ArticleGenome biology2014
Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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Who cites it
80 citing papers in PubMed, 124 citations in OpenAlex.
- miR-29b as an Anti-Fibrotic Therapeutic: Mechanisms, Disease Biology and Translational Opportunities.Cells · 2026Review
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo.Molecular cell · 2024Article
- Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.Analytical chemistry · 2024Article
- Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human.Nature genetics · 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
- Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes.Molecular microbiology · 2023Review
- Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs.Genome biology · 2023Article
- RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific.Scientific reports · 2023Article
- ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RNA degradation eliminates developmental transcripts during murine embryonic stem cell differentiation via CAPRIN1-XRN2.Developmental cell · 2022Article
- PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins.Nucleic acids research · 2022Article
- Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP.Genome biology · 2022Article
- Targeted RNA editing: novel tools to study post-transcriptional regulation.Molecular cell · 2022Review
- POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.Nucleic acids research · 2022Article
- Translational Applications of Linear and Circular Long Noncoding RNAs in Endometriosis.International journal of molecular sciences · 2021Review
- A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol.Nucleic acids research · 2021Article
- Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks.PLoS computational biology · 2021Article
- Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists.Computational and structural biotechnology journal · 2021Review
- TET2 chemically modifies tRNAs and regulates tRNA fragment levels.Nature structural & molecular biology · 2021Article
20 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundSequence specific RNA binding proteins are important regulators of gene expression. Several related crosslinking-based, high-throughput sequencing methods, including PAR-CLIP, have recently been developed to determine direct binding sites of global protein-RNA interactions. However, no studies have quantitatively addressed the contribution of background binding to datasets produced by these methods.
resultsWe measured non-specific RNA background in PAR-CLIP data, demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal among laboratories. We show that quantitative determination of background is essential for identifying targets of most RNA-binding proteins and can substantially improve motif analysis. We also demonstrate that by applying background correction to an RNA binding protein of unknown binding specificity, Caprin1, we can identify a previously unrecognized RNA recognition element not otherwise apparent in a PAR-CLIP study.
conclusionsEmpirical background measurements of global RNA-protein crosslinking are a necessary addendum to other experimental controls, such as performing replicates, because covalently crosslinked background signals are reproducible and otherwise unavoidable. Recognizing and quantifying the contribution of background extends the utility of PAR-CLIP and can improve mechanistic understanding of protein-RNA specificity, protein-RNA affinity and protein-RNA association dynamics.
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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.