ArticleMethods in molecular biology (Clifton, N.J.)2018
PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution.
Article in Methods in molecular biology (Clifton, N.J.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
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Who cites it
44 citing papers in PubMed.
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- Proximity labeling in neuroscience: decoding molecular landscapes for precision neurology.Translational neurodegeneration · 2026Review
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- CircTarget: a comprehensive database of circRNA-target RNA interactions across multiple cell types.Nucleic acids research · 2026Article
- Ancestral intronic splicing regulatory elements in the SCNbioRxiv : the preprint server for biology · 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
- RAP-RNA: A Methodological Approach to Study Base-Pairing Between Endogenous RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computational limitations and future needs to unravel the full potential of 2'-O-methylation and C/D box snoRNAs.RNA biology · 2025Review
- Eight Triplex-Binding Molecules from Four Chemical Classes Broadly Recognize the MALAT1 Triple Helix.Molecules (Basel, Switzerland) · 2025Article
- Epstein-Barr Virus Encoded lncRNAs Control the Viral Lytic Switch.bioRxiv : the preprint server for biology · 2025Article
- Direct circRNA-mRNA Binding Controls mRNA Fate: A New Mechanism for circRNAs.Non-coding RNA · 2025Review
- Harnessing Molecular Recognition for Small-Molecule-Mediated Reversible Photochemical Control Over mRNA Translation.Angewandte Chemie (International ed. in English) · 2025Article
- Mechanism of expression regulation of head-to-head overlapping protein-coding genes INO80E and HIRIP3.Communications biology · 2025Article
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments.Bioinformatics (Oxford, England) · 2024Article
- Bipartite viral RNA genome heterodimerization influences genome packaging and virion thermostability.Journal of virology · 2024Article
- Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation.Nature communications · 2024Article
- Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes.Briefings in functional genomics · 2024Review
- Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences.Genome biology · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
RNA has the intrinsic propensity to form base pairs, leading to complex intramolecular and intermolecular helices. Direct measurement of base pairing interactions in living cells is critical to solving transcriptome structure and interactions, and investigating their functions (Lu and Chang, Curr Opin Struct Biol 36:142-148, 2016). Toward this goal, we developed an experimental method, PARIS (Psoralen Analysis of RNA Interactions and Structures), to directly determine transcriptome-wide base pairing interactions (Lu et al., Cell 165(5):1267-1279, 2016). PARIS combines four critical steps, in vivo cross-linking, 2D gel purification, proximity ligation, and high-throughput sequencing to achieve high-throughput and near-base pair resolution determination of the RNA structurome and interactome in living cells. In this chapter, we aim to provide a comprehensive discussion on the principles behind the experimental and computational strategies, and a step-by-step description of the experiment and analysis.
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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.