Prevalence of Mutation-Prone Microhomology-Mediated End Joining in a Chordate Lacking the c-NHEJ DNA Repair Pathway

• Published in: Current biology 2018-10, Vol.28 (20), p.3337-3341.e4
• Main Authors: Deng, Wei, Henriet, Simon, Chourrout, Daniel
• Format: Article
• Language: English
• Subjects: chordates; CRISPR; DNA repair; evolution rate; genome evolution; MMEJ; NHEJ; Oikopleura; tunicates
• ISSN: 0960-9822; 1879-0445
• DOI: 10.1016/j.cub.2018.08.048

Classical non-homologous end joining (c-NHEJ), a fundamental pathway that repairs double-strand breaks in DNA, is almost universal in eukaryotes and involves multiple proteins highly conserved from yeast to human [1]. The genes encoding these proteins were not detected in the genome of Oikopleura dioica, a new model system of tunicate larvaceans known for its very compact and highly rearranged genome [2–4]. After showing their absence in the genomes of six other larvacean species, the present study examined how O. dioica oocytes and embryos repair double-strand DNA breaks (DSBs), using two approaches: the injection of linearized plasmids, which resulted in their rapid end joining, and a newly established CRISPR Cas9 technique. In both cases, end joining merged short microhomologous sequences surrounding the break (mainly 4 bp long), thus inducing deletions larger than for the tunicate ascidian Ciona intestinalis and human cells. A relatively high frequency of nucleotide insertions was also observed. Finally, a survey of genomic indels supports the involvement of microhomology-mediated repair in natural conditions. Overall, O. dioica repairs DSBs as other organisms do when their c-NHEJ pathway is experimentally rendered deficient, using another mode of end joining with the same effect as alternative NHEJ (a-NHEJ) or microhomology-mediated end joining (MMEJ) [5–7]. We discuss how the exceptional loss of c-NHEJ and its replacement by a more mutation-prone mechanism may have contributed to reshaping this genome and even been advantageous under pressure for genome compaction. •DNA repair by end joining is efficient in an organism naturally lacking c-NHEJ•DNA repair in Oikopleura dioica is microhomology dependent and more mutation prone•It probably contributed to compacting and rearranging the genome of tunicate larvaceans Deng et al. show that in Oikopleura dioica, a chordate that lacks genes of the DNA repair pathway c-NHEJ, double-strand DNA breaks are instead repaired using microhomology-mediated end joining. The exceptional loss of c-NHEJ, replaced by a more mutagenic mechanism, has enigmatic causes and probably contributed to divergent genome architecture.