Spatial genome reorganization is associated with chromosomal breakage regions and karyotype changes induced by programmed DNA elimination

Programmed DNA elimination (PDE) is a notable exception to genome integrity, characterized by significant DNA loss during development. In many nematodes, PDE is initiated by DNA double-strand breaks (DSBs), which lead to chromosome fragmentation and subsequent DNA loss. However, the mechanism of nematode DNA breakage remains largely unclear. Interestingly, in the human and pig parasitic nematode Ascaris , no conserved motif or sequence structures are present at chromosomal breakage regions (CBRs), suggesting the recognition of CBRs may be sequence-independent. Using Hi-C, we revealed that Ascaris CBRs engage in three-dimensional (3D) interactions before PDE, indicating that physical contacts of the break regions may contribute to the PDE process. The 3D interactions are established in both Ascaris male and female germlines, demonstrating inherent genome organization associated with the CBRs and to-be-eliminated sequences. In contrast, in the unichromosomal horse parasite Parascaris univalens , transient and pairwise interactions between two neighboring CBRs that would form the ends of future somatic chromosomes were observed only during PDE. Intriguingly, we found specific spatial compartmentalization changes in the Ascaris chromosomes after PDE converts 24 germline chromosomes into 36 somatic ones. Remarkably, Parascaris PDE generates the same set of 36 somatic chromosomes, and the compartment changes following PDE are consistent between the two species. Overall, our findings contribute to a model that the 3D genome facilitates the recognition of sequence-independent break sites for Ascaris PDE. It also suggests an evolutionary and developmentally conserved 3D genome reorganization of nematode somatic chromosomes following PDE.