Macromolecular Interplay and Traffic on DNA

A detailed understanding of the interplay between regulatory proteins and DNA targets is required to interpret transcriptomic data and to model the dynamics of genetic networks. This special issue deals with two key problems encountered in this respect: One is the control of macromolecular traffic on DNA, the other is the interplay between regulatory proteins acting on the same target gene. Is this issue Dutreix et al. discuss RecA-induced homologous DNA recombination as a paradigm for the search of a site on a long DNA molecule by a smaller molecule. The speed and efficiency of the reaction cannot be explained by brownian motion or molecular tracking, but presumably involves molecular translocations or inchworm local movements. Reinitz et al. present a refined three-layer model of transcriptional regulation. In particular, above direct DNA-binding by factors, the second layer involves adapter molecules binding to DNA-bound factors, while the third layer includes a physical model of how adapters initiate transcription. That second layer is reminiscent of the view presented by Benecke, which he proposes to exploit for genome-wide identification of human DNA targets that are controlled by a combination of certain regulatory factors. The article by Failla et al. introduces two new light microscopy approaches that allow unprecedented spatial resolution. These methods, together with modeling, suggest a relationship between chromosome organization and transcriptional status. Any life scientist interested in transcriptomics and the dynamics of genetic networks will benefit from the novel views and perspectives presented in this set of papers.