ReviewMethods (San Diego, Calif.)2019
Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.
Review in Methods (San Diego, Calif.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 20 citations in OpenAlex.
- let-7 miRNA and lin-46 mRNA are essential targets of the LIN28 RNA-binding protein in Caenorhabditis elegans developmental timing regulation.PLoS biology · 2026Article
- NUDT21 Drives T-Cell Acute Lymphoblastic Leukemia Through Dual Regulation of Alternative Polyadenylation and Transcriptional Activation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.RNA biology · 2025Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- Article
- KSHV promotes oncogenic FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation.bioRxiv : the preprint server for biology · 2024Article
- Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs.Genome biology · 2023Article
- A congenital hydrocephalus-causing mutation in Trim71 induces stem cell defects via inhibiting Lsd1 mRNA translation.EMBO reports · 2023Article
- Different congenital hydrocephalus-associated mutations in Trim71 impair stem cell differentiation via distinct gain-of-function mechanisms.PLoS biology · 2023Article
- Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding.Cell reports methods · 2021Article
- Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Frontiers in plant science · 2021Review
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
RNA-binding proteins are important players in post-transcriptional regulation, such as modulating mRNA splicing, translation, and degradation under diverse biological settings. Identifying and characterizing the RNA substrates is a critical step in deciphering the function and molecular mechanisms of the target RNA-binding proteins. High-throughput sequencing of the RNA fragments isolated by crosslinking immunoprecipitation (CLIP-seq) is one of the standard techniques to identify the in vivo transcriptome-wide binding sites of the target RNA-binding protein. This method is widely used in functional and mechanistic characterizations of RNA-binding proteins. In this review, we provide several practical considerations on performing and analyzing CLIP-seq experiments. Particularly, we focus on how to perform CLIP-seq experiments on endogenous RNA-binding proteins. In addition, we provide a practical summary on how to choose and use computational pipelines from an increasing number of computational methods and packages that are available for analyzing the sequencing datasets from the CLIP-seq experiments. We hope these practical considerations will facilitate experimental biologists in performing and analyzing CLIP-seq experiment to obtain biologically relevant mechanistic insights.
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