Repair of protein-linked DNA double strand breaks: Using the adenovirus genome as a model substrate in cell-based assays

DNA Repair (Amst). 2019 Feb;74:80-90. doi: 10.1016/j.dnarep.2018.12.001. Epub 2018 Dec 10.

Abstract

The DNA double strand breaks (DSBs) created during meiotic recombination and during some types of chemotherapy contain protein covalently attached to their 5' termini. Removal of the end-blocking protein is a prerequisite to DSB processing by non-homologous end-joining or homologous recombination. One mechanism for removing the protein involves CtIP-stimulated Mre11-catalyzed nicking of the protein-linked strand distal to the DSB terminus, releasing the end-blocking protein while it remains covalently attached to an oligonucleotide. Much of what is known about this repair process has recently been deciphered through in vitro reconstitution studies. We present here a novel model system based on adenovirus (Ad), which contains the Ad terminal protein covalently linked to the 5' terminus of its dsDNA genome, for studying the repair of 5' protein-linked DSBs in vivo. It was previously shown that the genome of Ad mutants that lack early region 4 (E4) can be joined into concatemers in vivo, suggesting that the Ad terminal protein had been removed from the genome termini prior to ligation. Here we show that during infection with the E4-deleted Ad mutant dl1004, the Ad terminal protein is removed in a manner that recapitulates removal of end-blocking proteins from cellular DSBs. In addition to displaying a dependence on CtIP, and Mre11 acting as the endonuclease, the protein-linked oligonucleotides that are released from the viral genome are similar in size to the oligos that remain attached to Spo11 and Top2 after they are removed from the 5' termini of DSBs during meiotic recombination and etoposide chemotherapy, respectively. The single nucleotide resolution that is possible with this assay, combined with the single sequence context in which the lesion is presented, make it a useful tool for further refining our mechanistic understanding of how blocking proteins are removed from the 5' termini of DSBs.

Keywords: Adenovirus; Chemotherapy; Concatemer; CtIP; DNA double strand break; End blocking; End processing; Endonuclease; Etoposide; Homologous recombination; Ligation; MRN; Mre11; Nonhomologous end joining; Protein-DNA adduct; Protein-linked DSB; Spo11; Terminal protein; Topoisomerase 2; dl1004.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenoviridae / genetics*
  • BRCA1 Protein / metabolism
  • Carrier Proteins / metabolism
  • DNA Breaks, Double-Stranded*
  • DNA Repair*
  • Endodeoxyribonucleases
  • Gene Knockdown Techniques
  • Genome, Viral / genetics*
  • HEK293 Cells
  • Humans
  • MRE11 Homologue Protein / metabolism
  • Nuclear Proteins / metabolism
  • Proteins / metabolism*

Substances

  • BRCA1 Protein
  • Carrier Proteins
  • MRE11 protein, human
  • Nuclear Proteins
  • Proteins
  • Endodeoxyribonucleases
  • MRE11 Homologue Protein
  • RBBP8 protein, human