From Rabl-like Architecture to Chromosome Territories: A Conserved Developmental Transition in Animal Genomes

In eukaryotes, chromosomes can be arranged with centromeres and/or telomeres clustered at opposite poles of the nucleus (Rabl-like, RBL) or as discrete spatial domains (chromosome territory, CT). These patterns were thought to be species specific, possibly linked to the presence or absence of condensin II subunits. Time-series embryonic chromatin maps from three distantly related animals reveal that RBL and CT reflect cell state rather than species identity, and a conserved RBL-to-CT transition has occurred during development. This shift is not significantly correlated with condensin II gene expression, but may be influenced by the genomic distribution of repetitive sequences. In late developmental stages, long-range cis- and trans-interactions between active A1 subcompartments progressively intensify, ultimately establishing CT as the dominant architecture. These results uncover a conserved, developmentally regulated reorganization of 3D genome structure across animals.