Oldridge, R. | bioRxiv Science

bioRxiv2026

A sequence motif for DNA double-strand break and telomere healing during programmed DNA elimination

Programmed DNA Elimination (PDE) is an exception to the paradigm of genome integrity, removing selected DNA sequences during development. PDE is observed in dozens of metazoan species from diverse phyla, but its molecular mechanisms and biological significance in most metazoa remain largely unknown. During PDE in the nematode Oscheius tipulae, DNA double-strand breaks (DSBs) are generated at subtelomeric regions, followed by the loss of DNA at chromosome ends and the healing of the DSBs by de novo telomere synthesis. DSBs occur at a 29-bp degenerate palindromic Sequence For Elimination (SFE) motif. We determined the sequence requirement for DSB generation and demonstrated that the conserved GGC/GCC sites are used for neotelomere formation. Introducing the SFE into a retained DNA region adjacent to a native SFE induces DNA cleavage, telomere healing, and loss of additional DNA between the two SFEs. Moreover, insertion of the SFE in the middle of the sex chromosome splits it into two functional somatic chromosomes, demonstrating that the function of SFE is not necessarily constrained by its genomic location. Overall, our data show that the SFE motif is both necessary and sufficient for the generation of DSBs and healing of DSB ends via telomere addition, providing molecular insights into the mechanisms of metazoan PDE.

genetics↗

bioRxiv2023

Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes

A growing list of metazoans undergo programmed DNA elimination (PDE), where a significant amount of DNA is selectively lost from the somatic genome during development. In some nematodes, PDE leads to the removal and remodeling of the ends of all germline chromosomes. In several species, PDE also generates internal breaks that lead to sequence loss and an increased number of somatic chromosomes. The biological significance of these karyotype changes associated with PDE and the origin and evolution of nematode PDE remain largely unknown. Here, we assembled the single germline chromosome of the horse parasite Parascaris univalens and compared the karyotypes, chromosomal gene organization, and PDE features among ascarid nematodes. We show that PDE in Parascaris converts an XX/XY sex-determination system in the germline into an XX/XO system in the somatic cells. Comparisons of Ascaris, Parascaris, and Baylisascaris ascarid chromosomes suggest that PDE existed in the ancestor of these parasites, and their current distinct germline karyotypes were derived from fusion events of smaller ancestral chromosomes. The DNA breaks involved in PDE resolve these fused germline chromosomes into their pre-fusion karyotypes, leading to alterations in genome architecture and gene expression in the somatic cells. Cytological and genomic analyses further suggest that satellite DNA and the heterochromatic chromosome arms play a dynamic role in the Parascaris germline chromosome during meiosis. Overall, our results show that chromosome fusion and PDE have been harnessed in these ascarids to sculpt their karyotypes, altering the genome organization and serving specific functions in the germline and somatic cells.

genomics↗