ArticleScientific reports2023
Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 12 citations in OpenAlex.
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- Agentomics: an agentic system that autonomously develops novel state-of-the-art solutions for biomedical machine learning tasks.Bioinformatics (Oxford, England) · 2026Article
- MiRformer: a dual-transformer-encoder framework for predicting microRNA-mRNA interactions from paired sequences.Bioinformatics (Oxford, England) · 2026Article
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- Mechanisms of Transfer RNA Fragments Functionality Within and Between Cells and Organisms.Cells · 2025Review
- Cellular miRNAs and viruses: trends in miRNA sequestering and target de-repression.Journal of virology · 2025Review
- miRBench: novel benchmark datasets for microRNA binding site prediction that mitigate against prevalent microRNA frequency class bias.Bioinformatics (Oxford, England) · 2025Article
- miRNA-Mediated Regulation of Gene Expression During Early Activation in Jurkat Cells.bioRxiv : the preprint server for biology · 2025Article
- rRFtargetDB: a database of Ago1-mediated targets of ribosomal RNA fragments.RNA (New York, N.Y.) · 2025Article
- Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional-Post-Transcriptional Regulatory Cross-Talk.Biology · 2025Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
Abstract
Argonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA 'guide' sequences, and identifies its targets primarily via a 'seed' mediated partial complementarity process. Despite numerous studies, a definitive experimental dataset of AGO2 'guide'-'target' interactions remains elusive. Our study employs two experimental methods-AGO2 CLASH and AGO2 eCLIP, to generate thousands of AGO2 target sites verified by chimeric reads. These chimeric reads contain both the AGO2 loaded small RNA 'guide' and the target sequence, providing a robust resource for modeling AGO2 binding preferences. Our novel analysis pipeline reveals thousands of AGO2 target sites driven by microRNAs and a significant number of AGO2 'guides' derived from fragments of other small RNAs such as tRNAs, YRNAs, snoRNAs, rRNAs, and more. We utilize convolutional neural networks to train machine learning models that accurately predict the binding potential for each 'guide' class and experimentally validate several interactions. In conclusion, our comprehensive analysis of the AGO2 targetome broadens our understanding of its 'guide' repertoire and potential function in development and disease. Moreover, we offer practical bioinformatic tools for future experiments and the prediction of AGO2 targets. All data and code from this study are freely available at https://github.com/ML-Bioinfo-CEITEC/HybriDetector/ .
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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.