ArticleNature protocols2021
Global in situ profiling of RNA-RNA spatial interactions with RIC-seq.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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.
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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
23 citing papers in PubMed, 57 citations in OpenAlex.
- hnRNPK condensates facilitate enhancer-promoter looping and RNA polymerase II recruitment.Nature genetics · 2026Article
- Cross-genus analysis reveals architecturally programmed sgRNA synthesis patterns in coronaviruses.Molecular systems biology · 2026Article
- High-Resolution Mapping of RNA-RNA Interactions Across the HIV-1 Genome With HicapR.Bio-protocol · 2026Article
- RNA modification-mediated multidimensional crosstalk: a novel perspective on gene expression regulation.Genome biology · 2026Review
- Integrative profiling of condensation-prone RNAs during early development.Cell genomics · 2026Article
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Mapping of RBP-Mediated RNA-RNA Interactome with RIC-Seq.Methods in molecular biology (Clifton, N.J.) · 2026Article
- IRGL-RRI: interpretable graph representation learning for plant RNA-RNA interaction discovery.Frontiers in plant science · 2025Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- A novel super-enhancer-related risk model for predicting prognosis and guiding personalized treatment in hepatocellular carcinoma.BMC cancer · 2024Article
- The selective sponging of miRNAs by OIP5-AS1 regulates metabolic reprogramming of pyruvate in adenoma-carcinoma transition of human colorectal cancer.BMC cancer · 2024Article
- Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq.Nucleic acids research · 2024Article
- Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Review
- lhCLIP reveals the in vivo RNA-RNA interactions recognized by hnRNPK.PLoS genetics · 2023Article
- RNA in situ conformation sequencing reveals novel long-range RNA structures with impact on splicing.RNA (New York, N.Y.) · 2023Article
- Article
- How does precursor RNA structure influence RNA processing and gene expression?Bioscience reports · 2023Review
- Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination.International journal of molecular sciences · 2023Review
- Enhancers dysfunction in the 3D genome of cancer cells.Frontiers in cell and developmental biology · 2023Review
- Long-range RNA structures in the human transcriptome beyond evolutionarily conserved regions.PeerJ · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Emerging evidence has demonstrated that RNA-RNA interactions are vital in controlling diverse biological processes, including transcription, RNA splicing and protein translation. RNA in situ conformation sequencing (RIC-seq) is a technique for capturing protein-mediated RNA-RNA proximal interactions globally in living cells at single-base resolution. Cells are first treated with formaldehyde to fix all the protein-mediated RNA-RNA interactions in situ. After cell permeabilization and micrococcal nuclease digestion, the proximally interacting RNAs are 3' end-labeled with pCp-biotin and subsequently ligated using T4 RNA ligase. The chimeric RNAs are then enriched and converted into libraries for paired-end sequencing. After deep sequencing, computational analysis yields interaction strength scores for every base on proximally interacting RNAs in the starting populations. The whole experimental procedure is designed to be completed within 6 d, followed by an additional 8 d for computational analysis. RIC-seq technology can unbiasedly detect intra- and intermolecular RNA-RNA interactions, thereby rendering it useful for reconstructing RNA higher-order structures and identifying direct noncoding RNA targets.
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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.