GEO DataSets

(Submitter supplied) While the issue of whether RNA interference (RNAi) ever forms part of the antiviral innate immune response in mammalian somatic cells remains controversial, there is considerable evidence demonstrating that few, if any, viral small interfering RNAs (siRNAs) are produced in infected cells. Moreover, total inhibition of RNAi by mutational inactivation of key RNAi factors, such as Dicer or Argonaut 2, has been shown to not enhance virus replication. more...

Organism:

Homo sapiens; Influenza A virus (A/hvPR8/34(H1N1))

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24703 GPL11154

13 Samples

Download data: BED

(Submitter supplied) We demonstrate that mature human somatic cells produce abundant virus-derived siRNAs co-immunoprecipitated with Argonaute proteins in response to IAV infection. We show that the biogenesis of viral siRNAs from IAV dsRNA precursors in infected cells is mediated by wild type human Dicer.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: FASTA, TXT

(Submitter supplied) While RNA interference (RNAi) functions as a potent antiviral innate immune response in plants and invertebrates, mammalian somatic cells appear incapable of mounting an RNAi response and few small interfering RNAs (siRNAs) can be detected. To examine why siRNA production is inefficient, we have generated double knockout human cells lacking both Dicer and PKR. Using these cells, which tolerate dsRNA expression, we show that mutant forms of human Dicer lacking the amino-terminal helicase domain can process dsRNAs to produce high levels of siRNAs that are readily detectable by Northern blot and that can effectively and specifically inhibit the expression of cognate mRNAs. more...

Organism:

Homo sapiens; Human poliovirus 1 strain Sabin

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL20271

21 Samples

Download data: BED, FA

(Submitter supplied) Plants and invertebrates protect themselves from viruses through RNA interference (RNAi), yet it remains unknown whether this defense mechanism exists in mammals. Antiviral RNAi involves the processing of viral long double-stranded (ds) RNA molecules into small interfering RNAs (siRNAs) by the ribonuclease (RNAse) III Dicer. These siRNAs are incorporated into effector complex(es) containing members of the Argonaute (Ago) protein family and guide silencing of complementary target viral RNAs. more...

Organism:

Mus musculus

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: TXT

(Submitter supplied) Dicer and Argonaute2 (Ago2) gene is involving in microRNA (miRNA) maturation. Knockdown of these genes has great impact on miRNA expression profiles. We used microarrays to detail the miRNA expression profiles in Dicer- and Ago2-knockdown HeLa cells and demonstarted that the significant difference between Ago2-knockdown and Dicer- and Ago2-co-knockdown HeLa cells were not found.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

5 Samples

Download data: CEL

(Submitter supplied) While mammalian somatic cells are incapable of mounting an effective RNA interference (RNAi) response to viral infections, plants and invertebrates are able to generate high levels of functional short interfering RNAs (siRNAs) of viral origin that can effectively control many infections. In Drosophila, the RNAi response is mediated by the Dicer 2 enzyme (dDcr2) acting in concert with two co-factors called Loqs-PD and R2D2. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: BED

(Submitter supplied) We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify ribonuclease L cleavage sites in host and viral RNAs.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

4 Samples

Download data: TXT

(Submitter supplied) We investigated the role of A. thaliana RDRs in the RNAi-mediated viral immunity by using a mutant of cucumber mosaic virus (CMV) that does not express the VSR protein 2b. CMV contains three positive-strand genomic RNAs and the 2b protein encoded by RNA2 is essential for infection by suppressing antiviral silencing initiated by either DCL4 or DCL2. Our results demonstrate an essential role for the amplification of viral siRNAs by either RDR1 or RDR6 in antiviral silencing. more...

Organism:

Arabidopsis thaliana; Cucumber mosaic virus (strain FNY)

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9951

6 Samples

Download data

(Submitter supplied) Viral infections affecting the upper or lower respiratory tract induce mucin production in the epithelial surfaces of the respiratory cells. However, a little is known about how mucins are produced on the surfaces of respiratory epithelial cells and affects viral replication. In the course of the investigation of the cellular responses in the early stage of Influenza A virus (IAV) infection, we found that two miRNAs, miR-221 and miR-17-3p, which target the mRNA of GalNAc transferase 3 (GALNT3), are rapidly down-regulated as early as 1.5 h post-infection.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14767

8 Samples

Download data: TXT

(Submitter supplied) In mammals, early resistance to viruses relies on interferons, which protect differentiated but not stem cells from viral replication. Many other organisms rely instead on RNA interference (RNAi) mediated by a specialised Dicer protein that cleaves viral double stranded RNA. Whether RNAi also contributes to mammalian antiviral immunity remains controversial. Here we identify an isoform of Dicer, named antiviral Dicer (aviD), that protects tissue stem cells from RNA viruses, including Zika virus and SARS-CoV-2, by dicing viral double-stranded RNA to orchestrate antiviral RNAi. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: TXT

(Submitter supplied) We focus our analyses on the description of viral small RNAs (FHVdeltaB2 or FHV) and based on genetic and molecular evidende, classify them and discuss their relevance in antiviral defense.

