RNA-dependent RNA polymerases in the black-legged tick produce Argonaute-dependent small RNAs and regulate genes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA762041 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15831571.fastq.gz | Fastqsanger.gz | |||
| SRR15831572.fastq.gz | Fastqsanger.gz | |||
| SRR15831573.fastq.gz | Fastqsanger.gz | |||
| SRR15831574.fastq.gz | Fastqsanger.gz | |||
| SRR15831575.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 37 |
Similar Datasets
Project description:Small regulatory RNAs (sRNAs) are involved in anti-viral defense and gene regulation. Although RNA-dependent RNA Polymerases (RdRPs) play essential roles in sRNA biogenesis in nematodes, plants and fungi, their involvement in other animals remains controversial. We identify abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs) expressed in the tick ISE6 cell line. The RdRP-dependent sRNAs are mainly derived from sense and antisense strands of RNA polymerase III-transcribed genes and repetitive elements. Knockdown of AGO/RdRP causes miregulation of protein-coding genes.These results demonstrate that arachnid RdRPs are important sRNA biogenesis factors, and the discovery of novel pathways underscores the importance of characterizing sRNA biogenesis in various organisms to understand virus-vector interactions and exploit RNAi for pest control.
2021-09-11 | GSE183810 | GEO
Project description:Alectoris rufa breed:red-legged partridge Genome sequencing
| PRJNA932231 | ENA
Project description:Argonaute (AGO) proteins interact with distinct classes of small RNAs to direct multiple regulatory outcomes. In many organisms, including plants, fungi and nematodes, cellular RNAdependent RNA polymerases (RdRPs) utilize AGO targets as templates for amplification of silencing signals. Here, we show that distinct RdRPs function sequentially to produce small RNAs that target endogenous loci in C. elegans. We show that DCR-1, the RdRP RRF-3, and the dsRNA-binding protein RDE-4, are required for the biogenesis of 26nt RNAs, termed 26GRNAs, and that 26G-RNAs engage the Piwi-clade AGO, ERGO-1. Our findings support a model in which targeting by ERGO-1 recruits a second RdRP (RRF-1 or EGO-1), which in turn transcribes 22G-RNAs that interact with worm-specific AGOs (WAGOs) to direct gene silencing. ERGO-1 targets exhibit a non-random distribution in the genome and appear to include many gene duplications, suggesting that this pathway may control over-expression resulting from gene expansion. 8 samples examined. Small RNA libraries generated from: C. elegans animals.
2010-02-25 | E-GEOD-18714 | biostudies-arrayexpress
Project description:Salp15 is one of the proteins in the saliva of the tick Ixodes scapularis. Together with other biomolecules injected into the mammalian host at the biting site, it helps the tick to sustain its blood meal for days. Salp15 interferes with the cellular immune response of the mammalian host by inhibiting the activation of CD4+ T-lymphocytes. This function is co-opted by pathogens that use the tick as a vector and invade the host when the tick bites, such as Borrelia burgdorferi, the causative agent of Lyme borreliosis. Because of the immunity-suppressing role of Salp15, it has been proposed as a candidate for therapeutic applications in disorders of the immune system. The protein is produced as a 135-residue long polypeptide and secreted without its N-terminal signal 1-21 sequence. Detailed structural studies on Salp15 are lacking because of the difficulty in producing large amounts of the folded protein. We report the production of Salp15 and its structural analysis by NMR. The protein is monomeric and contains a flexible N-terminal region followed by a folded domain with mixed α + β secondary structures. Our results are consistent with a three-dimensional structural model derived from AlphaFold, which predicts the formation of three disulfide bridges and a free C-terminal cysteine.
