IrCLIP-RNP reveals patterns of dynamic protein associations on RNA [CLIP-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1130390 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29661300.fastq.gz | Fastqsanger.gz | |||
| SRR29661400.fastq.gz | Fastqsanger.gz | |||
| SRR29661500.fastq.gz | Fastqsanger.gz | |||
| SRR29661301.fastq.gz | Fastqsanger.gz | |||
| SRR29661401.fastq.gz | Fastqsanger.gz |
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Project description:RNA binding proteins (RBPs) interact with RNA targets to control an array of processes, including RNA splicing, stability, transport, and translation1-3. Dysfunctional RNA-RBP interactions contribute to pathogenesis of a plethora of human diseases1,4,5, underscoring the need for a greater understanding of the nature and dynamics of RNA-protein assemblies. The capacity to study native RNA-dependent protein assemblies in living cells, however, has been limited. To address this, non-isotopic ligation-based ultraviolet crosslinking immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with specific RBPs of interest. irCLIP-RNP defined landscapes of complex and multimeric protein assemblies on RNA, uncovering previously unknown patterns of RBP associations on RNA. This included cell-type-selective patterned relationships between RDAPs and primary RBPs, such as cell context-dependent reciprocal impacts of HNRNPU and NONO on each other’s RDAP landscapes. irCLIP-RNP also defined dynamic RDAP remodeling patterns in response to epidermal growth factor (EGF) and uncovered EGF-induced recruitment of UPF1 adjacent to HNRNPC to effect splicing surveillance of mRNAs that mediate cell proliferation. The development of sequential immunoprecipitation irCLIP (RE-irCLIP) supported the same-RNA-molecule co-localization of irCLIP-RNP-identified associations. Thus, irCLIP-RNP and RE-irCLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.
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Project description:irCLIP-RNP reveals patterns of dynamic protein associations on RNA [RNA-seq]
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