Viral metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA648150 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12324923_1.fastq.gz | Fastqsanger.gz | |||
| SRR12324923_2.fastq.gz | Fastqsanger.gz | |||
| SRR12324924_1.fastq.gz | Fastqsanger.gz | |||
| SRR12324924_2.fastq.gz | Fastqsanger.gz |
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Project description:We identified cis-regulatory elements based on their dynamic chromatin accessibility during the gastrula-larva stages of sea urchin and sea star and studied their evolution in these echinoderm species
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Project description:Marine viral concentrates (VCs) contains a substantial amount of non-cellular biological particles, e.g. viruses, gene transfer agents (GTAs) and membrane vesicles that are ecological significant. Metagenomic sequencing of VCs has been extensively applied to study the diversity and function potential of natural virions whereas information of nonn-viral components are often excluded for investigation. Here we apply a shotgun proteomic approach to characterize the origin and function of proteins in the VCs collected from the deep chlorophyll maximum (DCM) of the South China Sea. Using a custom database, we identified 636 non-redundant proteins represented by a total of 7220 spectra from the two VC samples. Cyanophages, pelagiphages, Phycodnaviridae and a group of uncultured viruses (previouly collected from DCM of Mediterranean Sea) contributed the most in the viral proteome. Seldom proteins related to RNA viruses and known GTAs were found despites of the presence of their sequences in the protein-searching database, suggested that these particles might be low abundant in the samples. Over 60% of identified spectra could not be assigned to viruses. The non-viral spectra were dominated by microbial groups of SAR324, SAR11, Actinobacteria and picoeukaryotic algae such as prasinophytes.Interestingly, we found that periplasmic proteins such as diverse ABC and TRAP transporters, and 56 kDa selenium-binding proteins, were enriched in this fraction.Together with other detected non-viral proteins,we could identify significant microbial functions, such as the utilization of glycine betaine, 3-dimethylsulphoniopropionate,and taurine by SAR11,and urea by prochlorococcus, nitrous oxide production by ammonia-oxidizing archaea and peroxide detoxification by unkonwn gammaproteobacteria. Our study of marine VCs demonstrates the potential application of metaproteomics to link the nano-size materials to the diversity of virions and interesting microbial functions in the ocean.
2018-05-02 | PXD007174 | Pride
Project description:Due to the RNA nature of their genomes, influenza viruses have to utilize many RNA-binding proteins (RBPs) of both viral and host origin, for their replication. To uncover the comprehensive vRNA-host protein interactions, we performed affinity purification coupled with mass spectrometry (AP-MS) analysis of influenza vRNA complexes. The eight vRNA segments of H7N9 were transcribed and individually labeled with biotin in vitro and incubated with IAV virus-infected THP-1 cells, and vRNA complexes were enriched streptavidin magnetic beads and analyzed by mass spectrometry
2021-03-25 | PXD020723 | Pride
Project description:Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star and sea urchin orthologs. We sought to identify targets of sea urchin and sea star orthologs of Tbr. Because less is known about the function of Tbr during sea star development, we used RNA-seq in conjuction with ChIP-seq studies (GEO:xxxx) to determine the targets of sea star Tbr in early development. Methods: Sea star (Patiria miniata) embryos were injected with translation-blocking morpholino antisense oligonucleotides to knock-down PmTbr expression, as described previously. Control morpholinos were injected into sibling embryos. Embryos were allowed to develop until hatching (30-36 hpf) at which point injected embryos were collected and RNA was extracted. RNA-seq libraries were prepared, sequenced, and analyzed using standard protocols. Results: There are 2,562 genes that are significantly differentially expressed relative to control morpholino inected embryos (FDR < 0.05). There are roughly equivalent numbers of genes down-regulated (1,041) and up-regulated (1,521) by Pm-tbr knockdown, suggesting that PmTbr may act as both a transcriptional activator and repressor. 1,165 differentially expressed genes are located within 75 kb of a PmTbr binding site determined using ChIP-seq, and this set is used as a basis for comparison between sea star and sea urchin binding sites. Conclusions: 1,165 targets of the PmTbr transcription factor were identified based on differential expression following knockdown and the presence of transcription factor binding sites proximal to differentially expressed genes. There are an equal number of up- and down-regulated targets, suggesting Tbr may function as a transcriptional activator and repressor, depending on context and target gene. There was no clear association of motif utilization with either the direction of differential expression or ontological category of the target gene. There are only a small fraction of target genes (approximately 10%) that are in common between the sea star and sea urchin sets.
