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

ABSTRACT: 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).

ORGANISM(S): Homo sapiens

PROVIDER: GSE114825 | GEO | 2021/07/21

REPOSITORIES: GEO

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Mapping targets for small nucleolar RNAs in yeast

Project description:We report the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH).

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

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

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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.

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PAS-CLASH (PolyA Site-Crosslinking, Ligation and Sequencing of the Hybrid) analysis to detect RNA-RNA interaction at poly(A) site region

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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.

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Histone H3K27 methyltransferase EZH2 interacts with MEG3-lncRNA to directly regulate integrin signaling and endothelial cell function

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

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The EBV microRNA targetome

Project description:In EBV-associated tumors, such as gastric cancer (GC) and Burkitt’s lymphoma (BL), a high proportion of microRNAs are virally encoded. To explore the targets of both viral and host microRNAs, we performed Crosslinking, Ligation, and Sequencing of Hybrids (CLASH). With this approach, we were able to quantify each Argonaute-bound microRNA-mRNA interaction in a GC (SNU719), and BL (Akata) cell line.

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