MiRNA* loading on Ago2
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE12462 | GEO | 2010/08/03
SECONDARY ACCESSION(S): PRJNA113029
REPOSITORIES: GEO
Similar Datasets
Project description:In flies, microRNAs (miRNAs) are synthesized as a short imperfect duplex, where the miRNA is paired to another small RNA, dubbed the "miRNA*". Usually, miRNA*s are degraded in the last steps of miRNA maturation, but we found evidence that some of them can be loaded on the Ago2 protein. Small RNAs (18-29 nt) from fly heads (WT, ago2 mutants, dcr-2 homozygous and heterozygous mutants) were sequenced using a Solexa Genome Analyzer instrument. The ago2 cDNA library was loaded twice on the instrument, yielding two technical replicates.
2010-08-02 | E-GEOD-12462 | biostudies-arrayexpress
Project description:Drosophila Argonaute-1 and Argonaute-2 differ in function and small RNA content. AGO2 binds to siRNAs, whereas AGO1 is almost exclusively occupied by microRNAs. microRNA duplexes are intrinsically asymmetric, with one strand, the miR strand, preferentially entering AGO1 to recognize and regulate the expression of target mRNAs. The other strand, miR*, has been viewed as a by-product of microRNA biogenesis. Here, we show that miR*s are often loaded as functional species into AGO2. This indicates that each microRNA precursor can potentially produce two mature small RNA strands that are differentially sorted within the RNAi pathway. miR* biogenesis depends upon the canonical microRNA pathway, but loading into AGO2 is mediated by factors traditionally dedicated to siRNAs. By inferring and validating hierarchical rules that predict differential AGO loading, we find that intrinsic determinants, including structural and thermodynamic properties of the processed duplex, regulate the fate of each RNA strand within the RNAi pathway. These were independently processed and sequenced using the Illumina GAII platform. In total, five libraries were analyzed.
2009-11-15 | E-GEOD-17734 | biostudies-arrayexpress
Project description:Drosophila Argonaute-1 and Argonaute-2 differ in function and small RNA content. AGO2 binds to siRNAs, whereas AGO1 is almost exclusively occupied by microRNAs. microRNA duplexes are intrinsically asymmetric, with one strand, the miR strand, preferentially entering AGO1 to recognize and regulate the expression of target mRNAs. The other strand, miR*, has been viewed as a by-product of microRNA biogenesis. Here, we show that miR*s are often loaded as functional species into AGO2. This indicates that each microRNA precursor can potentially produce two mature small RNA strands that are differentially sorted within the RNAi pathway. miR* biogenesis depends upon the canonical microRNA pathway, but loading into AGO2 is mediated by factors traditionally dedicated to siRNAs. By inferring and validating hierarchical rules that predict differential AGO loading, we find that intrinsic determinants, including structural and thermodynamic properties of the processed duplex, regulate the fate of each RNA strand within the RNAi pathway.
2009-11-15 | GSE17734 | GEO
Project description:Target-directed degradation (TDD) of microRNAs (miRNAs) plays an important role in shaping miRNA abundances across bilateria. Some endogenous small interfering RNAs (siRNAs) of Drosophila cells have target sites resembling those that trigger miRNA TDD, raising the question as to whether they too might undergo such regulation. Here, we find that at least seven of these siRNAs are indeed sensitive to TDD when loaded into AGO1, the Argonaute paralog that preferentially associates with miRNAs. Despite this sensitivity when loaded into AGO1, these siRNAs are not detectably regulated by TDD because most molecules are loaded into AGO2, the Argonaute paralog that preferentially associates with siRNAs, and we find that siRNAs and miRNAs loaded into AGO2 are insensitive to TDD. One explanation for the protection of these small RNAs loaded into AGO2 is that these small RNAs are 2′-O-methylated at their 3′ termini. However, contrary to previous proposals, 2′-O-methylation does not protect these RNAs from TDD, which indicates that their protection is instead conferred by features of the AGO2 protein itself. Together, these observations clarify the requirements for regulation by TDD and revise our understanding of the role of 2′-O-methylation in small-RNA biology.
