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Next-generation sequencing of human snoRNA molecules associated with human cytomegalovirus virus.

ABSTRACT: Using Next-generation sequencing of total RNA isolated from human cytomegalovirus virions we have analyzed host (human) snoRNA molecules.

ORGANISM(S): Homo sapiens

PROVIDER: GSE168263 | GEO | 2021/03/05

REPOSITORIES: GEO

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Next-generation sequencing of human snoRNA molecules associated with human cytomegalovirus virus.

Project description:Next-generation sequencing of human snoRNA molecules associated with human cytomegalovirus virus.

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Identification of human tRNA molecules bound to human cytomegalovirus capsid using cryoEM and Next-generation sequencing

Project description:Using Next-generation sequencing of total RNA isolated from human cytomegalovirus virions we have identified host (human) tRNA molecules.

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Identification of human tRNA molecules bound to human cytomegalovirus capsid using cryoEM and Next-generation sequencing

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Mass spectrometry-based characterization of the virion proteome and phosphoproteome of human cytomegalovirus

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Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships

Project description:Background: Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. Results: We used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver and brain). We identify 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. 59% of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, compared to only 16% of the correlated non-coding host gene/snoRNA pairs. Conclusions: Our results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.

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Spatial, Quantitative and Functional Deconstruction of Virus and Host Protein Interactions Inside Intact Cytomegalovirus Particles

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2022-06-23 | PXD023444 | Pride

The host exosome biogenesis pathway is essential for human cytomegalovirus virion assembly and egress

Project description:Human Cytomegalovirus (HCMV) infects over 50% of humans, is a leading cause of congenital birth defects, and poses serious risks for immuno-compromised individuals. To expand the molecular knowledge governing virion assembly and egress, we initiated a proteomics-based investigation and identified a significant proportion of host exosome constituents in HCMV virions. Quantitative analysis of exosomes released from uninfected cells (765 proteins) revealed that over 99% of the protein cargo was subsequently integrated into virions, confirming near-complete acquisition of exosome biogenesis during infection. We confirmed VAMP3 is essential for viral trafficking and release of infectious progeny, further validating the intrinsic exploitation of the pathway by HCMV. Therefore, host exosomes serve as the molecular template for virion cargo addition, and provide an export mechanism for virion egress. Our discovery underpins future investigation of host exosome proteins as important modulators of viral maturation, and enhances the understanding of HCMV envelopment, trafficking, fusion and release.

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Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships

Project description:Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships

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Gene expression comparison between WT, U17 snoRNA knockdown and U17 overexpression NIH-3T3 cells to identify target mRNAs regulated by U17 snoRNA

Project description:Comparison of mRNA transcriptome after differential expression of U17 snoRNA. We hypothesiaed that if U17 snoRNA regulates cholesterol homeostasis by modulating the expression of target mRNAs, genes that are differentially expressed by the loss-of-function or gain-of-function of U17 snoRNA would be candidate U17 targets. Results revealed negative regulation of target genes by U17 snoRNA, in which increasing dosage of U17 snoRNA from U17 knockdown to WT to U17 overexpression lead to decreases in target levels. Total RNA were isolated by TRIzol reagent (Invitrogen) from WT, U17 snoRNA KD (ShSnhg3 stable clone), and U17 snoRNA OE (pMDβglobinU17b stable clone) cells grown in LPDS media for 24 hours.

2015-04-04 | E-GEOD-67569 | biostudies-arrayexpress

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