Abstract:

Transcriptional regulation is the complex system of interactions used to produce precise gene expression at specific times and locations. Encapsulating our understanding of these interactions in computational models allows the exploration and prediction of the cellular response to changing environments, which can provide invaluable support and guidance to experimental research. Computational models are needed for a wide range of applications such as predicting cellular response based on a patient’s genome in personalized medicine and designing the regulation for novel synthetic biological constructs. Cells use several different transcription regulation mechanisms including: transcription factor interactions, nucleosome positioning, chromatin remodeling, and transcriptional interference. These mechanisms are used individually or in combination to create complex regulation that can limit expression to a specific cellular environment. Additionally the transcription process itself modifies the regulation mechanisms by removing transcription factors and nucleosomes as it transcribes. We have combined the individual models of specific regulation methods into a single model.