ArticleNucleic acids research2024
Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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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
18 citing papers in PubMed, 22 citations in OpenAlex.
- Dysregulated circRNA expression profile and associated miRNA sponging in abnormal lung development in congenital diaphragmatic hernia.Clinical and translational medicine · 2026Article
- Circulating circRNAs at the frontier of cancer detection, prognosis, and therapy.Chinese medical journal · 2026Review
- Circular RNA-mediated regulation of key signaling pathways in cardiovascular diseases: a review.Journal of advanced research · 2026Review
- The circular RNA landscape: Biogenesis, functions, identification pipelines, and biomedical applications.Non-coding RNA research · 2026Review
- CircTarget: a comprehensive database of circRNA-target RNA interactions across multiple cell types.Nucleic acids research · 2026Article
- CIRCpedia v3: an interactive database for circular RNA characterization and functional exploration.Nucleic acids research · 2026Article
- Circular RNARNA biology · 2025Article
- Identification and characterization of tissue- and stress-specific circular RNAs (circRNAs) of tea to generate the largest tea circRNAs data repository.Scientific reports · 2025Article
- The role of circular RNAs in regulating cytokine signaling in cancer.FEBS open bio · 2025Review
- Internal ribosome entry sites enhance translation in trans in antisense non-coding SINEUP and circular RNAs.Nucleic acids research · 2025Article
- Direct circRNA-mRNA Binding Controls mRNA Fate: A New Mechanism for circRNAs.Non-coding RNA · 2025Review
- Decoding the regulatory roles of circular RNAs in cardiac fibrosis.Non-coding RNA research · 2025Review
- MicroRNA Signatures: Illuminating Minimal Residual Disease Monitoring in Juvenile Myelomonocytic Leukemia - A Review.Journal of hematology · 2025Review
- Back to the Origin: Mechanisms of circRNA-Directed Regulation of Host Genes in Human Disease.Non-coding RNA · 2024Review
- Circular RNA in cancer.Nature reviews. Cancer · 2024Review
- CircR-loop: a novel RNA:DNA interaction on genome instability.Cellular & molecular biology letters · 2024Review
- Review
- Experimental and Computational Tools for Mapping Circular RNA Modifications.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Although the functional role of circular RNA (circRNA) interaction with microRNAs and proteins has been studied extensively, circRNA interactions with the protein-coding mRNAs in intact cells remain largely unknown. Here, by employing AMT-mediated proximity ligation of RNA-RNA duplexes followed by circRNA enrichment and deep sequencing, we report a novel Cross-Linking Poly(A) Pulldown RNase R Sequencing (CLiPPR-seq) technology which identified hundreds of mRNA-interacting circRNAs in three different cell types, including βTC6, C2C12 and HeLa cells. Furthermore, CLiPP-seq without RNase R treatment was also performed to identify the mRNA expression in these cells. BLAST analysis of circRNAs in CLiPPR-seq sample with the mRNAs in CLiPP-seq samples determined their potential complementary sequences for circRNA-mRNA interaction. Pulldown of circRNAs and poly(A) RNAs confirmed the direct interaction of circRNAs with target mRNAs. Silencing of mRNA-interacting circRNAs led to the altered expression of target mRNAs in βTC6 cells, suggesting the role of direct interaction of circRNAs with mRNAs in gene expression regulation. CLiPPR-seq thus represents a novel method for illuminating the myriad of uncharacterized circRNA-mRNA hybrids that may regulate gene expression.
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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.