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Homo sapiens

ABSTRACT: DDX54 regulates transcriptome dynamics during DNA damage response [PAR-CLIP]

OTHER RELATED OMICS DATASETS IN: PXD005190PXD005189PXD005188GSE89369PXD005191PXD006093

PROVIDER: PRJNA351890 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR4734792.fastq.gz	Fastqsanger.gz
	SRR4734793.fastq.gz	Fastqsanger.gz
	SRR4734794.fastq.gz	Fastqsanger.gz
	SRR4734795.fastq.gz	Fastqsanger.gz
	SRR4734798.fastq.gz	Fastqsanger.gz

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DDX54 regulates transcriptome dynamics during DNA damage response

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Project description:DDX54 regulates transcriptome dynamics during DNA damage response [RNA-seq2]

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Project description:RNAs have versatile roles in DNA damage repair. We here report RAD51AP1 associated with RNAs by PAR-CLIP.

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Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution

Project description:The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as Crosslinking and Immunoprecipitation (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) in vivo. Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA and for the isolation of RNA crosslinked to RNA-BPs of interest. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.

2022-10-18 | MSV000090547 | MassIVE

PAR-CLIP of Slf1 and Sro9 during optimal growth and oxidative stress

Project description:We quantified the binding sites of the La related RNA-binding proteins Slf1 and Sro9 within RNAs using PAR-CLIP. Datasets were obtained for yeast cells during optimal growth and during the cellular response to peroxide stress.

2023-04-03 | GSE174707 | GEO

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Project description:U1 snRNP regulates alternative polyadenylation in DNA damage response

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A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (CLIP)

Project description:Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365 nm UV light. We found small differences in the accuracy of these methods in identifying binding sites of HuR, a protein that binds low-complexity sequences and Argonaute 2, which has a complex binding specificity. We show that crosslink-induced mutations lead to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect sufficiently their sites under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific ribonucleases strongly biases the set of recovered binding sites. We finally show that this bias can be substantially reduced by milder nuclease digestion conditions. We performed duplicate experiments for each variant of the CLIP protocol (CLIP, PAR-CLIP), each protein (HuR, Ago2), and enzymatic digestion (complete T1 digestion, mild MNase digestion). In addition, we performed a single PAR-CLIP experiment with mild T1 digestion.

2011-05-15 | E-GEOD-28859 | biostudies-arrayexpress

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