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Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP [dataset 2]

ABSTRACT: Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP [dataset 2]

PROVIDER: PRJNA935340 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23476216_1.fastq.gz	Fastqsanger.gz
	SRR23476216_2.fastq.gz	Fastqsanger.gz
	SRR23476217_1.fastq.gz	Fastqsanger.gz
	SRR23476217_2.fastq.gz	Fastqsanger.gz
	SRR23476218_1.fastq.gz	Fastqsanger.gz

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Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP [dataset 1]

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Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP [dataset 2]

Project description:RNA-binding proteins are instrumental for post-transcriptional gene regulation, yet transcriptome-wide methods to profile RNA-protein interactions remain technically challenging. We present an improved library preparation strategy for cross-linking and immunoprecipitation (CLIP) that involves tailing and ligation of cDNA molecules (TLC) for increased sensitivity and efficiency. TLC-CLIP eliminates time-consuming purifications, reduces sample loss, and minimises experimental steps, allowing precise profiling of RNA-protein interactions from limited starting material at nucleotide resolution.

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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.

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Subcellular refinement of RNA binding protein target interactions with colocalization CLIP [CLIP-seq]

Project description:RNA binding proteins (RBPs) are essential for RNA metabolism and have profound impacts in both health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP, a method that combines CrossLinking and ImmunoPrecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the well-studied RNA-binding protein HuR. Using this method, we uncover HuR's dynamic and location-specific interactions with RNA, revealing alterations in sequence preferences and interactions in the nucleus, cytosol, or stress granule compartments. We uncover HuR's unique binding preferences within stress granules during arsenite stress, illuminating intricate interactions that conventional methodologies cannot capture. Overall, coCLIP provides a powerful method for revealing RBP:RNA interactions based on localization, and lays the foundation for an advanced understanding of RBP models that incorporate subcellular location as a critical determinant of their functions.

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