Abstract

Dissecting the inner workings of a cell requires imaging methods with molecular specificity, molecular-scale resolution, and dynamic imaging capability such that molecular interactions inside the cell can be directly visualized. However, the diffraction-limited resolution of light microscopy is substantially larger than molecular length scales in cells, making many sub-cellular structures difficult to resolve. Another major challenge in imaging is the relatively low throughput in terms of the number of molecular species that can be simultaneously imaged, and genomic-scale throughput is desired for investigating many systems level questions. In this talk, I will describe two imaging methods that overcome these challenges and their biological applications. I will first describe stochastic optical reconstruction microscopy (STORM), a super-resolution imaging method that overcomes the diffraction limit. This approach has allowed multicolor and three-dimensional imaging of living cells with nanometer-scale resolution. I will present both technological advances and biological applications of STORM , with focus on some recent discoveries of novel sub-cellular structures enabled by STORM . I will also describe our recently developed single-cell transcriptome imaging method, multiplexed error-robust FISH (MERFISH), which allows thousands of RNA species to be quantified in a spatially resolved manner in individual cells. This approach enables single-cell transcriptomic analysis in the native context of tissues, facilitating the delineation of gene regulatory networks, the mapping of RNA distributions inside cells, and the mapping of distinct cell types in complex tissues. In addition, multiplexed FISH allowed us to trace the folding path of individual chromosomes, which has provided novel insights into the 3D organization of the genome.