BCIT Citations Collection | BCIT Institutional Repository

BCIT Citations Collection

Gene expression noise in embryonic spatial patterning
Proceedings of 2011 21st International Conference on Noise and Fluctuations in Toronto, ON, Canada on 12-16 June 2011. Fruit flies serve as a model for understanding the genetic regulation involved in specifying the complex body plans of higher animals. The head-to-tail (anterior-posterior) axis of the fly (Drosophila) is established in the first hours of development. Maternally supplied factors form concentration gradients which direct embryonic (zygotic) genes where to be activated to express proteins. These protein patterns specify the positions and cell types of the body's tissues. Recent research has shown, comparing between embryos, that the zygotic gene products are much more precisely positioned than the maternal gradients, indicating an embryonic error reduction mechanism. Within embryos, there is the additional aspect that DNA and mRNA operate at very low copy number, and the associated high relative noise has the potential to strongly affect protein expression patterns. In recent work, we have focused on the noise aspects of positional specification within individual embryos. We simulate activation of hunchback (hb), a primary target of the maternal Bicoid (Bcd) protein gradient, which forms an expression pattern dividing the embryo into anterior and posterior halves. We use a master equation approach to simulate the stochastic dynamics of hb regulation, using the known details of the hb promoter, the region of DNA responsible for transcribing hb mRNA. This includes the binding/unbinding of Bcd molecules at the promoter, hb transcription, subsequent translation to Hb protein, binding/unbinding of Hb at the promoter (self-regulation), and diffusion of the Bcd and Hb proteins. Model parameters were set by deterministically matching large scale pattern features for a series of experimental expression patterns: wild-type (WT) embryos; hb mutants lacking self-regulation; and constructs in which portions of the hb promoter were used to express a reporter gene (lacZ). The model was then solved stochastically to predict the noise output in these different experiments. In subsequent noise measurements we experimentally corroborated a number of the predictions. These include that mRNA is noisier than protein, and that Hb self-regulation reduces noise. Results indicate that WT (self-regulatory) Hb output noise is predominantly dependent on the transcription and translation dynamics of its own expression, and is uncorrelated with Bcd fluctuations. This contradicts prior work, which had assumed a complete dependence of Hb fluctuations on Bcd fluctuations. In the constructs and mutant, which lack self-regulation, we find that increasing the number and strength of Bcd binding sites (there are 6 in the core hb promoter) provides a rudimentary level of noise reduction. The model is robust to the various Bcd binding site numbers seen across different fly species. New directions in the project include incorporating a known inhibitor of hb, Krüppel, into the model to study its effect on the noise dynamics. Our study has identified particular ways in which hb output noise is controlled. Since these involve common modes of gene regulation (e.g. multiple regulatory sites, self-regulation), these results contribute to the general understanding of the reproducibility and determinacy of spatial patterning in early development., Conference paper, Published.
Stochastic dynamics of gene expression in developing fly embryos
Proceedings of 2017 International Conference on Noise and Fluctuations (ICNF), Vilnius, Lithuania on 20-23 June 2017. Segmentation of the developing insect body is preceded by cell-specific gene expression. In fruit flies (Drosophila), pair-rule genes are expressed in spatial stripes specifying segment fates. Transcription of the even-skipped (eve) pair-rule gene was recently shown to proceed in noisy bursts. Here, we develop a stochastic model of eve transcription from DNA to mRNA. This indicates that eve transcription proceeds at two rates, with a slow rate providing basal production and a fast rate allowing for high mRNA output. This two-rate transcription may afford more reliability in mRNA output, and therefore the protein levels which specify cell type, than a simple on-off (one-rate) mechanism., Conference paper, Published.