Dynamic interplay between genome organization and long noncoding RNAs in the regulation of gene expression

About This Grant

PROJECT SUMMARY In multicellular organisms, development and homeostasis require exquisitely precise, dynamic, and coordinated deployment of complex regulatory programs. As many genes are under the control of vast regulatory regions – with some enhancers located over a million base pairs away from target genes – we and others have explored to what extent the 3D organization of the genome facilitates the establishment of specific regulatory interactions. Additionally, regulatory regions are pervasively transcribed to generate a striking diversity of long noncoding (lnc)RNAs, which are emerging as important chromatin and transcriptional regulators. However, the molecular determinants and regulatory roles of genome organization remain unclear, and only a minute fraction of known lncRNAs have been ascribed any function. My recent work used innovative single-cell live imaging approaches to show that genome organization and cis-regulatory lncRNAs both play a key role in regulating the temporal dynamics of gene expression. My findings also suggest that lncRNAs may exploit – or even regulate – genome organization to exert long-range transcriptional control. The goal of my research is to understand how genome organization and lncRNAs regulate gene expression, and to investigate their mutual interplay. My lab will use our cutting-edge approaches to measure transcriptional dynamics in Drosophila embryos to investigate how long-range interactions are established; how lncRNAs operate in the context of long-range regulation and utilize genome organization; and how in turn lncRNAs can control genome organization. In my prior work, I identified novel “tethering elements” that foster specific long-range interactions to enable fast gene activation during development. In Project I, I will investigate the role of a well-known epigenetic repressor, Polycomb Repressive Complex 1, in facilitating transcriptional activation by mediating long-range interactions between tethering elements. Through a combination of genomics and live imaging, I will identify the molecular mechanisms establishing long-range interactions and determine their impact on gene expression. My recent work also showed that both long-range enhancers and tethering elements are pervasively transcribed genome- wide. In Project II, using methods I developed to visualize the transcription of endogenous lncRNAs in living embryos in combination with complex genetic perturbations, I will begin to determine the regulatory functions of select lncRNAs associated with important developmental genes and dissect their interplay with genome organization. In particular, I will investigate how lncRNAs regulate the recruitment of architectural factors and the establishment of long-range interactions. Finally, in Project III, I will use novel single-cell live imaging approaches that I developed to investigate how lncRNAs dynamically control local regulatory microenvironments to regulate genome organization and gene expression in vivo. Collectively, these three synergistic projects will enable my future research program by identifying guiding principles that will inform our understanding of the dynamics of gene regulation and be examined in future studies in other model systems and cellular and temporal contexts.