Ian Dodd

I am based in the laboratory of Assoc Prof Keith Shearwin (Biochemistry, Molecular and Biomedical Science) https://researchers.adelaide.edu.au/profile/keith.shearwin.

Research in the Shearwin lab integrates biochemistry, genetics and mathematical modelling to characterise fundamental mechanisms of gene control and how these mechanism are combined to create gene regulatory circuits with complex functions. Our primary experimental systems are two E. coli bacteriophages, lambda and 186. These temperate phages can replicate their genomes using alternative developmental pathways, lysis and lysogeny, and are some of the simplest organisms to make developmental decisions. Despite their relative simplicity, the phage systems combine a wide range of gene control mechanisms in complex ways and have many lessons to teach us.

The phage systems have been the springboard for my particular interests in DNA looping, molecular traffic on DNA and epigenetics.

DNA loops are created when proteins bound to separated sites on the same DNA interact with each other. These interactions can be critical in gene regulation (for example between eukaryotic promoters and enhancers), but it is still not understood how these loops can form efficiently, especially over long distances, and how certain looping interactions are chosen over others. Our research utilizes experiments with well-defined looping proteins in E. coli and mathematical modelling to find simple rules that govern looping efficiency and how this is affected by the positive or negative interactions between different DNA loops.

A simple picture of the transcription of a gene has RNA polymerase binding to the DNA at the promoter, initiating transcription and then transcribing uneventfully until reaching a terminator sequence and falling off the DNA. However, in reality the DNA is not a ‘freeway’ for RNA polymerase but is more like a crowded one-lane two-way street. As an RNA polymerase makes its way along the DNA, its progress can be affected by a myriad of ‘roadblock’ proteins bound to the DNA and also by other traffic such as RNA polymerases moving in the opposite direction. How can efficient transcription occur under such conditions? How are these obstacles used by the cell to regulate transcription? How is the function of the DNA-bound proteins affected by the passage of RNA polymerase? We examine these questions using synthetic gene expression constructs in E. coli cells and mathematical modelling.

Epigenetics allows cells with the same genome and that share the same environment to exist in distinct, persistent and heritable gene expression states. During development, cells with different identities are created by transient environmental signals causing changes in gene expression that persist after the signal disappears and are passed to the cell’s descendants. This epigenetic cell differentiation is needed to produce the many diffeent specialized cells required in multicellular organisms. Such stable and heritable alternative gene expression states can be generated by positive feedback in circuits of diffusible gene regulators. We study how the phage 186 and lambda regulatory proteins are wired to create bistable circuits and how this affects the choice between lytic and lysogenic development. We also design and test synthetic bistable circuits made from these phage components. The other major class of epigenetic mechanism is chromatin-based, where gene expression is regulated by self-sustaining modifications to chromatin, such as histone modifications or DNA methylation. My work in this area is solely theoretical, and is a collaboration with Prof Kim Sneppen, a physicist at the Niels Bohr Institute in Copenhagen. We mathematically model positive feedback, where nucleosomes carrying a particular modification stimulate formation of the same modification on nearby nucleosomes, or methylated CpG DNA sequences stimulate methylation of nearby CpGs. Our work demonstrates the need for this positive feedback to be ultrasensitive (cooperative) and to act beyond nearest neighbours (not a simple spreading), in order to generate distinct, stable and heritable states.