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.