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ABSTRACT: RNA associated with RNA helicase CrhR K57A mutant (UV-crosslinking experiment)

PROVIDER: PRJNA627099 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11578961_1.fastq.gz	Fastqsanger.gz
	SRR11578961_2.fastq.gz	Fastqsanger.gz
	SRR11578962_1.fastq.gz	Fastqsanger.gz
	SRR11578962_2.fastq.gz	Fastqsanger.gz
	SRR11578963_1.fastq.gz	Fastqsanger.gz

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Project description:RNA associated with RNA helicase CrhR (UV-crosslinking experiment)

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Defining the RNA Interactome by Total RNA-Associated Protein Purification

Project description:UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), relies on SILAC labelling to quantify RNA-associated protein recovery in the presence and absence of irradiation. We utilised TRAPP to study alterations in RNA-protein interactions upon exposure to weak acid stress in yeast. In addition, as UV irradiation induces short distance crosslinks between proteins and nucleic acids, the identity of crosslinked amino acids reveals the exact protein-RNA interacting interface. Precise sites of crosslinking at the level of individual amino acids (iTRAPP) were identified following phospho-peptide enrichment combined with a bioinformatic pipeline (Xi).

2019-03-26 | PXD011071 | Pride

RBM33 eCLIP

Project description:Enhanced UV crosslinking immunoprecipitation (eCLIP) was performed to identify direct RNA targets of RBM33

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iCLIP and NGS to map protein-RNA interactions for U1-snRNP proteins in Trypanosoma brucei

Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was performed to generate genome-wide binding maps of two U1-snRNP proteins: U1C and U1-70K in Trypanosoma brucei. 3 (2) biological replicates of U1C (U1-70K) -specific co-immunoprecipitated RNA after UV-crosslinking

2014-05-16 | E-GEOD-43848 | biostudies-arrayexpress

Regulation of alternative splicing by C9ORF78, a novel BRR2 interactor II

Project description:The RNA helicase BRR2 (SNRNP200) is one of the key remodeling factors of the spliceosome. Here we show its direct interaction with C9ORF78, a poorly characterized protein predicted to be largely intrinsically disordered. We present cryo-EM structures showing how C9ORF78 and the spliceosomal B-complex protein FBP21 wrap around the C-terminal helicase cassette of BRR2 and that binding of the two proteins is mutually exclusive. C9ORF78 associates with the spliceosome, as we confirm via proteomics and RNA UV-crosslinking. An siRNA mediated C9ORF78 knockdown reveals changes in alternative splicing of specific target pre-mRNAs, which in part depend on its interaction with BRR2. In particular, C9ORF78 regulates a substantial number of alternative 3’ splice sites, which might be facilitated through an additional interaction with human PRP22 (DHX8).

2021-12-31 | GSE189362 | GEO

Regulation of alternative splicing by a novel BRR2 interactor C9ORF78

2022-02-04 | GSE176464 | GEO

Regulation of alternative splicing by C9ORF78, a novel BRR2 interactor

2021-12-31 | GSE176517 | GEO

Individual-nucleotide resolution CLIP and high-throughput sequencing to map hnRNP L-RNA interactions in HeLa cells

Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of hnRNP L. Supplementary file GSE37560_hnRNPL_crosslink_site.bed includes filtered crosslink sites of hnRNPL: combining data from all 3 experiments. 3 biological replicates of hnRNP L-specific and control (Flag) co-immunoprecipitated RNA after UV-crosslinking in HeLa cells

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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).

2021-07-21 | GSE114825 | GEO

Enhanced RNA interactome capture (eRIC) of human malignant bone tumor cells and normal bone/mesenchymal cells

Project description:Patient-derived bone tumor (osteosarcoma and giant cell tumor of bone) cells, and the normal mesenchymal stem cells and osteoblasts were cultured and subjected to UV crosslinking (UV) at 254 nm or without crosslinking (noUV) as negative controls. Subsequently, RNA-binding proteins (RBPs) were identified by eRIC.

2024-02-28 | PXD038185 | Pride

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