Towards Single-Cell Systems Biology through Super-Resolution Imaging and Molecular Barcoding

Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral overlap between fluorophores. We have demonstrated a simple but general strategy to dramatically increase the capacity for multiplex detection in single cells by labeling with unique combinations of fluorophores using fluorescence in situ hybridization (FISH) and resolving these barcodes using optical super-resolution microscopy (SRM). We have used this technique to measure mRNA levels of 32 genes simultaneously in single Saccharomyces cerevisiae cells. Ongoing work to scale this methodology up for the high-throughput analysis of gene regulatory networks in single cells will be presented.