ArticleNucleic acids research2020
Robust partitioning of microRNA targets from downstream regulatory changes.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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
17 citing papers in PubMed, 35 citations in OpenAlex.
- Investigating Potential 5' UTR G-Quadruplexes Within NRF2 mRNA.Current issues in molecular biology · 2026Article
- The miR-16-1-3p passenger strand exhibits functional activity and suppresses malignant phenotypes in osteosarcoma.Frontiers in genetics · 2026Article
- Roles of exosomal miRNAs from different sources in knee osteoarthritis: exercise-regulated skeletal muscle-derived exosomal miRNAs as a prospective therapeutic avenue.Frontiers in medicine · 2026Review
- An efficient framework to decipher microRNA regulatory programs applied to T cells.Genes and immunity · 2025Article
- Loss of multiple micro-RNAs uncovers multi-level restructuring of gene regulation in rodents.BMC genomics · 2025Article
- The quantitative impact of 3'UTRs on gene expression.Nucleic acids research · 2025Article
- TP53I11 Functions Downstream of Multiple MicroRNAs to Increase ER Calcium Levels and Inhibits Cancer Cell Proliferation.International journal of molecular sciences · 2024Article
- Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.Nature biotechnology · 2024Article
- The miRNA-target interactions: An underestimated intricacy.Nucleic acids research · 2024Review
- MicroRNA-1 Deficiency Is a Primary Etiological Factor Disrupting Cardiac Contractility and Electrophysiological Homeostasis.Circulation. Arrhythmia and electrophysiology · 2024Article
- Subcytoplasmic location of translation controls protein output.Molecular cell · 2023Article
- Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model.BMC genomics · 2023Article
- On the rules of engagement for microRNAs targeting protein coding regions.Nucleic acids research · 2023Article
- Bone Marrow Mesenchymal Stem Cells-Derived miR-21-5p Protects Grafted Islets Against Apoptosis by Targeting PDCD4.Stem cells (Dayton, Ohio) · 2023Article
- Review
- Global and precise identification of functional miRNA targets in mESCs by integrative analysis.EMBO reports · 2022Article
- Dynamic and widespread control of poly(A) tail length during macrophage activation.RNA (New York, N.Y.) · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The biological impact of microRNAs (miRNAs) is determined by their targets, and robustly identifying direct miRNA targets remains challenging. Existing methods suffer from high false-positive rates and are unable to effectively differentiate direct miRNA targets from downstream regulatory changes. Here, we present an experimental and computational framework to deconvolute post-transcriptional and transcriptional changes using a combination of RNA-seq and PRO-seq. This novel approach allows us to systematically profile the regulatory impact of a miRNA. We refer to this approach as CARP: Combined Analysis of RNA-seq and PRO-seq. We apply CARP to multiple miRNAs and show that it robustly distinguishes direct targets from downstream changes, while greatly reducing false positives. We validate our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a comprehensive repertoire of targets. Using this approach, we identify miRNA-specific activity of target sites within the open reading frame. Additionally, we show that CARP facilitates the dissection of complex changes in gene regulatory networks triggered by miRNAs and identification of transcription factors that mediate downstream regulatory changes. Given the robustness of the approach, CARP would be particularly suitable for dissecting miRNA regulatory networks in vivo.
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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.