| S-EPMC8954417 | biostudies-literature
Project description:Argonaute (AGO) proteins interact with distinct classes of small RNAs to direct multiple regulatory outcomes. In many organisms, including plants, fungi and nematodes, cellular RNAdependent RNA polymerases (RdRPs) utilize AGO targets as templates for amplification of silencing signals. Here, we show that distinct RdRPs function sequentially to produce small RNAs that target endogenous loci in C. elegans. We show that DCR-1, the RdRP RRF-3, and the dsRNA-binding protein RDE-4, are required for the biogenesis of 26nt RNAs, termed 26GRNAs, and that 26G-RNAs engage the Piwi-clade AGO, ERGO-1. Our findings support a model in which targeting by ERGO-1 recruits a second RdRP (RRF-1 or EGO-1), which in turn transcribes 22G-RNAs that interact with worm-specific AGOs (WAGOs) to direct gene silencing. ERGO-1 targets exhibit a non-random distribution in the genome and appear to include many gene duplications, suggesting that this pathway may control over-expression resulting from gene expansion.
2010-02-25 | GSE18714 | GEO
Project description:By doing ChIP-seq with antibodies against two P23-45 RNA polymerases gp64 and gp96 we showed that both RNA polymerases interact with the phage genome at the early stage of infection. Gp96 interacts with pre-early P23-45 genes, while gp64 interacts with pre-early, early and some middle-stage genes.
2023-12-12 | GSE215810 | GEO
Project description:The hindgut, as a part of the tick excretory system, plays an important physiological role in maintaining homoeostases and waste elimination. Immunoreactive projections from the synganglion to the hindgut were found using antibodies against four different neuropeptides: FGLamide related allatostatin, myoinhibitory peptide, SIFamide, and orcokinin. The presence of FGLamide related allatostatin, myoinhibitory peptide and SIFamide in both synganglia (source) and hindgut (target organ) extracts was confirmed by MALDI-TOF. Tissue-specific PCR revealed the expression of four putative FGLamide related allatostatin receptors and an SIFamide receptor in the hindgut. An antibody against Ixodes scapularis SIFamide receptor detected immunoreactive spots in epithelial cells as well as the visceral muscles surrounding the rectal sac, while staining with the antibody against myoinhibitory peptide receptor 1 revealed that the immunoreactivity was only associated with the visceral muscles. In hindgut motility assays, SIFamide activated hindgut motility in a dose-dependent manner. None of other three neuropeptides (FGLamide related allatostatin, myoinhibitory peptide and orcokinin) activated hindgut motility when tested alone. Myoinhibitory peptide antagonised the SIFamide-stimulated hindgut mobility when it was tested in combination with SIFamide.
| S-EPMC4175087 | biostudies-literature
Project description:Life as we know it, simply would not exist without DNA replication. All living organisms utilize a complex machinery to duplicate their genomes and the central role in this machinery belongs to replicative DNA polymerases, enzymes that are specifically designed to copy DNA. "Hassle-free" DNA duplication exists only in an ideal world, while in real life, it is constantly threatened by a myriad of diverse challenges. Among the most pressing obstacles that replicative polymerases often cannot overcome by themselves are lesions that distort the structure of DNA. Despite elaborate systems that cells utilize to cleanse their genomes of damaged DNA, repair is often incomplete. The persistence of DNA lesions obstructing the cellular replicases can have deleterious consequences. One of the mechanisms allowing cells to complete replication is "Translesion DNA Synthesis (TLS)". TLS is intrinsically error-prone, but apparently, the potential downside of increased mutagenesis is a healthier outcome for the cell than incomplete replication. Although most of the currently identified eukaryotic DNA polymerases have been implicated in TLS, the best characterized are those belonging to the "Y-family" of DNA polymerases (pols η, ι, κ and Rev1), which are thought to play major roles in the TLS of persisting DNA lesions in coordination with the B-family polymerase, pol ζ. In this review, we summarize the unique features of these DNA polymerases by mainly focusing on their biochemical and structural characteristics, as well as potential protein-protein interactions with other critical factors affecting TLS regulation.
| S-EPMC5573590 | biostudies-literature
Project description:Comparision of mRNA abundance and translation efficiency mediated by cytoplasmic poly(A) polymerases in C. elegans comparision of different adults treated with RNAi
2014-10-02 | E-GEOD-58918 | biostudies-arrayexpress