Biography
My research focuses on the dynamics of post-transcriptional control of gene expression. After my undergraduate studies in Biochemistry at the University of Otago, Dunedin, New Zealand I pursued a PhD in Biochemistry at University College Cork, Ireland where I focused on elucidating non-canonical gene expression mechanisms in RNA viruses. During this time, I discovered and characterised novel mechanisms viruses use to generate previously unknown, but essential factors for infection. First, in the potyviruses - the largest family of plant viruses, I discovered and characterised a novel gene expression mechanism that results in the production of an essential viral protein PIPO (Pretty Interesting Potyvirius ORF), required for the virus to travel from cell to cell. Second, I discovered and characterised the TF protein of alphaviruses - a group of clinically important mosquito-transmitted arboviruses - where TF is important for the stability of the virus particles.
Following my studies on unusual protein synthesis mechanisms, and supported by Long-Term EMBO and Sir Henry Wellcome Postdoctoral Fellowships, I joined the Department of Plant Sciences, University of Cambridge, where I worked on deciphering the regulation of protein synthesis in plants, making use of the unicellular green algae Chlamydomonas to reveal the ancestral mechanism of miRNA-mediated translational regulation. Now, through a Medical Research Council Career Development Fellowship, I have established my research group in the Department of Pathology where my group aims to understand how living organisms utilise novel protein synthesis regulatory mechanisms to counteract external stresses, especially during host:pathogen interaction (animal) and in response to temperature fluctuation (plants).
Research
Group members:
Dr Jessica Powell
Dr Sherine Thomas
Matt Brember
Filip Lastovka
Dominykas Murza
George Wood
Ella Bishop
Visiting Scientists
Dr Ying Tian Deng (Baulcombe Lab, Department of Plant Sciences)
Publications
Public resource development
riboSeqR – Bioinformatic software package developed with Dr Thomas Hardcastle (Department of Plant Sciences) as part of the Bioconductor project, to assist the community in the analysis of Ribosome profiling data [Hardcastle and Chung 2022; Chung et al.2015 RNA]
Peer reviewed publications
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Thomas, S., Balcerowicz, M., Chung, B. (2022) RNA structure mediated thermoregulation: What can we learn from plants? Frontiers in Plant Sciences DOI: 10.3389/fpls.2022.938570
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Albarnaz, J., Ren, H.,, Torres, A.A., Shmeleva, E.V., Melo, C.A., Bannister, A.J., Brember, M.P., Chung, B.Y.W., Geoffrey L. Smith G.L. (2021) Viral mimicry of p65/RelA transactivation domain to inhibit NF-κB activation. Nature Microbiology DOI: 10.1038/s41564-021-01004-9
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Dumetz, F., Chow, E., Harris, L., Umar, M., Jensen, A., Chung, B., Chan, T., Merrick, C., Kwok, K., (2021) G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum. Nucleic Acids Research DOI:10.1093/nar/gkab1095
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Balcerowicz, M., Di Antonio, M., Chung, B., (2021) Hairpin temperature-dependent FRET. Bio-protocol DOI:10.21769/BioProtoc.3950
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Pearce, S., Cipullo, M., Chung, B., Brierley, I., Rorbach, J. (2021) Mitoribosome Profiling from Human Cell Culture: A High Resolution View of Mitochondrial Translation. Methods in Molecular Biology: Mitochondrial Gene Expression. 2192:p183-196 DOI:10.1007/978-1-0716-0834-0_14
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Chung, B. (co-corresponding author), Balcerowicz M, Antonio M.D., Jaeger K.E., Geng F., Franaszek K., Marriott P., Brierley I., Firth A.E., Wigge P.A., (2020) An RNA thermoswitch regulates daytime growth in Arabidopsis. Nature Plants, May;6(5):522-532, DOI: 10.1038/s41477-020-0633-3,
May issue with an accompanying News and Views highlight.
Selected for Faculty of 1000.
Hot and highly cited by Thompson Reuter
First case of an eukaryotic RNA thermoswitch that controls protein synthesis
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Chung, B. (co-corresponding author), Molnar, A., Deery M., Valli, A., Hardcastle, T., Howard J. and Baulcombe, D. (2019) Distinct roles of Argonaute in the green alga Chlamydomonas reveal an evolutionarily conserved mode of miRNA-mediated gene regulation. Sci. Rep., 9:22091, DOI:10.1038/s41598-019-47415-x
Part II of Chlamydomonas miRNA story – provides an explanation of miRNA CDS targeting and its evolutionary importance.
