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Dr Ian Brierley

Dr Ian Brierley

Reader in Molecular Virology

Translational control

Ribosomal frameshifting and readthrough

Virus gene expression

RNA structure and function

Department of Pathology
University of Cambridge
Tennis Court Road
Cambridge
CB2 1QP

Office Phone: +44 (0)1223 336914

Biography:

Following a PhD at the University of York, where I studied transcriptional activation and DNA bending of cyclic AMP receptor protein-responsive promoters under the supervision of Jim Hoggett, I have worked in Cambridge,  focusing principally on the role of RNA structures in the translational regulation of gene expression, using viruses as model systems. Most of my publications concern protein synthesis, especially the phenomenon of ribosomal frameshifting, a translational regulatory event employed by numerous viral and some cellular genes. The work includes the first demonstration of a role for RNA pseudoknots in the regulation of translational elongation (Cell 57, 537-547, 1989), the development of an exogenous tRNA-dependent rabbit reticulocyte lysate system (RNA 7, 765-773, 2001), the description of novel translational recoding events in cellular genes (Molecular Cell 13, 157-168, 2004; Nucleic Acids Res. 33, 1553-1563, 2005), the first visualisation of mammalian ribosomes stalled during translocation (Nature 441, 244-247, 2006) and the first demonstration of -2 frameshifting at a viral frameshifting signal (Nucleic Acids Res. 40, 8674-8689, 2012).   The Department of Pathology at the University of Cambridge provides excellent research facilities and a broad expertise in virology/molecular cell biology. Presently, our work focuses on protein-dependent ribosomal frameshifting signals and ribosome profiling of virus-infected cells (detailed in Research Interests section).

 

Research themes

Virology:

Translational control of virus gene expression.

Research Interests

Brierley Research
Cryo-EM image of ribosomal-stalling at a frameshift-promoting RNA pseudoknot (purple). Shown are 40S subunit (yellow), bent tRNA (green) and associated eEF2 (red; Namy 2006 Nature 441 p244ff).
The Brierley lab., in close collaboration with the group of Dr Andrew Firth, study the regulation of virus gene expression at the level of protein synthesis, especially the phenomenon of ribosomal frameshifting. During translation, ribosomes generally stay in register and decode each codon triplet by triplet. However, some viral mRNAs have embedded signals that instruct ribosomes to change register, ie: to frameshift, at a defined position and to continue translation in an overlapping reading frame. Frameshift signals are exploited by many viruses to co-ordinate gene expression from overlapping coding sequences. The best studied examples come from the retroviruses. Here, the coding region for the enzymatic functions of the virus (pol) often overlaps the upstream structural protein coding sequences (gag) and is in the -1 reading frame. Expression of the pol gene requires a -1 frameshift at the end of gag and the Pol protein is produced as a fusion with the Gag protein. Our aim is to understand the frameshift process with a view to inhibiting it and thus to prevent virus replication. Many other RNA viruses have been shown to utilise a frameshift strategy in their replication cycle and there are emerging examples in cellular genes. A closely related translational phenomenon, termination codon suppression (readthrough), has also been described. Here, viral mRNA signals cause the misreading of stop codons, and an amino acid is inserted instead, at a certain frequency, resulting in an elongated polypeptide.

 

We are studying frameshifting and readthrough using coronaviruses and retroviruses as model systems. A frameshift signal has two elements, a "slippery sequence" where the ribosome enters the new reading frame, followed, in most cases, by an mRNA structure, often an RNA pseudoknot. A bipartite signal is also employed in readthrough but here, the pseudoknot induces suppression of an upstream stop codon. Recently, we have also identified novel signals where there is no stimulatory RNA structure and frameshifting is stimulated by the binding of trans-acting proteins. Our aim is to determine the mechanism by which these stimulatory signals induce the ribosome to change frame/misread the stop codon. Further, we are interested in gaining an understanding of RNA pseudoknot structure and function. The pseudoknot motif has been described in all cellular RNAs described to date and pseudoknots are clearly key regulatory RNA elements. Projects are underway to study

(1) Transacting factors, both protein and RNA, which influence frameshifting/readthrough (2) the structure of frameshift and readthrough stimulatory RNAs and proteins (3) ribosome conformation during frameshifting/readthrough (4) the effect on virus replication of altering frameshift/readthrough efficiencies.

We are also using the technique of ribosome profiling to globally-analyse RNA virus translation and virus-host responses. We are particularly interested in identifying novel examples of translational control.

  • Research Associates:
    Sawsan Napthine, Nerea Irigoyen
  • Graduate Students:
    Krzysztof Franaszek

Collaborators

Key Publications

1. Napthine S, Treffers EE, Bell S, Goodfellow I, Fang Y, Firth AE, Snijder EJ, Brierley I. (2016). A novel role for poly(C) binding proteins in programmed ribosomal frameshifting. Nucleic Acids Research in press (Breakthrough Article).

2. Irigoyen N, Firth AE, Jones JD, Chung BY, Siddell SG, Brierley I. (2016). High-resolution analysis of coronavirus gene expression by RNA sequencing and ribosome profiling. PLoS Pathog. 12:e1005473.

3. Chung B, Hardcastle T, Jones J, Irigoyen N, Firth A, Baulcombe D, Brierley I. (2015). The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-Seq data analysis. RNA, 21:1731-1745.

4. Finch LK, Ling R, Napthine S, Olspert A, Michiels T, Lardinois C, Bell S, Loughran G, Brierley I, Firth AE. (2015). Characterization of ribosomal frameshifting in Theiler's murine encephalomyelitis virus. J. Virol. 89:8580-8589.

5. Csibra E, Brierley I, Irigoyen N. (2014). Modulation of stop codon read-through efficiency and its effect on the replication of murine leukemia virus. J. Virol. 88:10364-76.

6. Li Y, Treffers EE, Napthine S, Tas A, Zhu L, Sun Z, Bell S, Mark BL, van Veelen PA, van Hemert MJ, Firth AE, Brierley I, Snijder EJ, Fang Y. (2014). Transactivation of programmed ribosomal frameshifting by a viral protein. Proc. Natl. Acad. Sci. U S A. 111:E2172-81.

7. Brierley, I. (2013). Macrolide-induced ribosomal frameshifting: a new route to antibiotic resistance. Molecular Cell. 52: 613-615.