Pioneering activity of PBX transcription factors in murine embryonic development

• Applicant: Dr. Vera Laub
• Subject Area: Developmental Biology ; General Genetics and Functional Genome Biology ; Bioinformatics and Theoretical Biology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 566814459

Developmental processes are controlled by the activity of transcription factors, which are proteins that bind to DNA and interact with chromatin, helping to organize it in a highly dynamic way throughout space and time. When chromatin is accessible and bound by specific proteins, it allows for genes to be active, i.e. expressed, while regions of chromatin that are tightly packed tend to remain inactive. In inactive chromatin, histones keep the DNA tightly wrapped as nucleosomes, thus preventing the binding of most transcription factors. However, a special group of transcription factors, known as ‘pioneer’ factors, are able to bind to these tightly packed chromatin regions. These 'pioneer factors' thus make chromatin more accessible, essentially marking genes to be activated in later stages of development. The PBX proteins, key players in development, are thought to function as such a ‘pioneer’ factors. PBX proteins are essential for many crucial developmental processes, including the formation of the brain, face, heart, and limbs. In the development of hindlimb mesenchyme, a form of embryonic soft connective tissue, PBX1 and PBX2 work together with another transcription factor, HAND2, to control where and when specific genes are expressed. However, in this context, it is yet unresolved whether PBX proteins are pioneering the binding of HAND2, and whether presence of PBX proteins is a necessary condition for HAND2-association with chromatin. While it’s been shown that PBX1 can bind to certain developmental genes before they are activated and help determine distinct cell fates, its exact role as a pioneer factor is still under investigation. To explore PBX’s potential pioneering function, in this project I plan to use a range of approaches that combine developmental biology, genetics, genomics, bioinformatics and advanced imaging techniques to study chromatin structure in the four dimensions of space and time. This will allow me to observe how PBX potentially interacts with closed chromatin and contributes to its opening in the context of gene regulation. Specifically, I will investigate whether PBX (i) binds to key developmental factors in tightly packed chromatin, (ii) promotes the opening of chromatin through 3D-architecture reorganization to allow other proteins to associate with DNA, and (iii) recruits chromatin-remodeling proteins that prepare cells for changes in fate. By analyzing experimental data through bioinformatics, I will reconstruct the developmental process in silico, aiding to clarify PBX’s role as a potential pioneer factor in development.

• DFG Programme: WBP Fellowship
• International Connection: USA
• Host: Professorin Licia Selleri, Ph.D.