Richard Dean Wood

DNA polymerase ζ (Polζ) is essential for replication across damaged DNA, yet the mechanisms governing its regulation in mammalian cells remain incompletely understood. The catalytic subunit REV3L is nearly twice the size of its yeast counterpart owing to a large vertebrate-specific insertion, and recent studies reported that REV3L undergoes proteolytic cleavage by the endopeptidase TASP1. Here, we show that REV3L cleavage generates two stable fragments, Nter-p70 and Cter-p300, which reassociate into a long-lived heterodimeric complex with enhanced polymerase activity. This interaction is stabilized by key residues within the catalytically inactive EXO domain. The cleaved Polζ complex associates with chromatin, binds nascent DNA, and undergoes ATR-dependent phosphorylation in response to replication stress. Importantly, preventing REV3L cleavage markedly impairs Polζ activity, reduces cisplatin-induced mutagenesis, and increases RAD51 nuclear foci and sister chromatid exchange, consistent with a compensatory shift toward homologous recombination-mediated repair. Together, our findings suggest that the vertebrate-specific expansion of REV3L necessitated cleavage to restore structural organization and optimize catalytic function, representing an evolutionary adaptation in DNA damage tolerance pathways.

DNA polymerase theta (Pol θ)-mediated end joining (TMEJ) initiates DNA double-strand break repair by using short homologies (microhomologies) between single-stranded DNA tails. This repair process is particularly important in cancer cells defective in homologous recombination. The exonuclease function of DNA polymerase delta (Pol δ) has been identified as an essential component for TMEJ, functioning to remove unpaired bases flanking a microhomology (MH). It is not known if the exonuclease removes all unpaired bases at once and how this removal might affect subsequent MH selection. Here, we reconstituted a functional TMEJ repair process using purified human Pol θ and Pol δ. We find that when Pol δ exonuclease excises a nucleotide to generate a new 3′ terminus, Pol θ initiates a new MH search. Pol δ exonuclease removes a single nucleotide at a time, rather than cleaving an unpaired flap, and then transfers the DNA tail to the polymerase site of Pol θ. Specific primer-grasp amino acids in the polymerase domain of Pol θ are important for internal MH anchoring. The helicase-like domain of Pol θ harbors two activities which are recapitulated in reconstituted reactions: strand-capture to bring single-strand tails together and an ATPase activity that alleviates suppression of TMEJ by ssDNA binding protein RPA. This functional reconstitution of TMEJ advances the understanding of how two polymerases with three enzymatic activities orchestrate double-strand break repair.

DNA polymerase theta (Pol θ) initiates repair of DNA double-strand breaks by pairing single strands at short “microhomologies”. It is important to understand microhomology selection, as some cancer cells rely on Pol θ for survival. Here, we investigate end-joining by purified human Pol θ, employing DNA sequencing of products generated from oligonucleotide libraries having diverse 3′ ends. Pol θ overwhelmingly selects short internal microhomologies found within 15 nucleotides of the terminus of single-stranded DNAs, restricting deletion size during end-joining. Significantly, we find that the selected microhomologies are usually interrupted by mismatches and that base pairing within 6 nucleotides of the 3′ end is important for determining microhomology choice. Bidirectional synthesis is not necessary to initiate end-joining. The preference for mismatched microhomologies suggests a revision of the definition of microhomology to account for the unique properties of Pol θ. This could advance the analysis of mutations in cancer genomes.

Timely repair of chromosomal double-strand breaks is required for genome integrity and cellular viability. The polymerase theta-mediated end joining pathway has an important role in resolving these breaks and is essential in cancers defective in other DNA repair pathways, thus making it an emerging therapeutic target¹. It requires annealing of 2–6 nucleotides of complementary sequence, microhomologies, that are adjacent to the broken ends, followed by initiation of end-bridging DNA synthesis by polymerase θ. However, the other pathway steps remain inadequately defined, and the enzymes required for them are unknown. Here we demonstrate requirements for exonucleolytic digestion of unpaired 3′ tails before polymerase θ can initiate synthesis, then a switch to a more accurate, processive and strand-displacing polymerase to complete repair. We show the replicative polymerase, polymerase δ, is required for both steps; its 3′ to 5′ exonuclease activity for flap trimming, then its polymerase activity for extension and completion of repair. The enzymatic steps that are essential and specific to this pathway are mediated by two separate, sequential engagements of the two polymerases. The requisite coupling of these steps together is likely to be facilitated by physical association of the two polymerases. This pairing of polymerase δ with a polymerase capable of end-bridging synthesis, polymerase θ, may help to explain why the normally high-fidelity polymerase δ participates in genome destabilizing processes such as mitotic DNA synthesis² and microhomology-mediated break-induced replication³.

DNA polymerase θ (Pol θ) is a DNA repair enzyme widely conserved in animals and plants. Pol θ uses short DNA sequence homologies to initiate repair of double-strand breaks by theta-mediated end joining. The DNA polymerase domain of Pol θ is at the C terminus and is connected to an N-terminal DNA helicase–like domain by a central linker. Pol θ is crucial for maintenance of damaged genomes during development, protects DNA against extensive deletions, and limits loss of heterozygosity. The cost of using Pol θ for genome protection is that a few nucleotides are usually deleted or added at the repair site. Inactivation of Pol θ often enhances the sensitivity of cells to DNA strand–breaking chemicals and radiation. Since some homologous recombination–defective cancers depend on Pol θ for growth, inhibitors of Pol θ may be useful in treating such tumors.