ArticleNature2015
hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.
Article in Nature, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
157 citing papers in PubMed, 277 citations in OpenAlex.
- High-Resolution Mapping of RNA-RNA Interactions Across the HIV-1 Genome With HicapR.Bio-protocol · 2026Article
- rbpCNN: a biophysics-informed deep learning model for predicting piRNA and mRNA interactions.Scientific reports · 2026Article
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- The role of low-complexity repeats in RNA-RNA interactions and a deep learning framework for duplex prediction.Nature communications · 2026Article
- LncRNA CDIPTOSP-induced destabilization of KLF17 promotes ovarian cancer progression through STAU1-mediated mRNA decay.American journal of translational research · 2026Article
- Integrated Analysis of Cross-Link-Ligation Data for the Detection of RNA 2D/3D Structures and Interactions In Vivo.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Mapping of RBP-Mediated RNA-RNA Interactome with RIC-Seq.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Systematic mapping of small nucleolar RNA interactions in human cells.RNA biology · 2025Article
- Decoding the interactions and functions of non-coding RNA with artificial intelligence.Nature reviews. Molecular cell biology · 2025Review
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Regulatory Effects of RNA-Protein Interactions Revealed by Reporter Assays of Bacteria Grown on Solid Media.Biosensors · 2025Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- Noncanonical formation of SNX5 gene-derived circular RNA regulates cancer growth.Cell death & disease · 2024Article
- RNA-binding protein GIGYF2 orchestrates hepatic insulin resistance through STAU1/PTEN-mediated disruption of the PI3K/AKT signaling cascade.Molecular medicine (Cambridge, Mass.) · 2024Article
- Excessive STAU1 condensate drives mTOR translation and autophagy dysfunction in neurodegeneration.The Journal of cell biology · 2024Article
- Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq.Nucleic acids research · 2024Article
- The role of secondary structures in the functioning of 3' untranslated regions of mRNA: A review of functions of 3' UTRs' secondary structures and hypothetical involvement of secondary structures in cytoplasmic polyadenylation in Drosophila.BioEssays : news and reviews in molecular, cellular and developmental biology · 2024Review
- Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states.Cell chemical biology · 2024Review
- Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells.Molecular and cellular biology · 2024Article
- Staufen1 controls mitochondrial metabolism via HIF2α in embryonal rhabdomyosarcoma and promotes tumorigenesis.Cellular and molecular life sciences : CMLS · 2023Article
97 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans-acting factors. However, little is known about the in vivo structure of full-length mRNAs. Here we present hiCLIP, a biochemical technique for transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins (RBPs). Using this technique to investigate RNA structures bound by Staufen 1 (STAU1) in human cells, we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unexpected prevalence of long-range duplexes in 3' untranslated regions (UTRs), and a decreased incidence of single nucleotide polymorphisms in duplex-forming regions. We also discover a duplex spanning 858 nucleotides in the 3' UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.