HEARTBEAT Fuzzy Modeling

Introduction

The research field of regulation of gene expression in eukaryotes is a field of biological research growing rapidly [1,2]. Hereby the interaction of DNA with certain proteins known as transcription factors (TFs) plays an essential role for the complex mechanism of transcriptional activation [3,4]. One strong focus of synthetic biology aims at the reconstruction of such gene regulatory networks [5]. To act within the scope of synthetic biology’s duties, the iGEM Team Heidelberg 09 claims that any synthetic promoter can be constructed by using our two methods for the construction of synthetic promoters. However, the only efficient way to construct systems of high complexity (such as computers or airplanes) is simulating these systems on the computer prior to construction [6]. In our case, this strongly emphasizes the necessity of HEARTBEAT (Heidelberg Artificial Transcription Factor Binding Site Engineering and Assembly Tool) which comprises data analysis (data analysis (HEARTBEAT DB), a graphical user interface (HEARTBEAT GUI) and network modeling (HEARTBEAT fuzzy network (FN) modeling).

Contributing to the HEARTBEAT project, HEARTBEAT FN focuses on simulating the promoter activity by integrating a variety of signals and sequence characteristics as well as on predicting distinct pathway functionalities. This, especially in eukaryotic systems, is a tough challenge since transcriptional activity of a gene is not directly correlated to protein expression [7].

For this purpose we propose fuzzy logic (FL) modeling as an approach to logic-based modeling which is capable of incorporating qualitative data but producing quantitative predictions. New insights will be provided about the operation of gene regulatory networks and relationships between promoter sequence composition and TF-DNA interaction will be unraveled that is understood only marginally so far [8,9].

Background / Motivation

We present two different approaches for promoter design resulting in three different types of synthetic promoters: randomly assembled constitutive and inducible promoters as well as rationally designed promoters. As an additional type of promoters those occurring in nature can be integrated into vector systems. These heterogeneous cocktail of promoters can be combined for a precise regulation of pathways. This represents the power of our entire HEARTBEAT project. Synthesized promoters can be then used e.g. as a combinatorial gene therapy, i.e. several promoters that are of different types and/or have different strength will be applied as treatment agents. Therefore, a model that not only simulates single promoter activity and following gene expression but also accurately predicts gene expression from combined promoter sequences is indispensable.

We constructed a Fuzzy Logic model to provide a formal mathematical framework for prediction of combined activity of multiple promoters upon several stimuli and to gain insight into the mechanisms that generate diverse expression levels.

References

[1] Kelly, JR et al in Journal of Biological Engineering 3 (2009): "Measuring the activity of BioBrick promoters using an in vivo reference standard"
[2] http://www.promega.com/tbs/tm058/tm058.html