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Ribonucleotide incorporation enables repair of chromosome breaks by nonhomologous end joining

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Science  14 Sep 2018:
Vol. 361, Issue 6407, pp. 1126-1129
DOI: 10.1126/science.aat2477

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RNA takes over DNA repair

Damage to DNA genomes is normally thought to be repaired with DNA. Pryor et al. now describe a clear exception (see the Perspective by Modesti). They found that RNA is routinely incorporated during the repair of DNA double-strand breaks through the mammalian nonhomologous end–joining (NHEJ) pathway. In a variety of contexts, including V(D)J recombination and Cas9-induced genome engineering, two “DNA” polymerases specific to NHEJ preferentially added RNA in cells. These RNA additions facilitated the critical step of ligation and were later replaced by DNA to complete the NHEJ repair process.

Science, this issue p. 1126; see also p. 1069

Abstract

The nonhomologous end–joining (NHEJ) pathway preserves genome stability by ligating the ends of broken chromosomes together. It employs end-processing enzymes, including polymerases, to prepare ends for ligation. We show that two such polymerases incorporate primarily ribonucleotides during NHEJ—an exception to the central dogma of molecular biology—both during repair of chromosome breaks made by Cas9 and during V(D)J recombination. Moreover, additions of ribonucleotides but not deoxynucleotides effectively promote ligation. Repair kinetics suggest that ribonucleotide-dependent first-strand ligation is followed by complementary strand repair with deoxynucleotides, then by replacement of ribonucleotides embedded in the first strand with deoxynucleotides. Our results indicate that as much as 65% of cellular NHEJ products have transiently embedded ribonucleotides, which promote flexibility in repair at the cost of more fragile intermediates.

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