In order to fully understand transcription dynamics, we need microscope technologies that can image all the players involved with sufficient spatial resolution, over time.
We are designing novel microscopes to overcome the limitations of current instruments: for instance, our Multifocus Microscope (MFM ) can visualize the entire volume of the nucleus in one shot for fast tracking of individual molecules or 3D superresolution . The MFM is now available to the scientific community worldwide through the Janelia Advanced Imaging Center (AIC).
We have also built a drift-stabilized TIRF microscope that can be used for in vitro single molecule experiments in which the position of individual molecules can be tracked with nm precision over hours , allowing the quantification of single rounds of transcription on purified systems . The TIRF setup is also open to outside users through the Janelia Advanced Imaging Center (AIC).
In addition to these systems, we are also developing other approaches that will for example allow multiplexing the dynamics of multiple biological species simultaneously.
Our microscopes generate large datasets in which minute biological signals are emitted by individual molecules over important fluorescent background. In order to extract valuable biological data, we continuously devise innovative data analysis algorithms and techniques. These allow us to detect molecules, measure their trajectories with nanometer resolution so we can reconstitute the nucleus structural organization and its dynamics. Beyond data analysis, we also develop theoretical models in order to relate the genome architecture to transcription regulation.
Another key aspect of our work is data visualization: the Dahan lab recently developed a software dedicated to 3D superresolution data visualization (ViSP (El Beheiry and Dahan 2013)), and we continue to explore new ways to seamlessly navigate the multiple dimensions of data-rich movies.