Profile

Contact Details

Email: chunshen.lim@otago.ac.nz

University Links

Position: Research Fellow
Department: Department of Biochemistry
Research summary: Genomics and bioinformatics

Research

The regulation of gene expression is critical for the normal cellular function and the development of multicellular eukaryotes. It is also important in prokaryotes and virus-infected cells.

I am establishing my research into the fundamental steps of gene expression and how these can be manipulated in experimental systems. I have been researching different aspects of gene expression and regulation since my doctoral (2015-2018) and postdoctoral research (2018-2020).

For more details, see our homepage.

Why are some genes highly expressed? Why are some proteins poorly soluble? We are investigating the key sequence features that control gene expression and protein solubility.

How does the exon-intron gene structure emerge? Most of our genes are in pieces. The existence of the intervening sequences, so called introns, is still a mystery. We are comparing the genomes of various species to probe the origin of introns and their functions.

A new role of introns? We have recently found an undescribed mechanism that regulates gene expression, through splicing and translation. This links splicing and translation, key sequential cellular processes that occur in two separate cellular compartments. We estimate that ~30% of messenger RNAs are regulated by this new mechanism. We are developing computational and experimental methods (e.g., quantitative proteomics) to study this new mechanism.

What is the role of RNA splicing in viruses? Hepatitis B virus (HBV) affect 296million people worldwide. HBV is an unusual DNA virus. HBV produces the pregenomic RNA that is retro-transcribed into genomic DNA. While the introns of most human mRNAs are completely spliced out, the introns of HBV pregenomic RNA are partially spliced. We are investigating the sequence features and cellular processes that control splicing in HBV.

Publications

Lim, C. S., Bhandari, B. K., & Gardner, P. P. (2022). Fast and scalable prediction of protein-protein interactions. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go Conference Contribution - Published proceedings: Abstract

Smith-Beech, A. I. S., Delargy, E., Dearden, P. K., Lim, C. S., & Wilbanks, S. M. (2022). Phycourobilin and the evolution of the Florideophyte phycobilisome. Proceedings of the International Society of Photosynthesis Research (ISPR) 18th International Congress on Photosynthesis Research. (pp. 276). Retrieved from https://www.ps2022.nz Conference Contribution - Published proceedings: Abstract

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2021). TISIGNER.com: Web services for improving recombinant protein production. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 2). Retrieved from https://www.faobmb2021.org Conference Contribution - Published proceedings: Abstract

Lim, C. S., Wardell, S., Kleffmann, T., Weinstein, B., Roy, S., & Brown, C. (2021). The evolution and function of introns. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 161). Retrieved from https://www.faobmb2021.org Conference Contribution - Published proceedings: Abstract

Bhandari, B. K., Lim, C. S., Remus, D. M., Chen, A., van Dolleweerd, C., & Gardner, P. P. (2021). Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Computational Biology, 17(10), e1009461. doi: 10.1371/journal.pcbi.1009461 Journal - Research Article

2022

Conference Contribution - Published proceedings: Abstract

2021

Journal - Research Article

Lim, C. S., Weinstein, B. N., Roy, S. W., & Brown, C. M. (2021). Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species. Molecular Biology & Evolution, 38(10), 4166-4186. doi: 10.1093/molbev/msab094

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2021). TISIGNER.com: Web services for improving recombinant protein production. Nucleic Acids Research, 49, W654-W661. doi: 10.1093/nar/gkab175

Lim, C. S., Sozzi, V., Littlejohn, M., Yuen, L. K. W., Warner, N., Betz-Stablein, B., … Brown, C. M. (2021). Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes. Microbial Genomics, 7, 000492. doi: 10.1099/mgen.0.000492

Conference Contribution - Published proceedings: Abstract

2020

Journal - Research Article

Chapman, L. M., Spies, N., Pai, P., Lim, C. S., Carroll, A., Narzisi, G., … Zook, J. M. (2020). A crowdsourced set of curated structural variants for the human genome. PLoS Computational Biology, 16(6), e1007933. doi: 10.1371/journal.pcbi.1007933

Bhandari, B. K., Gardner, P. P., & Lim, C. S. (2020). Solubility-Weighted Index: Fast and accurate prediction of protein solubility. Bioinformatics, 36(18), 4691-4698. doi: 10.1093/bioinformatics/btaa578

Tan, L. P., Tan, G. W., Sivanesan, V. M., Goh, S. L., Ng, X. J., Lim, C. S., … the Malaysian Nasopharyngeal Carcinoma Study Group. (2020). Systematic comparison of plasma EBV DNA, anti-EBV antibodies and miRNA levels for early detection and prognosis of Nasopharyngeal Carcinoma. International Journal of Cancer, 146, 2336-2347. doi: 10.1002/ijc.32656

Working Paper; Discussion Paper; Technical Report

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2020). Improving recombinant protein production using TISIGNER.com. bioRxiv. doi: 10.1101/2020.07.09.196469

Bhandari, B. K., Gardner, P. P., & Lim, C. S. (2020). Protein solubility is controlled by global structural flexibility. bioRxiv. doi: 10.1101/2020.02.15.951012

