GENOMIC LANDSCAPE AND TRANSCRIPTIONAL REGULATION BY YAP AND MYC IN THE LIVER

This thesis is divided in three sections; the main project is described in the first part, while additional projects are developed in two appendixes. In the main project we studied YAP, the downstream effector of the Hippo pathway, a transcriptional co-factor that plays a fundamental role in de-differentiation, cell proliferation and transformation. While its upstream regulation has been extensively studied, its role as transcriptional co-factor is still poorly understood. We show that YAP co-adjuvates the transcriptional responses of Myc oncogene to promote cell proliferation and transformation; when both YAP and Myc are overexpressed, YAP is recruited on genomic sites pre-marked by Myc, TEAD and active chromatin and potentiate the expression of cell cycle genes regulated by Myc. In addition, we show that YAP promotes cell de-differentiation by antagonizing in cis the expression of liver-specific genes controlled by HNF4A master regulator, thus providing a mechanism on how YAP can revert the phenotype of a differentiated hepatocyte into a progenitor cell. In the first appendix we explain the mechanism of BRD4 inhibition, a promising strategy for the treatment of Myc-driven tumors. The efficacy of this strategy relies on the control of transcriptional elongation mediated by BRD4 on gene promoters, independently of the downregulation of Myc oncogene. Although the inhibition of BRD4 causes its genome-wide displacement on promoters, the effects on transcription are restricted to a subset of sensitive genes. This specificity relies on the fact that while most genes compensate the drop in elongation caused by BRD4 inhibition with further recruitment of RNA Pol2 on promoters and maintain a proficient mRNA transcription, vulnerable genes are not able to promote these compensatory effects, because RNA Pol2 recruitment on these promoters is already maximized. Our results show how the impairment of elongation genome-wide can affect specific transcriptional programs. In the second appendix we describe a new web application, Chrokit, aimed at analyzing genomic data in a fast and intuitive way. Chrokit handles a set of genomic regions of interest and performs several tasks on them, such as selecting particular subsets, computing overlaps and visualize reads enrichment of specific chromatin features interactively. The application is multiplatform and can be run on dedicated servers to maximize computational power and provide accessibility to multiple users simultaneously.