ArticleNucleic acids research2021
A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 49 citations in OpenAlex.
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- CLASHub is an integrated database and analytical platform for microRNA-target interactions.Nature communications · 2026Article
- Repurposed hnRNPC binds mature mRNAs and safeguards the mitotic transcriptome.Nucleic acids research · 2026Article
- U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs.Molecular cell · 2026Article
- The human DEAD-box protein DDX3X regulates host and viral mRNA translation during Sendai Virus infection.bioRxiv : the preprint server for biology · 2026Article
- Single-cell profiling reveals pervasive heterogeneity in subcellular RNA localization.bioRxiv : the preprint server for biology · 2026Article
- PCLIPtools: a robust framework for identifying RNA-protein interaction sites from PAR-CLIP experiments.Nucleic acids research · 2026Article
- RBProximity-CLIP: A Method for Profiling the Interactome of an RNA-Binding Protein at Subcellular Resolution.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution.bioRxiv : the preprint server for biology · 2025Article
- PCLIPtools: A Robust Framework for Identifying RNA-Protein Interaction Sites from PAR-CLIP experiments.bioRxiv : the preprint server for biology · 2025Article
- The MLLT3 YEATS domain is a dual reader of histone marks (H3K9/18/27ac/cr) and ncRNA (7SK), linking epigenetic and RNA signaling to regulate hematopoiesis.bioRxiv : the preprint server for biology · 2025Article
- Identification of RNA binding proteins that mediate a quality control mechanism of splicing.bioRxiv : the preprint server for biology · 2025Article
- Nuclear AGO2 supports influenza A virus replication through type-I interferon regulation.Nucleic acids research · 2025Article
- Transcriptome-Wide Characterization of Protein:RNA Interactions with UV-Crosslinking Immunoprecipitation and Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- reCRAC: A Stringent Method for Precise Mapping of Protein-RNA Interactions in Yeast.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Structural basis of MALAT1 RNA maturation and mascRNA biogenesis.Nature structural & molecular biology · 2024Article
- Nuclear PKM2 binds pre-mRNA at folded G-quadruplexes and reveals their gene regulatory role.Molecular cell · 2024Article
- Viral hijacking of hnRNPH1 unveils a G-quadruplex-driven mechanism of stress control.Cell host & microbe · 2024Article
- Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference.Nucleic acids research · 2024Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Crosslinking and immunoprecipitation (CLIP) methods are powerful techniques to interrogate direct protein-RNA interactions and dissect posttranscriptional gene regulatory networks. One widely used CLIP variant is photoactivatable ribonucleoside enhanced CLIP (PAR-CLIP) that involves in vivo labeling of nascent RNAs with the photoreactive nucleosides 4-thiouridine (4SU) or 6-thioguanosine (6SG), which can efficiently crosslink to interacting proteins using UVA and UVB light. Crosslinking of 4SU or 6SG to interacting amino acids changes their base-pairing properties and results in characteristic mutations in cDNA libraries prepared for high-throughput sequencing, which can be computationally exploited to remove abundant background from non-crosslinked sequences and help pinpoint RNA binding protein binding sites at nucleotide resolution on a transcriptome-wide scale. Here we present a streamlined protocol for fluorescence-based PAR-CLIP (fPAR-CLIP) that eliminates the need to use radioactivity. It is based on direct ligation of a fluorescently labeled adapter to the 3'end of crosslinked RNA on immobilized ribonucleoproteins, followed by isolation of the adapter-ligated RNA and efficient conversion into cDNA without the previously needed size fractionation on denaturing polyacrylamide gels. These improvements cut the experimentation by half to 2 days and increases sensitivity by 10-100-fold.
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