Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin

The organization of chromatin and transcription factors in the nucleus is essential for gene expression. Zygotic genome activation (ZGA) occurs during early embryonic development and involves substantial chromatin reprogramming. However, the organization of factors within the nucleus driving this process remain unclear. Here, we develop chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. Applying ChromExM to zebrafish embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and transcribing RNA Polymerase II (Pol II), which forms string-like nanostructures associated with nascent transcripts, providing direct visualization of transcriptional elongation. In the absence of elongation, more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers, indicating that enhancer-promoter contacts are transient and released by transcriptional elongation. Our results provide a new model of enhancer-promoter interaction called kiss-and-kick and demonstrate that ChromExM is broadly applicable to study nanoscale organization within the nucleus.