Functional Structures in RNA Viruses
A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".
Deadline for manuscript submissions: 30 November 2025 | Viewed by 12
Special Issue Editors
Interests: RNA secondary structure; machine-learning and AI; RNA viruses; lncRNAs; protein-RNA interactions
Special Issues, Collections and Topics in MDPI journals
Interests: computational modelling; phase-separation; solubility; ribonucleoprotein networks
Special Issues, Collections and Topics in MDPI journals
Interests: RNA viruses; phase-separation; RNA structure; protein-RNA interactions; RNA modifications
Special Issues, Collections and Topics in MDPI journals
Interests: protein-RNA interactions; post-transcriptional regulation; untranslated regions; circular RNAs; RNA processing and RNA modifications
Special Issues, Collections and Topics in MDPI journals
Special Issue Information
Dear Colleagues,
RNA viruses rely heavily on intricate RNA structures to regulate key steps of their life cycles, including replication, translation, packaging, interaction with proteins, and host defense evasion. These functional RNA structures are often more conserved than the viral sequences themselves, underscoring their essential role in viral fitness despite high mutation rates. Well-characterized examples include internal ribosome entry sites (IRESs) in picornaviruses, pseudoknots that mediate ribosomal frameshifting in coronaviruses, and XRN1-resistant RNA structures that promote immune evasion in the 3’ UTR of flaviviruses.
Advances in chemical probing techniques, particularly SHAPE, have significantly deepened our understanding of these elements and their dynamic roles. SHAPE was first used to understand the structural architecture of HIV-1 and has since been applied to numerous other viruses, including hepatitis C and dengue. In parallel, computational tools, especially machine learning-based predictors, are enabling de novo identification and large-scale analysis of conserved structural motifs, such as potential IRES elements across viral genomes. This growing understanding of viral RNA structures will enable novel therapeutic strategies and is likely to inform the rational design of next-generation RNA-based vaccines.
This Special Issue aims to highlight recent progress in identifying and characterizing functional RNA structures in RNA viruses, including their interactions with host proteins, with a focus on both experimental and computational approaches. We welcome original research, reviews, methods, databases, and perspectives, and encourage interdisciplinary contributions bridging virology, structural biology, and bioinformatics.
You may choose our Joint Special Issue in Biomolecules.
Dr. Riccardo Delli Ponti
Dr. Gian Gaetano Tartaglia
Dr. Andrea Vandelli
Dr. Laura Broglia
Guest Editors
Manuscript Submission Information
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.
Keywords
- RNA secondary structure
- RNA viruses
- machine learning
- SHAPE
- protein–RNA interactions
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