My independent research career was launched in January 2010 when I joined the department of Biochemistry and Molecular Biology at Monash. By the transfer of the final 3 years of my Australian Research Fellowship (ARC) and with support from the Department, I was able to embark on the most exciting (and sometimes terrifying) phase of my scientific career!
My background was in yeast cell-biology, initially studying the trafficking of proteins to the subcellular organelles and the role that protein translation plays in this. Then came a move to the U.S.A. for a post-doctoral term in the renowned lab of Prof. Randy Schekman (UC-Berkeley). This was a major turning point in my life; I was sharing the lab with 17 super-smart post-docs from around the world, each competing for that career-making CELL paper. It was an experience and opportunity for which I will always be grateful. It had all the great things; real scientific debate (untainted by concern for delicate egos), respect for proper controls, an appreciation of both technically and visually perfect data and the joy of long interactive lab meetings with nibbles and beer! But I also grew up scientifically, realizing (a bit late) that in vitro reconstitution was not really my thing after all. I could appreciate it for all its elegance, but kept being drawn to the amazing developments in live-cell-imaging and the newly feasible high-throughput technologies that were springing up all around me in the "Bay Area" of San Francisco. The idea that, instead of testing hypotheses based on our imperfect knowledge of what goes on in a cell, we could design experiments that allow the cells to show us what they actually do. So when the opportunity arose to return "home" to work on the genome-wide control of mRNA translation, I jumped. Thus, armed with a Howard Florey Centenary Fellowship (NHMRC) I headed for the Victor Chang Cardiac Research Institute (Sydney) and the newly formed lab of Thomas Preiss. Yikes, what a shock! Yeast biologist let loose amongst cardiologists... we spoke different languages. It took time to realize that I wasn't alone in feeling like this. In the labs next-door were Pete Currie's group doing evo-devo on limb development, David Martin and Cath Suter were studying epi-mutation by DNA silencing, and the bioinformatics team were working on structural disulfides in silico. It took even longer to realize that this was the point! Great research is often about mixing skills and technologies. And, a great research environment is bigger than the sum of its parts. Thus years went by happily tinkering in the lab with dismal failures and some wonderful private and professional successes.
Before long, circumstances made it seem right to move back to Melbourne, but where? Trevor Lithgow, my long-term mentor said "Monash is great" and he was right (as he always is). The head of department, Rob Pike said that the department would help out for 3 years "because that's what it takes", and as it turns out he was right too. Although, there seemed reason to doubt his optimism after the first crushing "un-fundable" grant outcomes in 2010. With hindsight, this was hardly surprising, the grants oozed enthusiasm, but held almost no feasibility data or evidence that I could actually run a project to a successful conclusion. 2011 was slightly better, still "unfunded" but at least in the fundable range. Finally, two successful NHMRC grants in 2012 is more than I had dared to dream. And best of all, the lab tinkering is throwing out some really cool stuff that is allowing me to do the cross-disciplinary work that the experience at the Victor Chang had prepared me for.
My specialty is RNA metabolism. What happens to mRNA after it is made? I am particularly interested in the UnTranslated Region at the end of the mRNA molecule (3'UTR). The reason for this is because the 3'UTR holds regulatory information. It can direct when, where and how often an mRNA is engaged by ribosomes to make protein. For example, 3'UTRs contains the vast majority of microRNA binding sites, the sequences/structural elements that interact with localization machinery and the motifs that regulate RNA stability. Much of my work in this area has been to develop technologies to monitor 3'UTR dynamics both of individual transcripts and across the transcriptome. My initial focus was on dynamic change in the length of the poly(A)-tail. Showing that genome-wide, a short poly(A)tail is generally associated with translational repression whereas robustly translated mRNA tend to have a long poly(A)-tail. But very recently the dynamic use of alternative polyadenylations sites has been added to my repertoire. About 50% of all eukaryotic mRNA are subject to condition dependent alternative polyadenylation. There is a general trend for a short 3'UTR in proliferative cells (stem cells) and a long 3'UTR in differentiated cells. Such longer 3"UTRs provide extra scope for regulation of translation. Switching to a short "embryonic 3'UTR" is rampant in Cancer cells. The shift to a shorter 3'UTR can mean that the platform for post-transcriptional silencing is lost and oncogenes become over-expressed. In 2011-12 with help from a small "impact fund" (Industry Engagement and Commercialisation) grant I developed a 3' focused RNA-seq method to simultaneously measure gene expression, the length of the poly(A)-tail and its position in the transcriptome by next generation sequencing. I now use this method to monitor gene expression and 3'UTR dynamics in all my work and have built a number of exciting collaborative projects with colleagues on my floor, within SoBS, Interstate and internationally applying this technique. My group thus now studies 3'UTR dynamics in model and pathogenic yeasts, in C. elegans worms, in murine brain development, the circadian rhythm of zebrafish and in the reprograming of induced pluripotent stem cells. There is even a dataset looking at 3'UTR switching in cardiac hypertrophy, something the director of the Victor Chang had always hoped would materialize out of the seemingly hotchpotch collection of researchers he assembled. It should be added that my floor (2/76) is just the same, with the departments of Biochemistry, Microbiology, Developmental biology and, most importantly for my work, the Victorian Bioinformatics Consortium (VBC) all mixed up together. Indeed, the biggest challenge for my own group, and other groups moving into high throughput areas of biology is the incorporation of bioinformatics into the experimental workflow. Once datasets grow too big for Excel it becomes essential to work in the command-line using "languages" that traditional biologists such as myself don't understand. Some computational aspects can and should be automated, but the interpretation of the data still requires biological insight. My mission now is to try to teach students to do both. As a first experimental step in this direction, Dr. David Powell (Life Science Computation Centre/VBC) and I are recruiting our first "biological computation" honors student for 2013. Let's see how that goes....
The Research Team
Research assistant: Amrei Jänicke
PhD student: Angavai Swaminathan