A development-specific POLX essential for programmed genome rearrangement in Paramecium tetraurelia

<p><span>During the sexual cycle, programmed genome rearrangement (PGR) in <em>Paramecium tetraurelia</em> involves the non-homologous end joining (NHEJ) DNA repair pathway to eliminate specific germinal Internal Eliminated Sequences (IESs) from the newly developing somatic nucleus. In addition to the core NHEJ factors Ku70/80 and Xrcc4/Lig4, additional enzymes are required to process the 4-base 5&rsquo;-protruding ends generated following DNA cleavage at IES boundaries, prior to their ligation. Here, we report that PolX (a,b,c,d), four <em>P. tetraurelia</em> distant orthologs of the human Pol</span><span>l</span><span> DNA polymerase, are involved in repair of IES excision junctions. During rearrangements, PolX-depleted cells accumulate genome-wide errors, such as unrepaired double-strand breaks, 1-nucleotide deletions and IES retention. Although all PolX paralogs can process DNA ends, two of them (PolXa&amp;b) are induced during PGR and have acquired tight nuclear anchoring properties through their N-terminal region, which contains a predicted BRCT domain. Finally, we show that PolXa accumulates in nuclear foci together with other NHEJ proteins and the Dicer-like enzyme Dcl5, which is involved in the biogenesis of IES-specific small RNAs. We propose</span><span><span> </span></span><span>that these &ldquo;DNA repair foci&rdquo; correspond to the sites where IES concatemers, a by-product of IES excision, are ligated together to produce the precursors of iesRNAs.</span></p>