Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Determinants of selectivity in the dicing mechanism

ABSTRACT: Determinants of selectivity in the dicing mechanism

PROVIDER: PRJNA1060650 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27407593_1.fastq.gz	Fastqsanger.gz
	SRR27407593_2.fastq.gz	Fastqsanger.gz
	SRR27407594_1.fastq.gz	Fastqsanger.gz
	SRR27407594_2.fastq.gz	Fastqsanger.gz
	SRR27407595_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Determinants of selectivity in the dicing mechanism

Project description:Determinants of selectivity in the dicing mechanism

| PRJNA1060648 | ENA

Determinants of selectivity in the dicing mechanism

Project description:Determinants of selectivity in the dicing mechanism

| PRJNA1060643 | ENA

Determinants of selectivity in the dicing mechanism III

Project description:Determinants of selectivity in the dicing mechanism III

| PRJNA1135181 | ENA

Determinants of selectivity in the dicing mechanism

Project description:The RNase III enzyme, DICER, is instrumental in the production of small RNAs, including miRNAs and siRNAs, by cleaving their precursors, such as pre-miRNAs, shRNAs, and long duplex RNAs. Utilizing High-throughput (HT) cleavage assays, our study delves into the cleavage activity of DICER. We challenge the widely accepted 2-nt loop counting rule in the previous study, revealing a divergent mechanism, the bipartite base pairing rule. This rule directs DICER's cleavage sites via the RNase III domain. Moreover, we demystify the recognition mechanism of the previously identified YCR motif. Building on this understanding, a secondary YCR motif that also influences DICER's cleavage sites has been discovered. We also address a long-debated issue concerning DICER's cleavage sites on long stem RNAs, such as pre-siRNAs or long shRNAs/pre-miRNAs. Our study shows that the dsRBD plays a crucial role in determining the cleavage sites of DICER in long-stem RNAs. In sum, our research provides a comprehensive understanding of several fundamental DICER mechanisms, challenging the long-standing model of the loop counting rule. This newfound knowledge reshapes our understanding of DICER's mechanisms, providing a robust foundation for future studies investigating the vast number of DICER mutations linked to various diseases.

2024-06-01 | GSE252433 | GEO

Determinants of selectivity in the dicing mechanism III

2024-07-13 | GSE272135 | GEO

Determinants of selectivity in the dicing mechanism

2024-06-01 | GSE252434 | GEO

Determinants of selectivity in the dicing mechanism

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-06-01 | GSE252435 | GEO

Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

Project description:In eukaryotes, small RNAs (sRNAs) play critical roles in multiple biological processes. Dicer endonucleases are central to sRNA biogenesis. In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24-nt small interfering RNAs (siRNAs) that determine the specificity of the RNA-directed DNA methylation (RdDM) pathway. Here, we determined structure of a DCL3-pre-siRNA complex in an active dicing-competent state. The 5′-phosphorylated-A1 of the guide strand and the 1-nt 3′-overhang of the complementary strand are specifically recognized by a positively charged pocket and an aromatic cap, respectively. The 24-nt siRNA length dependence relies on the separation between the 5′-phosphorylated-end of the guide RNA and dual cleavage sites formed by the paired RNaseIII domains. These structural studies, complemented by functional data, reveal insights into the dicing principle for Dicers in general.

2021-10-14 | GSE179616 | GEO

Genome-scale RNA interference profiling of Trypanosoma brucei sensitivity determinants for experimental phthalimide-based trypanocidal drug PHT-39

Project description:In a phenotypic screening approach of novel molecules composed of a synergistic combination of phthalimide, benzimidazole, and triazole scaffolds we discovered compounds with potent anti-leishmanial activity. The resulting early-lead compound PHT-39, which contains a trifluoromethyl substitution, demonstrated the highest efficacy in a Leishmania infantum intramacrophage assay, with an EC50 of 1.2+/- 3.2 μM.Cytotoxicity testing of PHT-39 in Hep-G2 cells indicated high selectivity of over 90-fold. To investigate the mechanism of action we carried out experiments in Trypanosoma brucei, which is also sensitive to PHT-39. Here we used a genome-wide RNAi library approach (PMID: 22278056; PMID: 21363968) to detect sensitivity determinants. This high-throughput phenotyping approach identified sensitivity determinants for PHT-39, which included a P-type ATPase that is crucial for the uptake of miltefosine and amphotericin, strongly indicating a shared route for cellular entry.

2024-03-08 | E-MTAB-13844 | biostudies-arrayexpress

Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

Project description:Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

| PRJNA744279 | ENA