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Project description:During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms. In this study, we applied metabolic labeling of newly transcribed RNA with 4-thiouridine (4sU-tagging) to dissect the real-time kinetics of cellular and viral transcriptional activity during lytic murine cytomegalovirus (MCMV) infection. Microarray profiling on newly transcribed RNA obtained from different times during the first six hours of MCMV infection revealed discrete functional networks of cellular genes regulated with distinct kinetics at surprising temporal resolution. Most of these were undetectable in total RNA, either due to low temporal sensitivity of standard gene expression profiling using total RNA, or due to rapid (viral) counter-regulation. Furthermore, metabolic labeling and purification of newly transcribed RNA detailed the real-time kinetics and regulation of viral gene expression in absence of any interfering virion-associated RNA. Both qRT-PCR and next-generation sequencing of newly transcribed RNA demonstrated an unexpected peak of viral gene expression during the first two hours of infection including transcription of immediate early, early and even well characterized late genes. Interestingly, this peak was subject to rapid gene silencing (independent of the multiplicity of infection) with similar transcriptional activity only reached late in infection. For some genes, e.g. m152, this resulted in massive down-regulation of transcriptional activity by 6 hours post infection, which was not even reversed late in infection. Our findings thus highlight the importance of transcriptional activity during the first few hours of CMV infection and hint at novel mechanisms governing the kinetics of viral gene expression. In conclusion, studying real-time transcriptional activity during lytic CMV infection provides intriguing new insights into the regulation of cellular and viral gene expression. In total 13 samples were examined: 3 samples of total RNA (mock, 25, 48 hours past MCMV infection), 3 samples pre-existing RNA (mock, 25, 48 hpi), and 7 samples newly-transcribed RNA (mock, 1-2, 5-6, 11-12, 18-19, 24-25, 47-48 hpi)
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Project description:Viral concentrates (VCs) contained both viral particles and cell-affiliated components. In this study, a shotgun metaproteomic approach was applied to characterize proteins in the VCs collected from chlorophyll maximum, mesopelagic (200 m) and bathypelagic (3000 m) waters in the South China Sea. Abundant viral proteins indicated the shift of viral community as depth. Whereas the remaining non-viral proteins suggested the diverse microbial metabolism distinct at different layers.
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Project description:Viruses are known for their extremely compact genomes composed almost entirely of protein-coding genes. Nonetheless, four long noncoding RNAs (lncRNAs) are encoded by human cytomegalovirus (HCMV). Although these RNAs accumulate to high levels during lytic infection, their functions remain largely unknown. Here, we show that HCMV-encoded lncRNA4.9 localizes to the viral nuclear replication compartment, and that its depletion restricts viral DNA replication and viral growth. RNA4.9 is transcribed from the HCMV origin of replication (oriLyt) and forms an RNA-DNA hybrid (R-loop) through its G+C-rich 5’ end, and this may be important for the initiation of viral DNA replication. Furthermore, interference with RNA4.9 expression drastically reduces the levels of the viral single-stranded DNA-binding protein (ssDBP), and overexpression of ssDBP alleviates the inhibition of viral DNA replication and growth caused by RNA4.9 depletion. We also identified a similar, oriLyt-embedded, G+C-rich lncRNA in murine cytomegalovirus (MCMV). Knockdown of this lncRNA interferes with MCMV ssDBP expression and viral DNA replication. These results indicate that HCMV RNA4.9 plays an important role in regulating viral DNA replication by coupling oriLyt activity to ssDBP levels, and that this novel activity may be conserved in other betaherpesviruses.
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