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AGO2 slicing of a domesticated retrotransposon is necessary for normal mammalian vasculature [RNA-Seq]

ABSTRACT: Argonaute (AGO) mediated slicing of RNA—also known as RNAi—is a highly conserved phenomenon that is evolutionarily linked to the repression of transposons and other repeats. Although RNAi is no longer a major mechanism of repeat control in mammals, AGO2 has retained cleavage competence and is able to efficiently cut RNAs with extensive complementarity to a bound guide. The regulatory roles this activity plays in mammals however remains poorly understood. Here we show that mice carrying two catalytically inactive Ago2 alleles have extensive developmental abnormalities including systemic vascular defects that are characterized by enlarged and leaky vessels and stem from endothelial cell dysfunction. Endothelial cell defects are caused by failure to repress Rtl1, a paternally-imprinted domesticated retrotransposon, whose cleavage in wild-type animals is triggered by miRNAs of the maternally-imprinted miR-433~127 cluster. Our data pinpoint an essential mRNA cleavage target of AGO2 and suggest that the repurposing of a TE-Argonaute regulatory interaction contributes to the retention of AGO catalytic competence in mammals.

ORGANISM(S): Mus musculus

PROVIDER: GSE291207 | GEO | 2025/03/10

REPOSITORIES: GEO

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AGO2 slicing of a domesticated retrotransposon is necessary for normal mammalian vasculature [smRNA-Seq]

Project description:Argonaute (AGO) mediated slicing of RNA—also known as RNAi—is a highly conserved phenomenon that is evolutionarily linked to the repression of transposons and other repeats. Although RNAi is no longer a major mechanism of repeat control in mammals, AGO2 has retained cleavage competence and is able to efficiently cut RNAs with extensive complementarity to a bound guide. The regulatory roles this activity plays in mammals however remains poorly understood. Here we show that mice carrying two catalytically inactive Ago2 alleles have extensive developmental abnormalities including systemic vascular defects that are characterized by enlarged and leaky vessels and stem from endothelial cell dysfunction. Endothelial cell defects are caused by failure to repress Rtl1, a paternally-imprinted domesticated retrotransposon, whose cleavage in wild-type animals is triggered by miRNAs of the maternally-imprinted miR-433~127 cluster. Our data pinpoint an essential mRNA cleavage target of AGO2 and suggest that the repurposing of a TE-Argonaute regulatory interaction contributes to the retention of AGO catalytic competence in mammals.

2025-03-10 | GSE291208 | GEO

Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference

Project description:In mammals, RNA interference (RNAi) is mostly studied as a cytoplasmic event, however, numerous reports convincingly show nuclear localization of the AGO proteins. Nevertheless, the mechanism of nuclear entry remains to be fully elucidated, and the extent of nuclear RNAi further explored. We found that reduced Lamin A levels significantly induced nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. The translocation of AGO2 was accompanied by aggravated cell proliferation and we further found that the loss of Lamin A leads to EGFR and Src kinase activation, which regulates the turnover and stability of cytoplasmic AGO2. Furthermore, Lamin A KO significantly reduced the activity of nuclear RNAi. This was evident by AGO fPAR-CLIP in WT and Lamin A KO cells, where we observed ca 60% less efficiency of RNAi. Mass spectrometry of AGO interactome, from the nuclear fraction, indicated that AGO2 is in complex with FAM120A, a known interactor of AGO2 that reduces the activity of RNAi by competing with AGO2 transcript binding. Therefore, loss of Lamin A starts a signaling cascade that mediates nuclear AGO2 translocation to rapidly inhibit RNAi in order to facilitate cancer proliferation

