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Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation [CLASH-seq]

ABSTRACT: Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation [CLASH-seq]

PROVIDER: PRJNA915020 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22863835.fastq.gz	Fastqsanger.gz
	SRR22863836.fastq.gz	Fastqsanger.gz
	SRR22863837.fastq.gz	Fastqsanger.gz

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Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation [CLASH-seq]

Project description:Here we present the CLASH analysis of AGO2 in HEK293 cells to address the small RNA repertoire and uncover their physiological targets. We developed an optimized bioinformatics approach of chimeric read identification to detect chimeras of high confidence. We report thousands of Ago2 target sites driven by microRNAs, but also a substantial number of Ago2 ‘drivers’ derived from fragments of other small RNAs such as tRNAs, snoRNAs, rRNAs and others. Target validation of several miRNAs delivered by 3’ Quantseq RNA-Seq.

2023-12-24 | GSE221572 | GEO

Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation [RNA-Seq]

2023-12-24 | GSE221573 | GEO

Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation

Project description:Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation

| PRJNA915014 | ENA

Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation [RNA-Seq]

Project description:Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation [RNA-Seq]

| PRJNA915022 | ENA

Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation

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

2023-12-24 | GSE221574 | GEO

Mapping targets for small nucleolar RNAs in human cells [CLASH/FLASH]

Project description:We report the identification of potential novel RNA targets for box C/D snoRNAs in human HEK293 cells, using the approaches of UV crosslinking and sequencing of hybrids (CLASH), and formaldehyde crosslinking and sequencing of hybrids (FLASH).

2021-07-21 | GSE114825 | GEO

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation [CLASH]

Project description:By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences. The sRNA-mRNA interactions identified by CLASH have strong base-pairing potential and are highly enriched for complementary sequence motifs, even those supported by only a few reads. Yet, steady state levels of most mRNA targets were not significantly affected upon over-expression of the sRNA regulator. Our results reinforce the idea that the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a regulatory outcome.

2020-05-01 | GSE123049 | GEO

CLASH for 15.5K and FBL proteins in HEK293T cells

Project description:We performed CLASH for 15.5K and FBL in HEK293T cells which overexpressed 15.5K and FBL, respectively.

2023-04-10 | GSE160636 | GEO

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation [CLASH]

Project description:Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation [CLASH]

| PRJNA507415 | ENA

The nuclear receptor ERbeta engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading

Project description:Background: The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNAsilencing pathways, exerting a pivotal role in microRNA maturation and activity, that in the cell nucleus is able to modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. The Estrogen Receptor beta (ERβ), a member of the nuclear receptor superfamily of trancriptional regulators, is endowed with oncosuppressive activities, antagonizing hormone-induced carcinogenesis and inhibiting growth and oncogenic functions in luminal-like breast cancers (BCs), where its expression correlates with a better prognosis of the disease. Results: Applying interaction proteomics coupled to mass spectrometry (MS) to characterize nuclear factors cooperating with ERβ in gene regulation, we identified AGO2 as a novel partner of ERβ in human BC cells. ERβ-AGO2 association was confirmed in vitro and in vivo both in the nucleus and cytoplasm. ChIP-Seq demonstrated AGO2 association to a large number of ERβ binding sites, and total and nascent RNA-Seq in ERβ+ vs ERβ- cells, and before and after AGO2 knock-down in ERβ+ cells, revealed a widespread involvement of this factor in ERβ-mediated regulation of gene transcription rate and RNA splicing. Moreover, isolation and sequencing by RIP-Seq of ERβ-associated long and small RNAs in the cytoplasm suggested involvement of the nuclear receptor in RISC loading, indicating that it may able to control directly also mRNA translation efficiency and stability. Conclusions: These results demonstrate that AGO2 is a pleiotropic functional partner of ERβ in BC cells, indicating that both factors are endowed with multiple roles in the control of BC cell functions.

2017-09-20 | PXD006280 | Pride

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