The linker region of a development-specific DNA polymerase X ensures efficient repair of programmed DNA double-strand breaks in Parameciumtetraurelia.

During the sexual cycle, programmed genome rearrangement in Paramecium tetraurelia involves the non-homologous end joining (NHEJ) DNA repair pathway to eliminate specific germinal internal eliminated sequences (IESs) from the newly developing somatic nucleus. Besides the core NHEJ factors Ku70/80 and Xrcc4/Lig4, additional enzymes are required to process the 4-base 5'-protruding ends generated following DNA cleavage at IES boundaries, prior to their ligation. Here, we report that PolXa,b,c,d, four P. tetraurelia distant orthologs of the human Polλ DNA polymerase, are involved in the repair of IES excision junctions. During rearrangements, PolX-depleted cells accumulate genome-wide errors, such as unrepaired double-strand breaks, one-nucleotide deletions, and IES retention. Although all PolX paralogs can process DNA ends, two of them (PolXa&b) are induced during rearrangements and have evolved a specific linker sequence downstream of their BRCT domain, which provides them with tight nuclear anchoring properties. We show that PolXa accumulates in nuclear foci together with other NHEJ actors and the Dicer-like enzyme Dcl5, which is involved in the biogenesis of IES-specific small RNAs. We propose that these 'DNA repair foci' correspond to the sites where IES concatemers, a by-product of IES excision, are ligated together to produce the precursors of these small RNAs.