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Mapping the targeting transcripts and binding sites of ALKBH5 by individual-nucleotide resolution UV crosslinking and immunoprecipitation-based sequencing (iCLIP-seq)

ABSTRACT: Mapping the targeting transcripts and binding sites of ALKBH5 by individual-nucleotide resolution UV crosslinking and immunoprecipitation-based sequencing (iCLIP-seq)

PROVIDER: PRJNA556264 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9737060.fastq.gz	Fastqsanger.gz
	SRR9737061.fastq.gz	Fastqsanger.gz
	SRR9737062.fastq.gz	Fastqsanger.gz
	SRR9737063.fastq.gz	Fastqsanger.gz

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Mapping the targeting transcripts and binding sites of ALKBH5 by individual-nucleotide resolution UV crosslinking and immunoprecipitation-based sequencing (iCLIP-seq)

Project description:To investigate whether the ALKBH5-mediated metabolic changes via demethylation of its target mRNA(s) is important in regulating viral response, we mapped the targeting transcripts and binding sites of ALKBH5 in the virus infected cells and uninfected cells by using iCLIP-seq. Biological replicates of iCLIP-seq confirmed that OGDH is the direct targeting transcript of ALKBH5 and the binding capacity of ALKBH5 to OGDH mRNA was decreased upon viral infection. By combining the ALKBH5-iCLIP-seq results with m6A-seq data, we identified that there are overlapped ALKBH5-iCLIP peaks and m6A-seq peaks on OGDH mRNA. Furthermore, other mRNAs, such as GOT2 mRNA, were also the ALKBH5’s targeting transcripts and m6A demethylation substrates. GOT2 is an important metabolic enzyme well known to be involved in host response to viral infection. These data demonstrated that ALKBH5-mediated metabolic rewiring via demethylation of target OGDH mRNA and other transcripts is important in regulating cellular viral replication.

2019-08-22 | GSE134754 | GEO

Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

Project description:Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

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U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

Project description:To better understand the mechanism of U1A functions in human cells, we performed U1A iCLIP-seq analysis in HeLa cells. iCLIP-seq is a previously well-established protocol that is believed to detect protein-RNA interaction at individual-nucleotide resolution. Indeed, successful completion of U1A iCLIP-seq has helped us to illuminate more detailed mechanism through which U1 snRNP prevents mRNA PCPA (premature cleavage and polyadenylation)

2020-02-28 | GSE146018 | GEO

U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

Project description:U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

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Identification of Meiotic-P26-bound RNAs in cutlured Drosophila SL2 cells by iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation)

Project description:Identification of Meiotic-P26-bound RNAs in cutlured Drosophila SL2 cells by iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation)

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Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

Project description:Purpose: to identify the AGO1-bound miRNAs and mRNAs in human endothelial cells subject to hypoxic condition (2% oxygen) Methods: human microvascular endothelial cells was cultured under normoxia (20% oxygen) or hypoxia (2%) oxygen for 24 hours. Total RNA was extracted and RNA and small RNA libraries were prepared for Seq. Results: We found substantial changes in AGO1-bound mRNAs due to hypoxia. A portion of CLIP-seq reads also reveal direct binding to miRNA to mRNA. Conclusions: hypoxia induces profound changes in mRNAs associated with AGO1.

2019-09-06 | GSE136907 | GEO

Identifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation

Project description:Identifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation

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iCLIP analysis of EZH2-interacting RNAs

Project description:RNAs directly interacting with EZH2 were isolated from human colorectal HCT116 cells using an in vivo crosslinking and immunoprecipitation strategy (iCLIP, König J et al, Nat Struct Mol Biol 2010) coupled to an ultrasequencing approach.

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Identifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation

Project description:To identify the substrates of METTL5, we used crosslinking-assisted immunoprecipitation of overexpressed, FLAG-METTL5 followed by high throughput sequencing.

2021-05-14 | GSE174435 | GEO

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.

Project description:Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a multifunctional RNA-binding protein that is involved in many different processes, such as regulation of transcription, translation, and RNA stability. We have previously characterized hnRNP L as a global regulator of alternative splicing, binding to CA-repeat, and CA-rich RNA elements. Interestingly, hnRNP L can both activate and repress splicing of alternative exons, but the precise mechanism of hnRNP L-mediated splicing regulation remained unclear. To analyze activities of hnRNP L on a genome-wide level, we performed individual-nucleotide resolution crosslinking-immunoprecipitation in combination with deep-sequencing (iCLIP-Seq). Sequence analysis of the iCLIP crosslink sites showed significant enrichment of C/A motifs, which perfectly agrees with the in vitro binding consensus obtained earlier by a SELEX approach, indicating that in vivo hnRNP L binding targets are mainly determined by the RNA-binding activity of the protein. Genome-wide mapping of hnRNP L binding revealed that the protein preferably binds to introns and 3' UTR. Additionally, position-dependent splicing regulation by hnRNP L was demonstrated: The protein represses splicing when bound to intronic regions upstream of alternative exons, and in contrast, activates splicing when bound to the downstream intron. These findings shed light on the longstanding question of differential hnRNP L-mediated splicing regulation. Finally, regarding 3' UTR binding, hnRNP L binding preferentially overlaps with predicted microRNA target sites, indicating global competition between hnRNP L and microRNA binding. Translational regulation by hnRNP L was validated for a subset of predicted target 3'UTRs.

| S-EPMC3973733 | biostudies-literature

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