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Bermudez-Santana CI, Gallego-Gómez JC. Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus. Viruses 2024; 16:804. [PMID: 38793685 PMCID: PMC11125801 DOI: 10.3390/v16050804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, the function of noncoding RNAs (ncRNAs) as regulatory molecules of cell physiology has begun to be better understood. Advances in viral molecular biology have shown that host ncRNAs, cellular factors, and virus-derived ncRNAs and their interplay are strongly disturbed during viral infections. Nevertheless, the folding of RNA virus genomes has also been identified as a critical factor in regulating canonical and non-canonical functions. Due to the influence of host ncRNAs and the structure of RNA viral genomes, complex molecular and cellular processes in infections are modulated. We propose three main categories to organize the current information about RNA-RNA interactions in some well-known human viruses. The first category shows examples of host ncRNAs associated with the immune response triggered in viral infections. Even though miRNAs introduce a standpoint, they are briefly presented to keep researchers moving forward in uncovering other RNAs. The second category outlines interactions between virus-host ncRNAs, while the third describes how the structure of the RNA viral genome serves as a scaffold for processing virus-derived RNAs. Our grouping may provide a comprehensive framework to classify ncRNA-host-cell interactions for emerging viruses and diseases. In this sense, we introduced them to organize DENV-host-cell interactions.
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Affiliation(s)
- Clara Isabel Bermudez-Santana
- Computational and theoretical RNomics Group, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Juan Carlos Gallego-Gómez
- Grupo de Medicina de Traslación, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
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Ursu A, Childs-Disney JL, Andrews RJ, O'Leary CA, Meyer SM, Angelbello AJ, Moss WN, Disney MD. Design of small molecules targeting RNA structure from sequence. Chem Soc Rev 2020; 49:7252-7270. [PMID: 32935689 PMCID: PMC7707016 DOI: 10.1039/d0cs00455c] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The design and discovery of small molecule medicines has largely been focused on a small number of druggable protein families. A new paradigm is emerging, however, in which small molecules exert a biological effect by interacting with RNA, both to study human disease biology and provide lead therapeutic modalities. Due to this potential for expanding target pipelines and treating a larger number of human diseases, robust platforms for the rational design and optimization of small molecules interacting with RNAs (SMIRNAs) are in high demand. This review highlights three major pillars in this area. First, the transcriptome-wide identification and validation of structured RNA elements, or motifs, within disease-causing RNAs directly from sequence is presented. Second, we provide an overview of high-throughput screening approaches to identify SMIRNAs as well as discuss the lead identification strategy, Inforna, which decodes the three-dimensional (3D) conformation of RNA motifs with small molecule binding partners, directly from sequence. An emphasis is placed on target validation methods to study the causality between modulating the RNA motif in vitro and the phenotypic outcome in cells. Third, emergent modalities that convert occupancy-driven mode of action SMIRNAs into event-driven small molecule chemical probes, such as RNA cleavers and degraders, are presented. Finally, the future of the small molecule RNA therapeutics field is discussed, as well as hurdles to overcome to develop potent and selective RNA-centric chemical probes.
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Affiliation(s)
- Andrei Ursu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Ryan J Andrews
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA.
| | - Collin A O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA.
| | - Samantha M Meyer
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA.
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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Luo Y, Hitz BC, Gabdank I, Hilton JA, Kagda MS, Lam B, Myers Z, Sud P, Jou J, Lin K, Baymuradov UK, Graham K, Litton C, Miyasato SR, Strattan JS, Jolanki O, Lee JW, Tanaka FY, Adenekan P, O'Neill E, Cherry JM. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res 2020; 48:D882-D889. [PMID: 31713622 PMCID: PMC7061942 DOI: 10.1093/nar/gkz1062] [Citation(s) in RCA: 365] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/18/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023] Open
Abstract
The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.
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Affiliation(s)
- Yunhai Luo
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Jason A Hilton
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Bonita Lam
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Zachary Myers
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Paul Sud
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Jennifer Jou
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Khine Lin
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | | | - Keenan Graham
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Casey Litton
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Stuart R Miyasato
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Jin-Wook Lee
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Forrest Y Tanaka
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Philip Adenekan
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - Emma O'Neill
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA 94305-5477, USA
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