Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of viral ncRNA-mRNA interactions in Herpesvirus saimiri-infected marmoset T cells

ABSTRACT: Viruses express several classes of non-coding (nc) RNAs1. For most of them, the functions and mechanisms by which they act are unknown. Herpesvirus saimiri (HVS), a g-herpesvirus that establishes latency in T cells of New World primates and has the ability to cause aggressive leukemias and lymphomas in non-natural hosts2, expresses seven small nuclear (sn), U-rich ncRNAs called HSURs in latently infected cells3-5. HSURs associate with Sm proteins and share biogenesis and structural features with cellular Sm-class snRNAs4,6. One of these viral snRNAs, HSUR 2, base-pairs with two host microRNAs (miRNAs), miR-142-3p and miR-167. However, HSUR 2 does not affect the abundance or activity of these two cellular miRNAs, suggesting alternative functions for these interactions. Here we show that HSUR 2 also base-pairs with messenger RNAs (mRNAs) in infected cells. We combined in vivo psoralen-mediated RNA-RNA crosslinking and high-throughput sequencing to identify mRNAs targeted by HSUR 2. HSUR 2 targets include mRNAs encoding Retinoblastoma (pRb) and factors involved in p53 signaling and apoptosis. We show that HSUR 2 represses expression of target mRNAs. Base-pairing between HSUR 2 and miR-142-3p and miR-16 is essential for HSUR 2-mediated mRNA repression, suggesting that HSUR 2 recruits these two cellular miRNAs to target mRNAs. Moreover, we show that HSUR 2 utilizes this mechanism to inhibit apoptosis. Our results uncover a role for a viral Sm-class RNA as a miRNA adaptor in post pre-mRNA-processing regulation of gene expression.

ORGANISM(S): Callithrix jacchus

PROVIDER: GSE79082 | GEO | 2017/10/01

SECONDARY ACCESSION(S): PRJNA314902

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Differential gene regulation by miR-142-3p and miR-K10a isomiRs

Project description:This study compares changes in gene expression induced by four interrelated miRNAs with similar but staggered 5'-ends: miR-142-3p, miR-142-3p-1, miR-K10a, and miR-K10a+1. miR-K10a and miR-K10a+1 are co-expressed by the Kaposi's sarcoma-associated herpesvirus. Total RNA was harvested from HEK293 cells transfected with individual miRNAs including a negative control miRNA mimic.

2015-07-31 | E-GEOD-66489 | biostudies-arrayexpress

Differential gene regulation by miR-142-3p and miR-K10a isomiRs

2015-07-31 | GSE66489 | GEO

Changes of Protein Expression after CRISPR/Cas9 Knockout of miRNA-142 in Cell Lines Derived from Diffuse large B-Cell Lymphoma // Proteome Dataset

Project description:MicroRNAs (miRNAs) post-transcriptionally regulate gene expression by inhibiting protein synthesis of target messenger RNAs (mRNAs). MicroRNA-142 (miR-142), which has tumor-suppressive properties, was functionally deleted by CRISPR/Cas9 knockout in cell lines derived from diffuse large B-cell lymphoma (DLBCL), a highly aggressive tumor that represents about 30% of non-Hodgkin lymphoma worldwide. Mutations in miR-142 affect about 20% of all cases of DLBCL. By proteome analyses, the miR-142 knockout resulted in a consistent up-regulation of 52 but also down-regulation of 41 proteins in the GC-DLBCL lines BJAB and SUDHL4. Various mitochondrial ribosomal proteins were up-regulated in line with their pro-tumorigenic properties, while proteins necessary for MHC-I presentation were down-regulated in accordance with the finding that miR-142 knockout mice have a defective immune response. Of the deregulated proteins/genes, CFL2, CLIC4, STAU1, and TWF1 are known targets of miR-142, and we could additionally confirm AKT1S1, CCNB1, LIMA1, and TFRC as new targets of miR-142-3p or -5p. We further show that seed-sequence mutations of miR-142 can be used to confirm potential targets and that miRNA knockout cell lines might thus be used to identify novel targets of miRNAs. Due to the complex contribution of miRNAs within cellular regulatory networks, in particular when a miRNA highly present in the RISC complex is deleted and can be replaced by other endogenous miRNAs, primary effects on gene expression may be covered by secondary layers of regulation

2023-03-10 | PXD037148 | Pride

Herpesvirus saimiri microRNAs Preferentially Target Host Cell-Cycle Regulators

Project description:In latently-infected marmoset T cells, Herpesvirus saimiri (HVS) expresses six microRNAs (known as miR-HSURs). The viral miR-HSURs are processed from chimeric primary transcripts, each containing a noncoding U-rich RNA (HSUR) and a pre-miRNA hairpin. To uncover functions of miR-HSURs, we identified mRNA targets in infected cells using High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation (HITS-CLIP). HITS-CLIP revealed hundreds of robust Argonaute (Ago) binding sites mediated by miR-HSURs in the host genome, but few in the HVS genome. Gene Ontology analysis showed that several pathways regulating the cell cycle are enriched among cellular targets of miR-HSURs. Interestingly, miR-HSUR4-3p represses expression of the p300 transcriptional co-activator by binding the open reading frame of its mRNA. miR-HSUR5-3p directly regulates BiP, an endoplasmic reticulum (ER) localized chaperone facilitating maturation of the Major Histocompatibility Complex I (MHC I) and the antiviral response. miR-HSUR5-3p also robustly downregulates WEE1, a key negative regulator of cell-cycle progression, leading to reduced phosphorylation of its substrate cyclin-dependent kinase (Cdk1). Consistently, inhibition of miR-HSUR5-3p in HVS-infected cells decreases their proliferation. Together, our results shed light on the roles of viral miRNAs in cellular transformation and viral latency.

