ReviewMethods (San Diego, Calif.)2017
Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins.
Review in Methods (San Diego, Calif.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed.
- LncPTPred: predicting lncRNA-protein interaction based on crosslinking and immunoprecipitation (CLIP-Seq) data.Briefings in bioinformatics · 2025Article
- Molecular insights into regulatory RNAs in the cellular machinery.Experimental & molecular medicine · 2024Review
- Role of Optimization in RNA-Protein-Binding Prediction.Current issues in molecular biology · 2024Article
- PAR-dCLIP: Enabling detection of RNA binding protein target transcripts bound at 5' termini through the incorporation of a decapping step.Methods in enzymology · 2024Article
- Bioinformatics analysis of markers based on m6A related to prognosis combined with immune invasion of rectal adenocarcinoma.Cancer biomarkers : section A of Disease markers · 2024Article
- Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells.RNA (New York, N.Y.) · 2023Article
- Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP.Nucleic acids research · 2023Article
- In vivo PAR-CLIP (viP-CLIP) of liver TIAL1 unveils targets regulating cholesterol synthesis and secretion.Nature communications · 2023Article
- A selective and sensitive detection system for 4-thiouridine modification in RNA.RNA (New York, N.Y.) · 2023Article
- Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives.Frontiers in molecular biosciences · 2023Review
- PAR-CLIP Assay in Ferroptosis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins.Nature communications · 2022Article
- The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7.Nucleic acids research · 2022Article
- ELAVL1 primarily couples mRNA stability with the 3' UTRs of interferon-stimulated genes.Cell reports · 2021Article
- RTEL1 influences the abundance and localization of TERRA RNA.Nature communications · 2021Article
- Convergence of mammalian RQC and C-end rule proteolytic pathways via alanine tailing.Molecular cell · 2021Article
- A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol.Nucleic acids research · 2021Article
- Analysis of RNA-protein networks with RNP-MaP defines functional hubs on RNA.Nature biotechnology · 2021Article
- Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing.Computational and structural biotechnology journal · 2021Review
- Crucial roles of different RNA-binding hnRNP proteins in Stem Cells.International journal of biological sciences · 2021Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in combination with next-generation sequencing is a powerful method for identifying endogenous targets of RNA-binding proteins (RBPs). Depending on the characteristics of each RBP, key steps in the PAR-CLIP procedure must be optimized. Here we present a comprehensive step-by-step PAR-CLIP protocol with detailed explanations of the critical steps. Furthermore, we report the application of a new PAR-CLIP data analysis pipeline to three distinct RBPs targeting different annotation categories of cellular RNAs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.