ERVE SIGNED
Systematic discovery of functional elements in RNA virus genomes: an Encyclopedia of RNA Virus Elements
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0ERVE project word cloud
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Project "ERVE" data sheet
The following table provides information about the project.
| Coordinator |
THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE
Organization address contact info |
| Coordinator Country | United Kingdom [UK] |
| Project website | http://www.firthlab.path.cam.ac.uk/index.html |
| Total cost | 1˙780˙000 € |
| EC max contribution | 1˙780˙000 € (100%) |
| Programme |
1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC)) |
| Code Call | ERC-2014-CoG |
| Funding Scheme | ERC-COG |
| Starting year | 2015 |
| Duration (year-month-day) | from 2015-09-01 to 2021-08-31 |
Partnership
Take a look of project's partnership.
| # | ||||
|---|---|---|---|---|
| 1 | THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE | UK (CAMBRIDGE) | coordinator | 1˙780˙000.00 |
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Project objective
Identification of the full complement of genes and other functional elements in any virus is crucial to fully understand its molecular biology and guide the development of effective control strategies. Our recent discoveries of new 'hidden' genes in the potyviruses, alphaviruses, arteriviruses, flaviviruses and influenza A virus have demonstrated that, even in the most well-studied and economically-important viruses, small overlapping genes can remain undetected throughout decades of research. Comparative computational analyses can be used to efficiently identify hidden features and target experimental analyses, thus saving time and cost, and minimizing animal experiments. With the rapid increase in sequencing data, for the first time it is now possible to map out at high resolution functional elements genome-wide in hundreds of important virus species.
Our research involves the development of powerful new tools for virus comparative genomics, and the application of these tools to uncover hidden genes and other functional elements in RNA virus and retrovirus genomes. Hidden genes are often translated via non-canonical mechanisms, such as programmed ribosomal frameshifting, and we are particularly interested in discovering and characterizing new types of non-canonical translation. Deciphering these 'exceptions-to-the-rule' enhances our understanding of the mechanics of protein synthesis. Further, these novel mechanisms may also be relevant to cellular gene expression.
The goals of this project are:
1) To computationally identify all 'hidden' genes and major functional non-coding elements in the genomes of RNA viruses and retroviruses of medical, veterinary and agricultural importance.
2) To experimentally characterize the most interesting new features.
3) To characterize novel translation mechanisms utilized by RNA viruses.
4) To develop web interfaces to our software and an interactive RNA virus comparative genomics database.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2018 |
Hazel Stewart, Katherine Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth Transcriptional and Translational Landscape of Equine Torovirus published pages: , ISSN: 0022-538X, DOI: 10.1128/JVI.00589-18 |
Journal of Virology 92/17 | 2020-02-12 |
| 2016 |
John F. Atkins, Gary Loughran, Pramod R. Bhatt, Andrew E. Firth, Pavel V. Baranov Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use published pages: gkw530, ISSN: 0305-1048, DOI: 10.1093/nar/gkw530 |
Nucleic Acids Research | 2020-02-12 |
| 2016 |
Steven M. Valles, David H. Oi, James J. Becnel, James K. Wetterer, John S. LaPolla, Andrew E. Firth Isolation and characterization of Nylanderia fulva virus 1, a positive-sense, single-stranded RNA virus infecting the tawny crazy ant, Nylanderia fulva published pages: 244-254, ISSN: 0042-6822, DOI: 10.1016/j.virol.2016.06.014 |
Virology 496 | 2020-02-12 |
| 2017 |
Roger Ling, Andrew E. Firth An analysis by metabolic labelling of the encephalomyocarditis virus ribosomal frameshifting efficiency and stimulators published pages: 2100-2105, ISSN: 0022-1317, DOI: 10.1099/jgv.0.000888 |
Journal of General Virology 98/8 | 2020-02-12 |
| 2017 |
Ingrida Olendraite, Nina I. Lukhovitskaya, Sanford D. Porter, Steven M. Valles, Andrew E. Firth Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses published pages: 2368-2378, ISSN: 0022-1317, DOI: 10.1099/jgv.0.000902 |
Journal of General Virology 98/9 | 2020-02-12 |
| 2017 |
Sawsan Napthine, Roger Ling, Leanne K. Finch, Joshua D. Jones, Susanne Bell, Ian Brierley, Andrew E. Firth Protein-directed ribosomal frameshifting temporally regulates gene expression published pages: 15582, ISSN: 2041-1723, DOI: 10.1038/ncomms15582 |
Nature Communications 8 | 2020-02-12 |
| 2017 |
Bradley Blitvich, Andrew Firth A Review of Flaviviruses that Have No Known Arthropod Vector published pages: 154, ISSN: 1999-4915, DOI: 10.3390/v9060154 |
Viruses 9/6 | 2020-02-12 |
| 2017 |
Jermilia Charles, Chandra S. Tangudu, Andrew E. Firth, Bradley J. Blitvich Complete genome sequences of two insect-specific flaviviruses published pages: 3913-3917, ISSN: 0304-8608, DOI: 10.1007/s00705-017-3552-5 |
Archives of Virology 162/12 | 2020-02-12 |
| 2018 |
Nerea Irigoyen, Adam M. Dinan, Ian Brierley, Andrew E. Firth Ribosome profiling of the retrovirus murine leukemia virus published pages: , ISSN: 1742-4690, DOI: 10.1186/s12977-018-0394-5 |
Retrovirology 15/1 | 2020-02-12 |
| 2017 |
Adam M. Dinan, John F. Atkins, Andrew E. Firth ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product? published pages: , ISSN: 1745-6150, DOI: 10.1186/s13062-017-0195-0 |
Biology Direct 12/1 | 2020-02-12 |
| 2016 |
Allan Olspert, John P. Carr, Andrew E. Firth Mutational analysis of the Potyviridae transcriptional slippage site utilized for expression of the P3N-PIPO and P1N-PISPO proteins published pages: 7618-7629, ISSN: 0305-1048, DOI: 10.1093/nar/gkw441 |
Nucleic Acids Research 44/16 | 2020-02-12 |
| 2016 |
Nerea Irigoyen, Andrew E. Firth, Joshua D. Jones, Betty Y.-W. Chung, Stuart G. Siddell, Ian Brierley High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling published pages: e1005473, ISSN: 1553-7374, DOI: 10.1371/journal.ppat.1005473 |
PLOS Pathogens 12/2 | 2020-02-12 |
| 2017 |
Gary Loughran, Michael T. Howard, Andrew E. Firth, John F. Atkins Avoidance of reporter assay distortions from fused dual reporters published pages: 1285-1289, ISSN: 1355-8382, DOI: 10.1261/rna.061051.117 |
RNA 23/8 | 2020-02-12 |
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