Speaker: Marianne Bauer, Ph.D., Delft University of Technology
Topic: Sensing transcription factors in the fly embryo
Transcription factor concentrations can be seen as signals that need to be sensed by organisms in order for them to express their genes as precisely as is required during development or during adjustment to different conditions. The low concentration of all the relevant molecules means that these measurements will be noisy, which sets a maximum that cells can extract. In embryonic development, as an example, there is a minimum of information that the organism needs in order to generate a complex body plan. I will present our work on how to extract this information using a “sensing scheme”, called the information bottleneck, which has recently gained popularity in neuroscience and machine learning. It helps us identify what optimal sensors of these transcription factors would look like. We find that these optimal sensors have important features in common with the fly enhancers. Our method thus provides a complement to mechanistic, bottom-up approaches for understanding why transcriptional elements are structured the way they are. If there is time, I will also discuss issues around optimal sensing given specific mechanistic constraints.