RNA-dependent chromatin organization during development

Embryonic development is characterized by controlled spatiotemporal remodeling of the nuclear landscape. To understand how this process is regulated, it is crucial to identify the factors controlling nano and mesoscale nuclear organization. Here, we developed an improved Chromatin Expansion Microscopy approach to visualize nuclear organization in developing zebrafish embryos at nanometer-scale resolution. We observe a stepwise emergence of chromatin compaction during early development, coincident with the onset of heterochromatin formation. Perturbation of the facultative heterochromatin mark H3K27me3 reveals that it is neither necessary nor sufficient for chromatin compaction in vivo. Instead, inhibiting transcription elongation disrupts chromatin compaction, while increasing nuclear RNA levels enhances compaction independently of transcriptional activity. Together, these results identify nuclear RNA as a major determinant of chromatin organization during development and support a model in which RNA promotes mesoscale chromatin compaction independently of canonical heterochromatin pathways.