Unveiling TF-RNA splicing regulatory networks in tissue development – TRren-D

Transcription Factors (TFs) are key players of cell fate by fine-tuning gene regulatory networks in precise cell and developmental contexts. While the current view states that they act on DNA regulatory elements, an emerging concept proposes that TFs bind RNA and modulate RNA fate at the transcription and splicing levels. Despite this central role in gene regulation, how TF-RNA regulatory function contributes to cell fate decision remains elusive. Alternative splicing is a remarkable process allowing the production of various mRNA isoforms from one single pre-mRNA. It relies on the dynamic assembly of the spliceosome and numerous accessory proteins that impel pre-mRNA fate in defined cell contexts and developmental stages. We hypothesise that one of the mechanisms by which TFs coordinate cell fate is by the cell-type specific assembly with RNA and the splicing machinery to regulate alternative splicing. To test our hypothesis, we will determine the RNA regulatory programs driven by TFs in the dynamic context of tissue development. To do so, we will use the Drosophila Hox TF Ultrabithorax (Ubx) as a model, for which we uncovered a novel function in splicing. Ubx interacts with a specific set of splicing factors in vivo in different tissue types. Importantly, Ubx modulates transcription and splicing to coordinate distinct cell functions in the mesoderm of Drosophila embryos. Here, we propose to reveal the RNA-wide binding profile and splicing protein networks of Ubx, using integrative approaches of genetic, transcriptomics, proteomics and in silico model to ultimately reconstruct Ubx-RNA splicing regulatory networks in muscle development. By decrypting how TFs modulate RNA fate during morphogenesis, our project will extend our insights into the molecular mechanisms underlining the building of multicellular organisms.