Responding to the NIH's 4D Nucleome FOA for Imaging Tools, we propose here two novel imaging methods. When combined, these methods provide nanometer spatial resolution, and millisecond to hour temporal resolution of dynamic chromatin architecture rearrangement and its relation to cell activation and transcription. The first novel technique, termed SUSHI (SUb-zero-Stochastic-High-resolution-Imaging platform), enables quantitative, stochastic, single molecule imaging by combining intelligent labeling design with cryogenic fluorescence and emitter control using polarized excitation and depletion. This results in 1-5 nanometer isotropic structural resolution of nuclear chromatin, and the ability to discern DNA elements such as enhancers, suppressors or gene loci that can be mapped and tracked. The second method, termed 3D-SMRT Microscopy (three-dimensional Single-Molecule Real-Time microscopy, manuscript submitted), is an expansion on the recently described MFM (multi-focus microscopy). It provides real-time, simultaneous, multicolor, 30-80 nanometer-resolution tracking in the living cell at a millisecond to hour timescale. By implementing a well thought out labeling strategy, this method also allows for the detection of DNA elements and their nuclear movement in time and space. To be able to analyze hundreds of cells in different activation states, we also describe our streamlined image processing workflows for both SUSHI and 3D-SMRT, permitting the automated analysis of multiple loci of hundreds of single cells and many activation states. We will make the imaging platforms available to all members of the 4D Nucleome consortium by placing the microscopes in a core facility at UMMS, and will share all data processing techniques via code sharing. We focus on the FOS gene locus, as this immediate-early response gene has low to no expression of c-Fos mRNA and protein at rest. Upon activation, however, there is a rapid induction of c-Fos, which persists only for a few hours. Heat maps depicting intrachromosomal interaction matrices around the FOS gene indicate extensive looping at this locus. By labeling DNA in a living cell, we can resolve chromatin looping changes around the locus and its surrounding enhancers, determine potential gene locus positional movements toward the nuclear periphery and nuclear pores, and correlate this with mRNA expression and export, both at rest and upon activation. By collaborating with members of the 4D Nucleome consortium, we envision the final stage of this project to include direct correlation with biochemical, structural and genome-wide mapping derived data, thereby shedding light on how genomic information specifies proper execution of spatial and temporal gene expression at rest, upon activation, during cellular development and in diseased states.
We aim to correlate ensemble data collected from methods developed to map nuclear DNA: DNA interactions, with what is happening at the single molecule level in the individual cell. To do so we propose novel light microscopy methods that achieve 1 nanometer resolution (a value up until now only possible with electron microscopy) and a time resolution of 0.00002 seconds. Combined, these tools, termed SUSHI and 3D-SMRT respectively, allow us to directly investigate genome architecture and its change in reaction to activation, development and disease.
| Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan et al. (2018) CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods 15:928-931 |
| Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan et al. (2016) Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 34:528-30 |
| Smith, Carlas; Huisman, Max; Siemons, Marijn et al. (2016) Simultaneous measurement of emission color and 3D position of single molecules. Opt Express 24:4996-5013 |
| Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan et al. (2016) CRISPR-Cas9 nuclear dynamics and target recognition in living cells. J Cell Biol 214:529-37 |
