ArticleNucleic acids research2017
From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 35 citations in OpenAlex.
- A Distinct Population of Mitochondrial miRNA in Human Male Skeletal Muscle Assessed Before and After Exercise.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Endothelial miR-7052 Safeguards Blood-Brain Barrier Integrity During Endotoxemia by Co-repressing ANGPT2 and PDE5A.Molecular neurobiology · 2026Article
- Serpine1 mRNA confers mesenchymal characteristics to the cell and promotes CD8+ T cells exclusion from colon adenocarcinomas.Cell death discovery · 2024Article
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- Review
- Sequence determinants as key regulators in gene expression of T cells.Immunological reviews · 2021Review
- Specific arterio-venous transcriptomic and ncRNA-RNA interactions in human umbilical endothelial cells: A meta-analysis.iScience · 2021Article
- Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding.Nucleic acids research · 2021Article
- Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists.Computational and structural biotechnology journal · 2021Review
- Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.GigaScience · 2020Article
- Circulating microRNA trafficking and regulation: computational principles and practice.Briefings in bioinformatics · 2020Review
- Trends in the development of miRNA bioinformatics tools.Briefings in bioinformatics · 2019Review
- Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.Methods (San Diego, Calif.) · 2019Review
- CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals.Nucleic acids research · 2018Article
- Recent computational developments on CLIP-seq data analysis and microRNA targeting implications.Briefings in bioinformatics · 2018Review
- Data Science Issues in Studying Protein-RNA Interactions with CLIP Technologies.Annual review of biomedical data science · 2018Article
- The Nefarious Nexus of Noncoding RNAs in Cancer.International journal of molecular sciences · 2018Review
- uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins.Nature communications · 2018Article
- Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq.Nature communications · 2017Article
- Re-evaluating Strategies to Define the Immunoregulatory Roles of miRNAs.Trends in immunology · 2017Review
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq). Since the quality of peaks is of pivotal importance for the final output of the proposed method, we provide a comprehensive benchmarking of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, on four publicly available Ago2-HITS-CLIP datasets and one unpublished in-house Ago2-dataset in stem cells. We measured the sensitivity, the specificity and the position accuracy toward miRNA binding sites identification, and the agreement with TargetScan. Secondly, we developed a new pipeline, called miRBShunter, to identify canonical and non-canonical miRNA-binding sites based on de novo motif identification from Ago2 peaks and prediction of miRNA::RNA heteroduplexes. miRBShunter was tested and experimentally validated on the in-house Ago2-dataset and on an Ago2-PAR-CLIP dataset in human stem cells. Overall, we provide guidelines to choose a suitable peak detection program and a new method for miRNA-target identification.
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