Unveiling the invisible genomic dynamics

CRISPR-based imaging technologies have emerged as powerful tools for visualizing specific genomic loci, providing groundbreaking insights into chromatin structure and dynamics. Here, in this Review, we discuss the development and recent advances in these techniques, highlighting key strategies such as signal amplification, background reduction, multiplexing and enhanced genomic resolution. By engineering Cas proteins and guide RNAs, and incorporating peptide and aptamer tags, researchers have remarkably improved the sensitivity, specificity and resolution of CRISPR-based imaging, enabling the detection of nonrepetitive genomic regions and single-nucleotide polymorphisms. Recent studies have further pushed the boundaries of CRISPR-based imaging with the introduction of degron-mediated fluorogenic labeling and light-controllable background reduction. Despite remaining challenges, such as the bulkiness of signal amplification systems, limitations in guide RNA design and the effects of fixation on chromatin-protein interactions, CRISPR-based imaging holds great promise for advancing our understanding of chromatin dynamics, genomic interactions and their roles in various biological processes.