دورية أكاديمية
Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes
| العنوان: | Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes |
|---|---|
| المؤلفون: | Srivastava, Mansi, Dukeshire, Matthew R., Mir, Quoseena, Omoru, Okiemute Beatrice, Manzourolajdad, Amirhossein, Janga, Sarath Chandra |
| المساهمون: | BioHealth Informatics, School of Informatics and Computing |
| المصدر: | PMC |
| بيانات النشر: | Oxford University Press |
| سنة النشر: | 2024 |
| المجموعة: | Indiana University - Purdue University Indianapolis: IUPUI Scholar Works |
| مصطلحات موضوعية: | Gene regulation, RNA structure, Post-transcriptional control, RNA interactions, Viral genomics, Sub-genomic RNA, Pseudoknot |
| الوصف: | Long-range ribonucleic acid (RNA)–RNA interactions (RRI) are prevalent in positive-strand RNA viruses, including Beta-coronaviruses, and these take part in regulatory roles, including the regulation of sub-genomic RNA production rates. Crosslinking of interacting RNAs and short read-based deep sequencing of resulting RNA–RNA hybrids have shown that these long-range structures exist in severe acute respiratory syndrome coronavirus (SARS-CoV)-2 on both genomic and sub-genomic levels and in dynamic topologies. Furthermore, co-evolution of coronaviruses with their hosts is navigated by genetic variations made possible by its large genome, high recombination frequency and a high mutation rate. SARS-CoV-2’s mutations are known to occur spontaneously during replication, and thousands of aggregate mutations have been reported since the emergence of the virus. Although many long-range RRIs have been experimentally identified using high-throughput methods for the wild-type SARS-CoV-2 strain, evolutionary trajectory of these RRIs across variants, impact of mutations on RRIs and interaction of SARS-CoV-2 RNAs with the host have been largely open questions in the field. In this review, we summarize recent computational tools and experimental methods that have been enabling the mapping of RRIs in viral genomes, with a specific focus on SARS-CoV-2. We also present available informatics resources to navigate the RRI maps and shed light on the impact of mutations on the RRI space in viral genomes. Investigating the evolution of long-range RNA interactions and that of virus–host interactions can contribute to the understanding of new and emerging variants as well as aid in developing improved RNA therapeutics critical for combating future outbreaks. |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| العلاقة: | Briefings in Functional Genomics; Srivastava M, Dukeshire MR, Mir Q, Omoru OB, Manzourolajdad A, Janga SC. Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes. Brief Funct Genomics. 2024;23(1):46-54. doi:10.1093/bfgp/elac050; https://hdl.handle.net/1805/41377Test |
| الإتاحة: | https://doi.org/10.1093/bfgp/elac050Test https://hdl.handle.net/1805/41377Test |
| حقوق: | Publisher Policy |
| رقم الانضمام: | edsbas.14EB9211 |
| قاعدة البيانات: | BASE |
| الوصف غير متاح. |