2021-01-05 | GSE163938 | GEO
Project description:The proposed method uses enriched de novo motifs on the peak sequences of Ago2-CLIP to determine miRNA-RNA heteroduplex for either canonical or non-canonical miRNA-binding sites. miRNA-RNA heteroduplex are ranked based on a duplex score. Since the quality of the peak detection is of pivotal importance for the final output of the proposed method, we also provide an illustrative comparative evaluation of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, for four publicly available Ago2-datasets and one previously unpublished in-house Ago2-dataset in stem cells. The experimental validation was carried out on the in-houseAgo2 dataset by gene reporter assay.
2017-03-01 | GSE85219 | GEO
Project description:We used miRNA microarrays to detail the miRNA content in A549 Ago2-KO/HA-Ago2Wt, Ago2-KO/HA-Ago2KA, and Ago2-KO/HA-Ago2Δ (Dm) cells
2024-04-18 | GSE255941 | GEO
Project description:The reduced sperm count observed in Ago2 cKO mice implies that AGO2 has non-redundant functions in the male germ line. Because AGO2 is a key protein in the RNA interference (RNAi) pathway, we first postulated that AGO2 loss disrupts normal transcriptional and translational dynamics of target mRNAs relevant to sperm maturation. To address this hypothesis, we took advantage of the apparently normal spermatogenesis in Ago2 cKO mice, which allowed us to purify matched meiotic and post-meiotic germ cells from Ago2 cKO and wild type controls. We examined changes in the transcriptome and proteome of these two spermatogenic stages in Ago2 cKO relative to control mice using RNA-seq and quantitative mass spectrometry (MS). To further examine if the changes in mRNA and protein levels detected in Ago2 cKO germ cells was due to a loss of regulation by the canonical AGO2-miRNA pathway, we characterized AGO2 protein interactors by AGO2 immunoprecipitation-mass spectrometry (IP-MS) in cytoplasmic and nuclear fractions of post-meiotic cells
2022-08-01 | PXD027935 | Pride
Project description:microRNAs (miRNAs) are typically generated as ~22-nucleotide double-stranded RNAs via processing of precursor hairpins by the RNase III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form RNA-induced silencing complex (RISC). However, the biogenesis of miR-451, an erythropoietic miRNA conserved in vertebrates, does not require Dicer processing. Instead, the short pre-miR-451 precursor hairpin is directly loaded into Ago, followed by cleavage of the 3' arm and trimming of the 3' end to the mature length by PARN. Here we show the in vivo activity of miR-430 Ago2-hairpin, a canonical microRNA engineered to fit the structure of miR-451 and hence become Ago2-dependent. Moreover, we test a modified miR-430 Ago2-haipin with 3x phoshorothioate bonds that impairs trimmng. Surprisingly, our data show that trimming of Ago-cleaved pre-miRNAs is not essential for target silencing, indicating that RISC is functional with miRNAs longer than 22-nucleotides. Rescue of MZdicer zebrafish mutant with the injection of trimmable and nontrimmable miR-430 Ago2 hairpins: Transcriptome of wild type, MZdicer mutant, and MZdicer mutant micoinjected with miR-430 duplex, miR-430 (Ago2-haripin), miR-430 (Ago2-haripin 3xPhosphorothioate)
2013-11-13 | E-GEOD-51036 | biostudies-arrayexpress
Project description:Among the four Argonaute family members in mammals, only AGO2 protein retains endonuclease activity, and facilitates cleavage of target RNAs base-pairing with highly complementary guide RNAs. Despite the deeply conserved catalytic activity, only a small number of targets have been reported to extensively base pair with cognate miRNAs to be cleaved by AGO2. Here, we analyzed AGO2-bound RNAs by CrossLinking ImmunoPrecipitation (CLIP) of genetically modified cells that express epitope-tagged AGO2 from the native genomic locus. We found that HMGA2 mRNA is cleaved by AGO2 loaded with let-7 and miR-21. In contrast to the generally accepted notion, the base-pairing from the seed region to the cleavage site, rather than perfect or near perfect complementarity, was required for cleavage of the target mRNA in cells. Non-templated addition of nucleotides at the 3’ end of the cleaved RNA was observed, further supporting the AGO2-mediated cleavage. Based on the observation that the limited complementarity is the minimum requirement for cleavage, we found that AGO2-mediated cleavage of targets is more common than previously thought. Our result may explain the vital role of endonuclease activity in controlling miRNA-mediated gene regulation.
2017-10-05 | GSE93644 | GEO
Project description: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.
2015-09-30 | GSE67992 | GEO