Enhancers are complex regulatory regions that consist of many binding sites for several Transcription Factors(TFs). They are ubiquitous in all organisms, and are in particular associated in controlling gene expression during development.
Recently, we showed that enhancers are modular objects that can be divided into three modules or segments:
- The driver module – akin to your computer’s power switch – without the presence of this TF, expression will not possible.
- The program module – this is the area on the DNA that integrates binding sites for many TFs. The presence or absence of TFs either increases (activates) or decreases (represses) the probability for transcription. Thus, this module is akin to the software installed on your computer
- The CPU module – this is the actual promoter region which typically binds a poised RNA polymerase holoenzyme complex. Transcription will commence only if DNA looping will take place and the driver forms a contact with the promoter. As a result, this region is responsible for integrating all the inputs and executing a computational like process, yielding an RNA transcript in a particular time and place.
This computational process is not typically digital, but rather analog.
In this effort, we would like to focus on several subjects:
- Design program modules that activate or increase the probability of expression (i.e. so far we have been successful in understanding repression).
- Design synthetic enhancer gene regulatory circuits. Here we will “wire” together two enhancers to form a gene circuit that will execute some type of computational operation. Examples include:
- We would like to build the intra-cellular detect circuit. Namely, a piece of DNA that will be transformed into an organism or various cell types (otherwise indistinguishable), and based on the proteome content will decide whether or not to execute a program.
- Spatial domains. We would like to develop gene circuits that generate three-dimensional patterns in microfluidic devices with artificial morphogen gradient environments. Is it possible to generate intricate geometric patterns with bacteria cells?