Mechanisms of transcription regulation by CREB, with a focus on disordered domains

Transcription factors are proteins which regulate the expression of genes within our cells, often by being in close proximity to the DNA. Many transcription factors are intrinsically disordered proteins, meaning they have no setshape, which has made them difficult to study structurally. The bZIP family of disordered transcription factors, the second largest transcription factor family, binds the DNA as dimers like "a pair of chopsticks" through the major grooves using their bZIP domain. CREB (cAMP regulatory element (CRE) binding protein) is a disordered bZIP transcription factor of special interest, being overexpressed in cancers and helping regulate many physiological processes like the circadian clock. Hence, CREB is an ideal protein to study why disorder is important in transcription factors, being also very physiologically relevant. Recently, Shammas lab have investigated the nature of target search using bZIP domain constructs. In this project, we would use full-length CREB to reveal the role of the rest of the CREB sequence in this process, and transcriptional regulation in general. How does disorder contribute to transcription factor activity, and what happens when disorder is affected? Do they bind the DNA and search for their target site (CRE DNA, for CREB) as a monomer or a dimer? What roles do CREB partners play in the regulation of transcription? To answer these questions, we would study the DNA-CREB interaction under various conditions, for instance by mutating CREB, using biophysical techniques like stopped-flow or fluorescence anisotropy, confirming the results by using fluorescence microscopy and cell-based assays.