2024-10-17 | PXD042899 | Pride

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases

Project description:Messenger RNAs are regulated by a variety of degradation mechanisms in mammalian cells. In the canonical animal microRNA pathway, microRNAs in complex with Argonaute proteins bind to many mRNA targets with imperfect complementarity, leading to degradation of the mRNA through the regular decay machinery. The ancestral “slicer” endonuclease activity of Argonaute2 itself, which requires more extensive complementarity with the target RNA, is not used in this pathway, and has only been observed in two microRNA-guided cases. Nevertheless, the cleavage capacity of mammalian Ago2 is conserved and essential for viability. Here, we assess the endonucleolytic function of Ago2 and other nucleases by identifying cleavage products retaining 5`-phosphate groups in mouse ES cells on a transcriptome-wide scale. We detect a significant signature of Ago2-dependent cleavage events and validate several targets. Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in this mode of mRNA regulation. Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events, including one in the Dgcr8 mRNA, that functionally regulate mRNA levels in mES cells. Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals. Global 5`-phosphate-dependent RACE in WT, Ago2-KO and Drosha-excised mouse ES cells and human 293S cells

2010-06-25 | E-GEOD-21975 | biostudies-arrayexpress

Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference

Project description:In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event, however, in the last decade growing number of reports convincingly show nuclear localization of the AGO proteins. Nevertheless, the mechanism and the extent of nuclear RNAi remains to be fully elucidated. We found that reduced Lamin A levels significantly induced nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 evident by changes in cell morphology, increased cell proliferation and oncogenic miRNA expression. Furthermore, in SHSY5Y cells, AGO fPAR-CLIP in Lamin A KO cells revealed significantly reduced activity of RNAi. Further exploration of the nuclear AGO interactome by mass spectrometry indicated that AGO2 is in complex with FAM120A, an RNA binding protein and known interactor of AGO2. By performing FAM120A fPAR-CLIP we discovered that FAM120A co-binds AGO targets and that this competition reduces the activity of RNAi. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, RNAi impairment and selective upregulation of oncogenic miRNAs to facilitate cancer cell proliferation.

2024-03-21 | GSE261593 | GEO

Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference

2024-03-21 | GSE261422 | GEO

Loss of Lamin A leads to nuclear translocation of AGO2 mediated by EGFR signaling and inactivation of RNAi

Project description:In mammals, RNA interference (RNAi) is mostly studied as a cytoplasmic event, however, numerous reports convincingly showed nuclear localization of AGO proteins. Nevertheless, the mechanism of the nuclear entry remains to be fully elucidated, and the extent of nuclear RNAi explored. The nuclear import of large proteins requires active transport through the nuclear envelope (NE). Therefore, we hypothesized that the NE, and its composition, is important for nuclear AGO2 translocation. Lamin A knockout significantly induced nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cells. We unravelled that the loss of Lamin A leads to EGFR and Src kinase activation, which regulates the turnover and stability of cytoplasmic specifically AGO2. Furthermore, EGFR mediated phosphorylation at Y393 inhibits the activity of nuclear RNAi. This was evident by AGO fPAR-CLIP in WT and KO cells, where we observed a decrease in RNAi potential. Mass spectrometry of AGO interactome, from the nuclear fraction, indicated that AGO2 is in complex with FAM120A, which may further reduced the activity of RNAi by competing with AGO2 transcript binding. Therefore, loss of Lamin A starts a signalling cascade that mediates nuclear AGO2 translocation to rapidly inhibit RNAi.

2023-06-22 | GSE235156 | GEO

miRNAs associated with the different human Argonaute proteins

Project description:microRNAs (miRNAs) are small non-coding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3’ untranslated region (UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer-independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected. Examination of miRNAs associated with endogenous human Ago1-4 in HeLa cells

2013-03-29 | E-GEOD-45506 | biostudies-arrayexpress

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases

2010-06-25 | GSE21975 | GEO

PARN mediates 3'-end trimming of Argonaute-cleaved precursor microRNAs

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

Antiviral RNA interference in mammalian cells

Project description: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. Here, we detect the accumulation of phased Dicer-dependent virus-derived siRNA (viRNAs) and demonstrate their loading into Ago2 after infection of mouse embryonic stem (ES) cells with Encephalomyocarditis virus (EMCV). We further show that the production of these viRNAs is drastically reduced, yet not completely abolished, if ES cells are first induced to differentiate before infection. Finally, we reveal that the mammalian virus Nodamura virus (NoV) encodes for a protein that counteracts such antiviral RNAi in ES cells supporting the existence of an effective RNAi-based immunity in mammals.

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