Overview
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).
Projects
A new role of introns?
We have recently found an undescribed mechanism that regulates gene expression, through splicing and translation of mRNAs (Lim et al., 2018). 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. We are looking for students interested in this interdisciplinary project.
What is the role of splicing in viruses?
Hepatitis B virus (HBV) affect 296 million people worldwide. HBV is an unusual DNA virus. HBV produces the pregenomic RNA that is retro-transcribed into genomic DNA. We have experimentally characterised the spliced pregenomic RNAs of HBV and shown that these spliced RNAs are specific to the different genotypes of HBV (Lim et al., 2021). We also identify similar genotype-specific expression profiles in human liver and infected primary cells (501 public RNA-seq libraries), suggesting the viral spliced RNAs could be functionally important.
How does the exon-intron gene structure emerge?
We have reconstructed the evolutionary history of intron presence/absence in fungi and found a general bias towards intron loss over intron gain (Lim et al., 2021). We estimate that all modern species have experienced a net reduction in intron number from an initially highly intron-rich fungal ancestor (>8 introns per kilobase, more than modern humans). Interestingly, we find that these intron gain and loss events have given rise to exons that are 6-fold larger than average exons. Some introns are well conserved across species and even harbour functional noncoding RNAs.
How to enhance gene expression and protein solubility?
Why are some genes highly expressed? Why are some proteins poorly soluble? We sought to understand the key sequence features that control gene expression and protein solubility. We identify that the ‘accessibility’ of the mRNA regions around initiation codons correlates with gene expression (Bhandari and Lim et al., 2021). For protein solubility, we find that ‘flexible’ proteins tend to be more soluble (Bhandari et al., 2020). We have developed user-friendly web services to harness these features for optimising recombinant protein expression and solubility of genes of interest (Bhandari et al., 2021).
Computational tools
Web services for improving recombinant protein production
Comparison of the ability of open reading frames to recruit ribosomes within individual transcripts
Experimental resources
Funding
I am currently supported by the Royal Society of New Zealand Te Apārangi (Marsden grant 19-UOO-040, Are molecular mis-interactions a major constraint on the evolution of cellular and genomic complexity? PI Paul Gardner).
My postdoctoral study (2018-2020) was supported by the MBIE Smart Idea grant (UOOX1709, Building bioinformatic software for controlling protein expression, PI Paul Gardner).
My PhD study (Roles of Introns, 2015-2018) was supported by the Dr Sulaiman Daud 125th Jubilee Postgraduate Scholarship.
