ArticlePLoS computational biology2017
Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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.
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Who cites it
25 citing papers in PubMed, 31 citations in OpenAlex.
- Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation.Nature communications · 2026Article
- Recent advances in the detection and functional analysis of circRNAs with short-read RNA sequencing-based methods.Molecular biology reports · 2026Review
- Encapsulin-Protected Immunotherapeutic Complexes: Bacteria-Derived Nanoparticles for mRNA Delivery to Eukaryotic Cells.ChemMedChem · 2026Article
- IRES-TrAPPr reveals novel insights into viral and cellular mRNA translation.bioRxiv : the preprint server for biology · 2026Article
- IRESeek: structure-informed deep learning method for accurate identification of internal ribosome entry sites in circular RNAs.NAR genomics and bioinformatics · 2025Article
- A foundation language model to decipher diverse regulation of RNAs.Genome biology · 2025Article
- Internal ribosome entry sites enhance translation in trans in antisense non-coding SINEUP and circular RNAs.Nucleic acids research · 2025Article
- A capless hairpin-protected mRNA vaccine encoding the full-length Influenza A hemagglutinin protects mice against a lethal Influenza A infection.Gene therapy · 2025Article
- Evaluation of Eukaryotic mRNA Coding Potential.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Circular RNA-Encoded Proteins in Disease Pathogenesis.International journal of biological sciences · 2025Review
- DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs.Briefings in bioinformatics · 2024Article
- Host-like RNA Elements Regulate Virus Translation.Viruses · 2024Review
- Internal Ribosome Entry Site (IRES)-Mediated Translation and Its Potential for Novel mRNA-Based Therapy Development.Biomedicines · 2022Review
- CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs.BMC bioinformatics · 2022Article
- Review
- Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans.Database : the journal of biological databases and curation · 2021Article
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- Control of Translation at the Initiation Phase During Glucose Starvation in Yeast.International journal of molecular sciences · 2019Review
- IRESpy: an XGBoost model for prediction of internal ribosome entry sites.BMC bioinformatics · 2019Article
- Functional assays for transcription mechanisms in high-throughput.Methods (San Diego, Calif.) · 2019Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be involved in this process. However due to the small number of IRESs known, there have been no systematic investigations of the determinants of IRES activity. With the recent discovery of thousands of novel IRESs in human and viruses, the next challenge is to decipher the sequence determinants of IRES activity. We present the first in-depth computational analysis of a large body of IRESs, exploring RNA sequence features predictive of IRES activity. We identified predictive k-mer features resembling IRES trans-acting factor (ITAF) binding motifs across human and viral IRESs, and found that their effect on expression depends on their sequence, number and position. Our results also suggest that the architecture of retroviral IRESs differs from that of other viruses, presumably due to their exposure to the nuclear environment. Finally, we measured IRES activity of synthetically designed sequences to confirm our prediction of increasing activity as a function of the number of short IRES elements.
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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.