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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.

2021-02-19 | GSE167037 | GEO

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

Project description: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

Project description:The assembly of human cytomegalovirus (HCMV) virions is an orchestrated process that requires, as an essential prerequisite, the complex crosstalk between viral structural proteins. So far, however, the mechanisms governing the successive steps in the constitution of virion protein complexes remained elusive. Protein phosphorylation is a key regulator determining the sequential changes in conformation, binding, dynamics and stability of proteins in the course of multiprotein assembly. Here, we present new results to complete knowledge on HCMV virion proteome and phosphoproteome. Thus, a novel dataset of viral and cellular proteins contained in HCMV virions has been generated, providing a basis for future analyses of individual phosphorylation steps and sites involved in the orchestrated assembly of HCMV virion-specific multiprotein complexes.

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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.

2021-05-13 | GSE157846 | GEO

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

Project description:Viral infections involve packaging of the viral genome and proteins into virions. Knowing virion composition and structure is critical to understand viral pathogenesis. However, an integrated picture of virion proteome organization of large viruses, such as Herpesviruses, is lacking. Here we use cross-linking mass spectrometry to derive a spatially resolved structural interactome of intact human cytomegalovirus virions. We capture interactions of 82 host and 33 viral proteins, allowing us to de novo allocate them into distinct virion-layers and identify several host proteins as constitutive virion components recruited via specific protein interactions. The abundant viral protein pp150 forms domain-specific interactions with all virion layers and scaffolds numerous viral and host proteins such as PP1 phosphatase and 14-3-3 proteins, which are incorporated via nearby short linear motifs in pp150’s C-terminus. PP1 recruitment antagonizes 14-3-3 proteins and is pivotal during early and late viral replication steps. Collectively, this study gives a spatial and quantitative inventory of the system-wide organization and functional relevance of protein interactions inside native herpesvirus particles.

2023-06-14 | PXD031911 | Pride

Intermittent bulk release of human cytomegalovirus

Project description:Human Cytomegalovirus (HCMV) significantly remodels host cell processes and membranes to enable effective production of virus progeny. Nascent capsids exit the nucleus and undergo a final morphogenesis process in the cytoplasm where they associate with tegument and membranes. During this process called secondary envelopment, fully assembled virions are formed which are wrapped inside of host vesicles. Both the origin of the receiving membrane as well as the dynamic organization of the envelopment and exocytosis process are not well understood. Enveloped virus particles can be both found individually wrapped in small vesicles but also as accumulations in multivesicular bodies (MVBs). While individually wrapped particles are believed to exit the cell by exocytosis, it is unclear if particles in MVBs ever leave the cell or are actually targeted for lysosomal degradation. Using a novel correlative light and electron microscopy workflow that allows three-dimensional imaging of whole cells, we present evidence that HCMV capsids can bud into MVBs, generating large intracellular accumulations of enveloped virions. Immunofluorescence and fusion assays suggest that these MVBs are positive for markers of the exosomal pathway. Time-lapse as well as functional live-cell imaging showed that MVBs fuse with the plasma membrane and release patch-like accumulations of virus particles. Our data suggests a so far undescribed envelopment and exocytosis pathway of HCMV, possibly involving the late-endosome/exosome pathway, leading to the intermittent bulk release of virus particles.

2022-06-23 | PXD023444 | Pride

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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Genomic and functional characteristics of human cytomegalovirus revealed by next-generation sequencing.

Project description:The complete genome of human cytomegalovirus (HCMV) was elucidated almost 25 years ago using a traditional cloning and Sanger sequencing approach. Analysis of the genetic content of additional laboratory and clinical isolates has lead to a better, albeit still incomplete, definition of the coding potential and diversity of wild-type HCMV strains. The introduction of a new generation of massively parallel sequencing technologies, collectively called next-generation sequencing, has profoundly increased the throughput and resolution of the genomics field. These increased possibilities are already leading to a better understanding of the circulating diversity of HCMV clinical isolates. The higher resolution of next-generation sequencing provides new opportunities in the study of intrahost viral population structures. Furthermore, deep sequencing enables novel diagnostic applications for sensitive drug resistance mutation detection. RNA-seq applications have changed the picture of the HCMV transcriptome, which resulted in proof of a vast amount of splicing events and alternative transcripts. This review discusses the application of next-generation sequencing technologies, which has provided a clearer picture of the intricate nature of the HCMV genome. The continuing development and application of novel sequencing technologies will further augment our understanding of this ubiquitous, but elusive, herpesvirus.

| S-EPMC3970138 | biostudies-literature

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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