![]() ![]() A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Human plasma and serum extracellular small RNA reference profiles and their clinical utility. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. This is the first plant iCLIP study and identifies RNA-binding partners of an hnRNP-like protein in the reference plant A. Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7. Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation. In vivo and transcriptome-wide identification of RNA binding protein target sites. This study gives a detailed description of the CLIP protocol, establishes the CLIP workflow and explains the stages of RNase optimization, SDS-PAGE purification conditions and cDNA library preparation that are used by most later variants. CLIP: a method for identifying protein–RNA interaction sites in living cells. Advances in CLIP technologies for studies of protein–RNA interactions. Methods to study RNA–protein interactions. Beyond CLIP: advances and opportunities to measure RBP–RNA and RNA–RNA interactions. In this study, subcellular compartment-specific proximity labelling is combined with CLIP to monitor RNA–protein interactions at specific locations in the cell. Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments. This study establishes a method to identify RNA binding sites of RBPs through fusion with ADARcd and analysis of RNA editing. TRIBE: hijacking an RNA-editing enzyme to identify cell-specific targets of RNA-binding proteins. This study reviews computational methods and presents the analysis of RNA splicing maps as a way to assess the sensitivity and specificity of CLIP data. Data science issues in studying protein–RNA interactions with CLIP technologies. M., Haberman, N., Praznik, A., Luscombe, N. This study describes the development of iCLIP, which enables amplification of truncated cDNAs and identification of cross-link sites with analysis of truncations. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. This study describes the development of PAR-CLIP, which enables identification of cross-link sites from the nucleotide substitutions in the sequenced cDNAs. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. This study introduces HITS-CLIP and validates the RNA map of splicing regulation by Nova proteins. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. CLIP identifies Nova-regulated RNA networks in the brain. Reversible cross-linking combined with immunoprecipitation to study RNA–protein interactions in vivo. Niranjanakumari, S., Lasda, E., Brazas, R.Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus. RNA-binding proteins in human genetic disease. Gebauer, F., Schwarzl, T., Valcárcel, J.Finally, we present open questions in the field and give directions for further development and applications. We discuss the prospect of integrating data obtained by CLIP with complementary methods to gain a comprehensive view of RNP assembly and remodelling, unravel the spatial and temporal dynamics of RNPs in specific cell types and subcellular compartments and understand how defects in RNPs can lead to disease. We outline the various applications of CLIP and available databases for data sharing. We summarize the main challenges of computational CLIP data analysis, how to handle various sources of background and how to identify functionally relevant binding regions. In this Primer, we discuss the main variants of these protein-centric methods and the strategies for their optimization and quality assessment, as well as RNA-centric methods that identify the protein partners of a specific RNA. To identify the sites bound by a specific RNA-binding protein on endogenous RNAs, cross-linking and immunoprecipitation (CLIP) and complementary, proximity-based methods have been developed. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA, coordinates all processes in which the RNA is involved. RNA molecules start assembling into ribonucleoprotein (RNP) complexes during transcription. ![]()
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