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

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

PROVIDER: PRJNA472770 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7207800.fastq.gz	Fastqsanger.gz
	SRR7207791.fastq.gz	Fastqsanger.gz
	SRR7207801.fastq.gz	Fastqsanger.gz
	SRR7207792.fastq.gz	Fastqsanger.gz
	SRR7207802.fastq.gz	Fastqsanger.gz

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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).

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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).

2018-08-17 | GSE114680 | GEO

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Mapping targets for small nucleolar RNAs in human cells

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Mapping targets for small nucleolar RNAs in human cells [RNA-seq]

Project description:Mapping targets for small nucleolar RNAs in human cells [RNA-seq]

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Mapping targets for small nucleolar RNAs in yeast.

Project description:Background: Recent analyses implicate changes in the expression of the box C/D class of small nucleolar RNAs (snoRNAs) in several human diseases. Methods: Here 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) with the snoRNP proteins Nop1, Nop56 and Nop58. We also developed a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions. Results: We recovered 241,420 hybrids, out of which 190,597 were classed as reproducible, high energy hybrids. As expected, the majority of snoRNA interactions were with the ribosomal RNAs (rRNAs). Following filtering, 117,047 reproducible hybrids included 51 of the 55 reported rRNA methylation sites. The majority of interactions at methylation sites were predicted to guide methylation. However, competing, potentially regulatory, binding was also identified. In marked contrast, following CLASH performed with the RNA helicase Mtr4 only 7% of snoRNA-rRNA interactions recovered were predicted to guide methylation. We propose that Mtr4 functions in dissociating inappropriate snoRNA-target interactions. Numerous snoRNA-snoRNA interactions were recovered, indicating potential cross regulation. The snoRNAs snR4 and snR45 were recently implicated in site-directed rRNA acetylation, and hybrids were identified adjacent to the acetylation sites. We also identified 1,368 reproducible snoRNA-mRNA interactions, representing 448 sites of interaction involving 39 snoRNAs and 382 mRNAs. Depletion of the snoRNAs U3, U14 or snR4 each altered the levels of numerous mRNAs. Targets identified by CLASH were over-represented among these species, but causality has yet to be established. Conclusions: Systematic mapping of snoRNA-target binding provides a catalogue of high-confidence binding sites and indicates numerous potential regulatory interactions.

| S-EPMC6171561 | biostudies-literature

Screening of miR-379 target RNAs by comparison of WT and miR-379 KO mouse primary kidney mesangial cells by using CLASH technique [CLASH-Seq]

Project description:We screened for miR-379 targets in primary mesangial cells from wild-type vs. miR-379KO mice using unbiased CLASH sequencing approach and identified the redox protein thioredoxin (Txn1) and mitochondrial fission-1 protein (Fis1).

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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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