Emerging oligo-based imaging methods to study chromatin organization in cells and tissue

Over the past decades, vast progress in sequencing and imaging has transformed our understanding of chromatin organization in the cell nucleus and its relevance in development and disease. Imaging methods have regained popularity in recent years, as they inherently facilitate single-cell resolution and visualization of subnuclear spatial distances and morphology. An exceptional strength of imaging is the relative ease of designing multimodal experiments, as DNA and RNA fluorescence in situ hybridization (FISH) can be combined with immunofluorescence staining for joint visualization of genomic loci, transcripts, and proteins. In this mini-review, we highlight recent imaging developments that advance our views on 3D genome organization, focusing primarily on oligonucleotide-based DNA FISH and emerging applications (e.g. chromatin tracing, live-cell imaging, lineage reconstruction, and optical pooled screening). To help novices navigate this rapidly expanding field, we provide a comprehensive overview of the main oligo-based FISH methods.