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

5 Samples

Download data: TXT

(Submitter supplied) Mosquito-borne flaviviruses maintain life cycles in mammals and mosquitoes. RNA interference (RNAi) has been demonstrated as an anti-flavivirus mechanism in mosquitoes; however, whether and how flavivirus induces and antagonizes RNAi-mediated antiviral immunity in mammals remains unknown. Here we showed that NS2A of Dengue virus-2 (DENV2) act as a viral suppressor of RNAi (VSR). When NS2A-mediated RNAi suppression was disabled, the resulting mutant DENV2 induced Dicer-dependent production of abundant DENV2-derived siRNAs in differentiated mammalian cells. more...

Organism:

Aedes aegypti; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21020 GPL11154

6 Samples

Download data: TXT

(Submitter supplied) RNA interference (RNAi) functions as the major host antiviral defense in insects, while less is understood about how to utilize antiviral RNAi in controlling viral infection in insects. Enoxacin belongs to the family of synthetic antibacterial compounds based on a fluoroquinolone skeleton that has been previously found to enhance RNAi in mammalian cells. In this study, we showed that enoxacin efficiently inhibited viral replication of Drosophila C virus (DCV) and Cricket paralysis virus (CrPV) in cultured Drosophila cells. more...

Organism:

Drosophila melanogaster; Drosophila C virus strain EB

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL30984

2 Samples

Download data: TXT

(Submitter supplied) High-throughput sequencing of Drosophila melanogaster small RNAs from S2 cells. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data

(Submitter supplied) High-throughput sequencing of Drosophila melanogaster small RNAs from S2R+ cells. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

2 Samples

Download data

(Submitter supplied) Influenza A virus (IAV), one of the most prevalent respiratory diseases, causes pandemics around the world. The multifunctional non-structural protein 1 (NS1) of IAV is a viral antagonist that suppresses host antiviral response. However, the mechanism by which NS1 modulates the RNA interference (RNAi) pathway remains unclear. Here, we identified interactions between NS1 proteins of Influenza A/PR8/34 (H1N1; IAV-PR8) and Influenza A/WSN/1/33 (H1N1; IAV-WSN) and Dicer’s cofactor TAR-RNA binding protein (TRBP). more...

Organism:

Mus musculus; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

5 Samples

Download data: TXT

(Submitter supplied) Influenza A virus exhibits high rates of replicative failure due to a variety of genetic defects. As such, most viral particles cannot complete the life cycle. However, despite this failure, this virus is incredibly successful in the suppression of innate immune detection and the production of interferons, succeeding at remaining undetected in >99% of cells in tissue-culture models of infection. As the same variation that leads to replication failure can, by chance, inactivate the major innate immune antagonist in influenza A virus, NS1, what features prevent these events from triggering massive amounts of interferon production? By studying how genetic and phenotypic variation in a viral population lacking NS1 correlates with interferon production, we have built a model of the "worst-case" failure from an improved understanding of the steps at which NS1 acts in the viral lifecycle to prevent triggering of an innate immune response. more...

Organism:

Influenza A virus (A/WSN/1933(H1N1)); Homo sapiens; Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL25643 GPL32752

14 Samples

Download data: MTX, TSV

(Submitter supplied) m6A and YTHDF1, YTHDF2, YTHDF3 mapping of IAV RNA with PAR-CLIP and pA-m6A-seq

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL11154

5 Samples

Download data: BED

(Submitter supplied) RNA interference (RNAi) is a cell-intrinsic antiviral defense conserved in diverse organisms. However, the mechanism by which mammalian antiviral RNAi is regulated is largely unknown. Herein, we uncover that STUB1, an E3 ubiquitin ligase, interacts with and ubiquitinates AGO2, the core component of RNAi pathway, resulting in the degradation of AGO2 via ubiquitin-proteasome system. Additionally, STUB1 can induce the degradation of the other mammalian AGO proteins including AGO1, AGO3, and AGO4. more...

Organism:

Enterovirus A71; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL30983

2 Samples

Download data: TXT

(Submitter supplied) In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. more...

Organism:

Sindbis virus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20301 GPL33716

26 Samples

Download data: BW, TXT