Tracking Chromosome Conformation in Live Cells with CRISPR Imaging

In each cell cycle, chromosomes go through dramatic large-scale structural changes, oscillating between being relatively open at interphase and highly compact at metaphase. However, little is known about how they change between the two extremes. Therefore it is desirable to monitor the long-term dynamics of chromosome structure in live cells. Here we use a modified CRISPR system to directly image specific genomic loci in hundreds of live cells with high temporal and spatial resolution. By following dozens of diffraction-limited fluorescence spots sparsely decorating a single chromosome, specific genomic elements can be localized with a precision of ∼30 nm. We study how topological domains and long range interactions between chromosome loci are maintained or re-established through cell cycle. As CRISPR imaging allows us flexibility and specificity in imaging any genomic loci, the method developed here could be easily adapted to explore other systems where long-term live cell imaging is required.