2015-08-19 | GSE71806 | GEO

microRNA Targetome Analysis of Latently KSHV-infected Primary Effusion Lymphoma Cell lines Using PAR-CLIP [Illumina]

Project description:Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and, often, EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in viral latency and lymphomagenesis. Here we report the direct and transcriptome-wide identification of miRNA target sites for all miRNAs expressed in PEL cell lines. The resulting dataset revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs encoding proteins that function in pathways with relevance to KSHV pathogenesis. Moreover, ~50% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, these experiments identify an extensive list of mRNAs targeted by KSHV miRNAs and indicate that these are likely to strongly influence viral replication and pathogenesis. small RNA sequencing, 3 samples Ago2 (EIF2C2) PAR-CLIP, 2 samples

2011-11-16 | E-GEOD-32109 | biostudies-arrayexpress

microRNA Targetome Analysis of Latently KSHV-infected Primary Effusion Lymphoma Cell lines Using PAR-CLIP [Illumina]

2011-11-16 | GSE32109 | GEO

mRNA microarray analysis of uveal melanoma cell lines SP6.5 and M17 transfected with miR-142-3p or negative control

Project description:MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs of about 22 nt in length. Uveal melanoma is the most common intraocular malignant tumor in adults. Our previous result of microarray analysis showed that miR-142-3p was distinctly downregulated in uveal melanoma cells on which miR-142-3p was speculated to have important regulatory effect. In order to better understand the function of miR-142-3p in uveal melanoma and identify its gene targets, we performed transcriptomic microarray analysis. This was done by comparing gene expression profile changes in uveal melanoma cells transfected with miR-142-3p with that transfected with a negative control.

2019-02-28 | E-MTAB-6725 | biostudies-arrayexpress

56afc434-ec9b-4228-9939-fc0a3871593d - samples

Project description:Microglia were derived from iPSCs and treated with mimics and inhibitors of the miRNAs hsa-miR-150-5p, hsa-miR-193a-3p and hsa-miR-19b-3p. RNA-sequencing was then performed to examine the effects of up- and down-regulation of the respective miRNAs.

| EGAD00001006842 | EGA

Identification of differentially expressed microRNAs in liver tissue of Hepatitis B virus (HBV) infected hepatocellular carcinoma (HCC)

Project description:Global expression profiling of miRNAs in liver tissue of HBV infected HCC and chronic hepatitis B (CHB) with no fibrosis was evaluated. A total of 40 differentially expressed miRNAs were identified in HCC. Top 10 miRNAs are validated in more numbers of HCC tisuues by qRT PCR. Finally six miRNAs (miR-15a, miR-16, miR-21,miR-29b-3p, miR-126, miR-142-3p, miR-193a-5p) showed similar expression pattern in both microarray and qRT PCR

2015-04-15 | GSE67882 | GEO

MicroRNA-183-3p is a predictor of worsening heart failure in adult patients with transposition of the great arteries and a systemic right ventricle

Project description:AIM: MicroRNAs (miRNAs) have been shown to play an important role in the progression of heart failure (HF). The aim of our study was to analyze miRNAs in the blood of patients with transposition of the great arteries and a systemic right ventricle (TGA-RV) in order to identify those that predict worsening HF. MATERIALS AND METHODS: In 36 patients with TGA-RV, SurePrint™ 8×60K Human v21 miRNA arrays were used to determine the miRNA abundance profiles and compared to 35 age- and gender-matched healthy volunteers (HVs). MiRNAs that were most significantly abundant or best related to worsening HF were further validated by RT-qPCR. RESULTS: Using miRNA array analysis, a total of 50 down-regulated and 56 up-regulated miRNAs were found to be differentially abundant in TGA-RV patients compared to HVs. 6 of these 106 miRNAs were significantly related to worsening HF. After validation by RT-qPCR, 4 miRNAs turned out to be significantly associated with worsening HF, namely miR-150-5p, miR-1255b-5p, miR-423-3p, and miR-183-3p. In the stepwise multivariable Cox regression analysis, ejection fraction of the systemic RV and miR-183-3p were found to be independent predictors of worsening HF (P<0.001 and P=0.008, respectively). CONCLUSIONS: In patients with TGA-RV, miR-183-3p is an independent predictor of worsening HF and thus may be used as additional biomarker in the risk assessment of these patients.

2021-09-29 | GSE179105 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data