions on all cellular mRNAs revealed slightly increased accumulation of ribosomes downstream of start codons in RPLP1/2-depleted cells, suggesting that RPLP1/2 enhance elongation efficiency. Importantly, we found that ribosome density on mRNAs encoding multiple TMDs was disproportionately affected by RPLP1/2 knockdown, suggesting a role for RPLP1/2 in transmembrane protein biogenesis. Together, our findings reveal insights into the function of RPLP1/2 in DENV and cellular translation.

2019-06-21 | GSE133111 | GEO

scRNAseq analysis of DENV-2 infected B cells

Project description:Dengue virus (DENV) is the causative agent of dengue, a mosquito-borne disease that represents a significant and growing public health burden around the world. A unique pathophysiological feature of dengue is immune-mediated enhancement, wherein preexisting immunity elicited by a primary infection can enhance the severity of a subsequent infection by a heterologous DENV serotype. A leading mechanistic explanation for this phenomenon is antibody dependent enhancement (ADE), where sub-neutralizing concentrations of DENV-specific IgG antibodies facilitate entry of DENV into FcR expressing cells such as monocytes, macrophages, and dendritic cells. Accordingly, this model posits that phagocytic mononuclear cells are the primary reservoir of DENV. However, analysis of samples from individuals experiencing acute DENV infection reveals that B cells are the largest reservoir of infected circulating cells, representing a disconnect in our understanding of immune-mediated DENV tropism. In this study, we demonstrate that the expression of a DENV-specific B cell receptor (BCR) renders cells highly susceptible to DENV infection, with the infection-enhancing activity of the membrane-restricted BCR correlating with the ADE potential of the IgG version of the antibody. In addition, we observed that the frequency of DENV-infectable B cells increases in previously flavivirus-naïve volunteers after a primary DENV infection. These findings suggest that BCR-dependent infection of B cells is a novel mechanism immune-mediated enhancement of DENV-infection.

2024-10-21 | GSE276766 | GEO

scRNAseq analysis of DENV-2 infected B cells

Project description:scRNAseq analysis of DENV-2 infected B cells

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Ribosome profiling of ZPR1-depleted S.cerevisiae cells

Project description:Ribosome profiling of ZPR1-depleted S.cerevisiae cells

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Detection of DENV infected cells following natural dengue infection

Project description:Detection of DENV infected cells following natural dengue infection

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Salivary glands from Aedes aegypti infected with DENV, ZIKV, and CHIKV

Project description:Aedes aegypti mosquitoes were orally infected with DENV, ZIKV or CHIKV virus, and once virus infection reached salivary gland tissues, these glands were dissected out and i-TRAQ performed to identify differentially expressed proteins during virus infection.

2021-06-02 | MSV000087564 | MassIVE

Ribosome profiling of ZPR1-depleted S.cerevisiae cells

Project description:The aim of this study was to gain insight into the ribosome occupancy on different genes and codons in Zpr1-depleted cells vs. WT Zpr1 cells

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Ribosome profiling of astrovirus-infected cells

Project description:Ribosome profiling of astrovirus-infected cells

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Detection of DENV infected cells following natural dengue infection

Project description:Viable T cells (CD3+ CD19-) and B cells (CD3- CD19+) were sorted from PBMC samples obtained from 1 individual experiencing a natural secondary DENV infection. Single cell RNA sequencing analysis was performed on 3 time points

2020-05-17 | GSE147104 | GEO

Unravelling tRNA Fragments in DENV Pathogenesis: Insights from RNA Sequencing

Project description:tRNA-derived small RNA including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs) plays significant roles in the various molecular mechanisms that underlie certain human diseases. of the generation of tRFs/tiRNAs and their potential roles during Dengue virus (DENV) infection is not yet known. Here, we have performed small RNA sequencing to identify the generation and alterations in tRF expression profiles of DENV infected Huh7 cells. Our results suggest that 733 tiRNAs/tRFs were found to be differentially expressed during DENV infection. Interestingly, 3’tRF population were found to be upregulated and i-tRF population were found to be downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to analyze the impact of differentially expressed tRFs on DENV pathogenesis. Our results suggest the significant involvement in transcriptional regulation via RNA polymerase II promoter and metabolic pathways. Overall, our study contributes significantly to our understanding of the roles played by tRFs in the complex dynamics of DENV infection.

2024-08-10 | GSE245081 | GEO

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