Genome-scale imaging: from the subcellular structure of chromatin to the 3D organization of the peripheral olfactory system

Abstract

Information within an organism flows across multiple length-scales ranging from the molecular events within individual cells to the large-scale coordination between different organs. At each of these scales there are many interacting components from thousands of genes and genomic regulatory elements within cells to thousands of cell types organized into hundreds of tissues and organs. Recent efforts, particularly powered by advances in sequencing-based technologies, have started cataloguing in ever improving detail the different components (i.e., the expressed genes, the accessible regulatory regions, the different cell types etc.). However, measuring how these components physically interact and are organized in their native structural and functional context remains a challenge. My thesis summarizes the work towards developing an imaging platform capable of measuring in a highly multiplexed manner the 3D organization of the different relevant components across these length scales within intact cells and tissue samples. Specifically, I first focus on measuring the 3D structure of chromatin at different scales within the cell - from resolving the structure of single genomic loci with super-resolution to measuring the organization of chromatin at the genomic-scale. Then I connect the chromatin organization with the instantaneous transcriptional output and proximity to key nuclear landmarks by simultaneously imaging >1000 DNA loci, together with >1000 RNA transcription foci and with core protein components of nuclear speckles and nucleoli. Finally, I adapt this multiplexed imaging platform to the larger scale by measuring the expression of the entire olfactory gene family within two organs - the olfactory epithelium and the olfactory bulb, to address two long-standing questions of olfaction: which olfactory receptor genes respond to different ethological odors? and what is the organization of olfactory sensory neurons within the olfactory epithelium and their connectivity into the brain?