Exploring the contribution of transcription to native chromatin looping and genome conformation

The precise spatiotemporal control of gene expression is critical for cell identity and cell homeostasis. We now understand that this control is exerted also via the three-dimensional organization of the genome. Thus, the converging and conflicting dynamic forces that act on chromosomes in order to regulate their architecture are of utmost importance in understanding gene regulation. A number of transcription factors and “structural“ proteins has been extensively studied for the contribution to genomic architecture. However, an enzyme that is essential for life and is a powerful molecular machine central to chromatin processes, the RNA polymerase, has not been analyzed in detail to date. It is, therefore, necessary to bridge this gap-of-knowledge and study the direct impact of the different RNA polymerases on chromatin dynamics and vice versa, to finally unveil the full 3D regulatory repertoire of mammalian cells. This requires generation of mammalian cell lines with specific, inducible, and reversible degradation of RNA polymerase II and/or III, and subsequently the implementation of our “native” chromosome conformation capture technology in conjunction with a novel and truly integrative pipeline for in silico analysis on the basis of unsupervised “deep” machine learning. We expect that this project will resolve the debate on the contribution of active transcription to chromatin looping, and lay the ground for identifying new paths via which mammalian genomes are organized and regulated in a spatiotemporal manner.