2019

Conference Contribution - Published proceedings: Abstract

Bhandari, B. K., Lim, C. S., & Gardner, P. (2019). Protein expression is controlled by the accessibility of translation initiation sites. Proceedings of the 16th Asian Conference on Transcription. (pp. 43). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02

Lim, C. S., Bhandari, B. K., & Gardner, P. P. (2019). Highly accessible translation initiation sites are predictive of successful heterologous protein expression. Proceedings of the 16th Asian Conference on Transcription. (pp. 75-76). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/

Bhandari, B., Lim, C. S., & Gardner, P. (2019). SoDoPE: Soluble domain for protein expression. Proceedings of the 16th Asian Conference on Transcription. (pp. 66). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/

Lim, C. S., Bhandari, B. K., & Gardner, P. P. (2019). Improving the expression and solubility of recombitant proteins by smart sequence design algorithms. Proceedings of the 16th Asian Conference on Transcription. (pp. 52). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/

Conference Contribution - Poster Presentation (not in published proceedings)

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2019, August-September). TIsigner: Controlling protein expression with designer translation initiation regions. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Lim, C. S., Bhandari, B. K., & Gardner, P. P. (2019, August-September). Highly accessible translation initiation sites are predictive of successful heterologous protein expression. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2019, August-September). Protein expression is controlled by the accessibility of translation initiation sites. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2018

Journal - Research Article

Lim, C. S., Wardell, S. J. T., Kleffmann, T., & Brown, C. M. (2018). The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Research, 46(9), 4575-4591. doi: 10.1093/nar/gky282

Journal - Research Other

Lim, C. S., & Brown, C. M. (2018). Know your enemy: Successful bioinformatic approaches to predict functional RNA structures in viral RNAs. Frontiers in Microbiology, 8, 2582. doi: 10.3389/fmicb.2017.02582

Conference Contribution - Published proceedings: Abstract

Brown, C., Chyou, T.-y., Lim, C. S., Padilla, E., Nilsen, A., Liu, S., … Summerfield, T., … Orlovich, D. (2018). The functions of non-coding RNAs and elements in fungal genomes: New roles in the regulation of gene expression. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 53). Retrieved from https://www.nzmsconference.org.nz

Lim, C. S., & Gardner, P. (2018). How can we increase the success rate of recombinant protein expression in Escherichia coli? Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 38-39). Retrieved from https://www.nzmsconference.org.nz

Conference Contribution - Poster Presentation (not in published proceedings)

Lim, C. S., & Brown, C. M. (2018, August). Analysis of transcript splicing. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Lim, C. S., & Gardner, P. P. (2018, August). Avoidance of stochastic mRNA:ncRNA interactions in successful recombinant protein expression in Escherichia coli. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Other Research Output

Lim, C. S. (2018, July). New roles of introns in translation. Department of Biochemistry, University of Otago, Dunedin, New Zealand. [Department Seminar].

Awarded Doctoral Degree

Lim, C. S. (2018). Roles of introns (PhD). University of Otago, Dunedin, New Zealand. Retrieved from http://hdl.handle.net/10523/8464

2017

Journal - Research Other

Lim, C. S., & Brown, C. (2017). A new class of ribozyme from hepatitis B virus. FEBS Journal, 284(8), 1182-1183. doi: 10.1111/febs.14062

Conference Contribution - Published proceedings: Abstract

Lim, C. S., & Brown, C. (2017). Independent loss of introns during evolution across multiple fungal clades. Proceedings of the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB). 680. Retrieved from http://gen2017.w.events4you.currinda.com

2016

Journal - Research Article

Lim, C. S., & Brown, C. M. (2016). Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element. RNA Biology, 13(9), 743-747. doi: 10.1080/15476286.2016.1166330

2015

Journal - Research Article

Lim, C. S., Goh, S. L., Kariapper, L., Krishnan, G., Lim, Y.-Y., & Ng, C. C. (2015). Inclusion bodies of recombinant Epstein–Barr virus capsid antigen p18 as potential immobilized antigens in enzyme immunoassays for detection of nasopharyngeal carcinoma. Clinica Chimica Acta, 448, 206-210. doi: 10.1016/j.cca.2015.07.008

Lim, K.-S., Tan, A.-H., Lim, C.-S., Chua, K.-H., Lee, P.-C., Ramli, N., … Ng, C.-C. (2015). R54C mutation of NOTCH3 gene in the first Rungus family with CADASIL. PLoS ONE, 10(8), e0135470. doi: 10.1371/ journal.pone.0135470

2014

Journal - Research Article

Lim, C. S., Goh, S. L., Krishnan, G., & Ng, C. C. (2014). Recombinant production of Epstein-Barr virus BZLF1 trans-activator and characterization of its DNA-binding specificity. Protein Expression & Purification, 95, 8-12. doi: 10.1016/j.pep.2013.11.007

2013

Journal - Research Other

Lim, C. S., Krishnan, G., Sam, C. K., & Ng, C. C. (2013). On optimizing the blocking step of indirect enzyme-linked immunosorbent assay for Epstein-Barr virus serology [Short communication]. Clinica Chimica Acta, 415, 158-161. doi: 10.1016/j.cca.2012.08.031