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Cross-linking ligation and sequencing of hybrids (qCLASH) reveals an unpredicted miRNA targetome in melanoma cells

ABSTRACT: Cross-linking ligation and sequencing of hybrids (qCLASH) reveals an unpredicted miRNA targetome in melanoma cells

PROVIDER: PRJEB35798 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3761153.fastq.gz	Fastqsanger.gz
	ERR3761154.fastq.gz	Fastqsanger.gz
	ERR3761155.fastq.gz	Fastqsanger.gz

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Similar Datasets

Cross-linking ligation and sequencing of hybrids (qCLASH) reveals an unpredicted miRNA targetome in melanoma cells

Project description:In the quick cross-linking ligation and sequencing of hybrids (qCLASH) protocol, RNA-protein (RNP) complexes of interest are UV cross-linked in living cells. The protein of interest is purified by immunoprecipitation (in this case, AGO bound to the miRNA and the target gene). The two interacting RNA molecules (e.g. miRNA-mRNA) are physically bound to each other by intermolecular RNA-RNA ligation, followed by library preparation and sequencing oh hybrids.

2020-12-15 | E-MTAB-8591 | biostudies-arrayexpress

Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells.

Project description:MicroRNAs are key post-transcriptional gene regulators often displaying aberrant expression patterns in cancer. As microRNAs are promising disease-associated biomarkers and modulators of responsiveness to anti-cancer therapies, a solid understanding of their targetome is crucial. Despite enormous research efforts, the success rates of available tools to reliably predict microRNAs (miRNA)-target interactions remains limited. To investigate the disease-associated miRNA targetome, we have applied modified cross-linking ligation and sequencing of hybrids (qCLASH) to BRAF-mutant melanoma cells. The resulting RNA-RNA hybrid molecules provide a comprehensive and unbiased snapshot of direct miRNA-target interactions. The regulatory effects on selected miRNA target genes in predicted vs. non-predicted binding regions was validated by miRNA mimic experiments. Most miRNA-target interactions deviate from the central dogma of miRNA targeting up to 60% interactions occur via non-canonical seed pairing with a strong contribution of the 3' miRNA sequence, and over 50% display a clear bias towards the coding sequence of mRNAs. miRNAs targeting the coding sequence can directly reduce gene expression (miR-34a/CD68), while the majority of non-canonical miRNA interactions appear to have roles beyond target gene suppression (miR-100/AXL). Additionally, non-mRNA targets of miRNAs (lncRNAs) whose interactions mainly occur via non-canonical binding were identified in melanoma. This first application of CLASH sequencing to cancer cells identified over 8 K distinct miRNA-target interactions in melanoma cells. Our data highlight the importance non-canonical interactions, revealing further layers of complexity of post-transcriptional gene regulation in melanoma, thus expanding the pool of miRNA-target interactions, which have so far been omitted in the cancer field.

| S-EPMC7961530 | biostudies-literature

Modified cross-linking, ligation, and sequencing of hybrids (qCLASH) identifies KSHV microRNA targets in endothelial cells

Project description:KS lesions consist of endothelial cells latently infected with KSHV which express the KSHV miRNAs. Identifying the targets of the KSHV miRNAs will help us understand their role in viral oncogenesis. Cross-Linking and Sequencing of Hybrids (CLASH) is a method for unambiguously identifying miRNA targetomes. We developed a streamlined version of CLASH, called quick CLASH (qCLASH). qCLASH requires a lower initial input of cells than its parent protocol. Additionally, a new fast-growing KSHV-negative endothelial cell line, named TIVE-EX-LTC cells, was established. qCLASH was performed on TIVE-EX-LTC cells latently infected with WT KSHV or a mutant virus lacking miR-K12-11/11*. A number of novel targets of the KSHV miRNAs were identified, including targets of miR-K12-11, the ortholog of cellular oncomiR miR-155. Many of the miRNA targets were involved in processes related to oncogenesis, such as glycolysis, angiogenesis, and cell cycle control.

2018-01-25 | GSE101978 | GEO

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast.

Project description:Many protein-protein and protein-nucleic acid interactions have been experimentally characterized, whereas RNA-RNA interactions have generally only been predicted computationally. Here, we describe a high-throughput method to identify intramolecular and intermolecular RNA-RNA interactions experimentally by cross-linking, ligation, and sequencing of hybrids (CLASH). As validation, we identified 39 known target sites for box C/D modification-guide small nucleolar RNAs (snoRNAs) on the yeast pre-rRNA. Novel snoRNA-rRNA hybrids were recovered between snR4-5S and U14-25S. These are supported by native electrophoresis and consistent with previously unexplained data. The U3 snoRNA was found to be associated with sequences close to the 3' side of the central pseudoknot in 18S rRNA, supporting a role in formation of this structure. Applying CLASH to the yeast U2 spliceosomal snRNA led to a revised predicted secondary structure, featuring alternative folding of the 3' domain and long-range contacts between the 3' and 5' domains. CLASH should allow transcriptome-wide analyses of RNA-RNA interactions in many organisms.

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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.

2020-08-01 | GSE147228 | GEO

single step cross-linking ChIP-seq

Project description:single step cross-linking ChIP-seq

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two steps cross-linking ChIP-seq

Project description:two steps cross-linking ChIP-seq

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High-throughput identification of miRNA targets using CLASH (crosslinking, ligation and sequencing of hybrids)

Project description:High-throughput identification of miRNA targets using CLASH (crosslinking, ligation and sequencing of hybrids)

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

Project description:We profiled EZH2-RNA interactions using formaldehyde/UV assisted cross-linking ligation and sequencing of hybrids (FLASH-seq) in primary human ECs. Transcriptome-wide EZH2-associated ncRNAs and RNA–RNA interactome were obtained.

2024-04-12 | GSE230112 | GEO

Salvelinus Microarray experiment: cross-specific transcriptome in hybrids

Project description:The genetic mechanisms underlying hybridization are poorly understood despite their potentially important roles in speciation processes, adaptative evolution, and agronomical innovation. In this study, transcription profiles were compared among three populations of brook charr and their hybrids using microarrays to assess the influence of hybrid origin on modes of transcription regulation inheritance and on the mechanisms underlying growth. We found that twice as many transcripts were differently expressed between the domestic strain and the two wild populations (Rupert and Laval) than between wild ones, despite their deeper genetic distance. This could reflect the consequence of artificial selection during domestication. We detected that hybrids exhibited strikingly different patterns of mode of transcription regulation, being mostly additive (94%) for domestic × Rupert, and non-additive for Laval × domestic (45.7%) and Rupert × Laval hybrids (37.5%). Both heterosis and outbreeding depression for growth were observed among the crosses. Our results indicated that prevalence of dominance in transcription regulation seems related to growth heterosis, while prevalence of transgressive transcription regulation may be more related to outbreeding depression. Our study clearly shows, for the first time in vertebrates, that the consequences of hybridization on both the transcriptome level and the phenotype are highly dependent on the specific genetic architectures of crossed populations and therefore hardly predictable. Comparison between six crosses using a loop design: direct comparison of hybrids vs parental populations fishes for 8 families. Each individual was technically replicated on two bi-coloured distinct microarrays and dye-swapped.

2010-07-01 | E-GEOD-22008 | biostudies-arrayexpress

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