Chromosomes fold into distinct domains that regulate transcription, replication and repair. In addition to well-characterized topologically associating domains (TADs) and compartments, the diversity of heterochromatin domains remains poorly defined at the sequence level.

Using single-molecule tracing of nascent heterochromatin in Caenorhabditis elegans, the study identifies three classes of megabase-scale domains: sharp-boundary, condensin I-dependent TAD-like domains; similarly sized condensin-independent domains; and decompacted diffuse structures that are abundant but likely missed by crosslinking-based assays.

The results uncover previously unrecognized heterochromatin architectures and suggest that maternal transcriptional activity helps shape domain boundaries in early embryos.