ArticleRNA (New York, N.Y.)2017
Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq.
Article in RNA (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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.
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
35 citing papers in PubMed, 1 synthesis or guideline pooled it, 49 citations in OpenAlex.
- An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops.Briefings in bioinformatics · 2022Pooled it
- Effects of genetic ablation and pharmacological inhibition of HuR on gene expression, iron metabolism, and hormone levels.BMC biology · 2025Article
- The RNA binding protein DND1 is elevated in a subpopulation of pro-spermatogonia and targets chromatin modifiers and translational machinery during late gestation.PLoS genetics · 2023Article
- Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management.International journal of molecular sciences · 2023Review
- Analyzing RNA-Protein Interactions by Cross-Link Rates and CLIP-seq Libraries.Current protocols · 2023Article
- MicroRNAs, Tristetraprolin Family Members and HuR: A Complex Interplay Controlling Cancer-Related Processes.Cancers · 2022Review
- Phospho-RNA sequencing with circAID-p-seq.Nucleic acids research · 2022Article
- RNA regulatory mechanisms that control antiviral innate immunity.Immunological reviews · 2021Review
- CBRPP: a new RNA-centric method to study RNA-protein interactions.RNA biology · 2021Article
- STAU2 binds a complex RNA cargo that changes temporally with production of diverse intermediate progenitor cells during mouse corticogenesis.Development (Cambridge, England) · 2021Article
- A Survey of Current Resources to Study lncRNA-Protein Interactions.Non-coding RNA · 2021Review
- Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein-RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing.International journal of molecular sciences · 2021Review
- RNA-Centric Approaches to Profile the RNA-Protein Interaction Landscape on Selected RNAs.Non-coding RNA · 2021Review
- RNA-Binding Proteins as Regulators of Migration, Invasion and Metastasis in Oral Squamous Cell Carcinoma.International journal of molecular sciences · 2020Review
- Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA.RNA (New York, N.Y.) · 2020Article
- Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners.Biochemical Society transactions · 2020Review
- The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation.International journal of molecular sciences · 2020Article
- PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.Communications biology · 2020Article
- Ribonucleoprotein Immunoprecipitation (RIP) Analysis.Bio-protocol · 2020Article
- Approaches for measuring the dynamics of RNA-protein interactions.Wiley interdisciplinary reviews. RNA · 2020Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA-binding proteins (RBPs) and noncoding RNAs orchestrate post-transcriptional processes through the recognition of specific sites on targeted transcripts. Thus, understanding the connection between binding to specific sites and active regulation of the whole transcript is essential. Many immunoprecipitation techniques have been developed that identify either whole transcripts or binding sites of RBPs on each transcript using cell lysates. However, none of these methods simultaneously measures the strength of each binding site and quantifies binding to whole transcripts. In this study, we compare current procedures and present digestion optimized (DO)-RIP-seq, a simple method that locates and quantifies RBP binding sites using a continuous metric. We have used the RBP HuR/ELAVL1 to demonstrate that DO-RIP-seq can quantify HuR binding sites with high coverage across the entire human transcriptome, thereby generating metrics of relative RNA binding strength. We demonstrate that this quantitative enrichment of binding sites is proportional to the relative in vitro binding strength for these sites. In addition, we used DO-RIP-seq to quantify and compare HuR's binding to whole transcripts, thus allowing for seamless integration of binding site data with whole-transcript measurements. Finally, we demonstrate that DO-RIP-seq is useful for identifying functional mRNA target sets and binding sites where combinatorial interactions between HuR and AGO-microRNAs regulate the fate of the transcripts. Our data indicate that DO-RIP-seq will be useful for quantifying RBP binding events that regulate dynamic biological processes.
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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.