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Chung, B. (co-corresponding author), Deery, M., Groen, A., Howard, J., and Baulcombe, D. (2017) Endogeneous miRNA in the green alga Chlamydomonasregulate translation repression through CDS-targeting. Nature Plants. Oct; 3(10):787-794 DOI:10.1038/s41477-017-0024-6
October issue with an accompanying News and Views highlight.
First demonstration of the global effects and targeting efficacy of endogenous miRNA on gene expression in plants.
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Valli, A., Santos, B., Hnatova, S., Bassett, A., Molnar, A., Chung, B., and Baulcombe, D. (2016) Most microRNAs in the single-cell alga Chlamydomonas reinhardtiiare produced by Dicer like 3- mediated cleavage of introns and untranslatable regions of coding RNAs. Genome Research26(4): 519-529, DOI: 10.1101/gr.199703.115
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Irigoyen, N., Firth, A., Jones, J., Chung, B., Siddell, S., and Brierley, I. (2016) High-resolution analysis of Coronavirus gene expression through RNA sequencing and ribosome profiling. PLoS Path.12(2):e1005473. DOI: 10.1371/journal.ppat.1005473
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Chung, B. (co-corresponding author), Hardcastle, T., Jones, J., Irigoyen, N., Firth, A., Baulcombe, D., and 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, DOI: 10.1261/rna.052548.115
Development of a non-organism specific rRNA depletion method for ribosome profiling and a software package for simultaneous analysis of ribosome profiling and corresponding RNA-seq.
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Olspert, A., Chung, B., Carr, J., and Firth, A. (2015) Transcriptional slippage in the positive-sense RNA virus family Potyviridae. EMBO Rep, 16: 995-1004,with an accompanying News and Views highlight DOI: 10.15252/embr.201540509
Deciphered the non-canonical expression mechanism of P3N-PIPO, an overlapping gene in the largest plant virus family.
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Smirnova, E., Firth, A., Scheidecker, D., Brault, V., Reinbold, C., Rakotondrafara, A., Chung, B., Miller, W., and Ziegler-Graff, V. (2015) Discovery of a small non-AUG-initiated ORF in Poleroviruses and Luteoviruses that is required for long-distance movement. PLoS Path, 11: e1004868, DOI: 10.1371/journal.ppat.1004868
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Cook, A., Chung, B. (joint first author), Bass, D., Moureau, G., Mcalister, E., Culverwell, L., Glucksman, E., Wang, H., Brown, T., Gould, E., Harbach, R., De Lamballerie, X. and Firth, A. (2013)Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts. PLoS ONE, 8: e80720, DOI: 10.1371/journal.pone.0080720
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Kuchibhatla, D., Sherman, W., Chung, B., Cook, S., Schneider, G., Eisenhaber, B. and Karlin, D. (2013) Powerful sequence similarity search methods and in-depth manual analyses identify remote homologs in many apparently “orphan” viral proteins. J Virol88: 10-20, DOI:10.1128/JVI.02595-13
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Chung, B., Firth, A. and Atkins, J. (2010) Frameshifting in Alphaviruses: a diversity of 3′ stimulatory structures. J Mol Biol, 397: 448-456. DOI:10.1016/j.jmb.2010.01.044
Characterization of cis-elements utilized for programmed ribosome frameshifting in Alphaviruses
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Firth, A., Chung, B. (joint first author), Fleeton, M. and Atkins, J. (2008) Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma. Virol J, 5: 108, DOI: 10.1186/1743-422X-5-108
Discovery of the overlapping gene (TF) in the important animal virus Alphavirus genus as well as characterization of its non-canonical expression mechanism via ribosome frameshifting
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Chung, B., Miller, W., Atkins, J., and Firth, A. (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci, 105: 5897-5902, DOI: 10.1073/pnas.0800468105,
Selected by Faculty of 1000.
Discovery of an essential overlapping gene in the largest plant virus family
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Chung, B., Simons, C., Firth, A., Brown, C. and Hellens, R. (2006) Effect of 5′ UTR introns on gene expression in Arabidopsis thaliana, Genomics, 7: 120, DOI: 10.1186/1471-2164-7-120