Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements.

Rajula Elango,Beth Osia,Ewa Malc,Victoria Harcy,Steven A Roberts,Anna Malkova,Piotr A Mieczkowski

doi:10.1093/nar/gkz651

Abstract

Break induced replication (BIR) is a double strand break repair pathway that can promote genetic instabilities similar to those observed in cancer. Instead of a replication fork, BIR is driven by a migration bubble where asynchronous synthesis between leading and lagging strands leads to accumulation of single-stranded DNA (ssDNA) that promotes mutation. However, the details of the mechanism of mutagenesis, including the identity of the participating proteins, remain unknown. Using yeast as a model, we demonstrate that mutagenic ssDNA is formed at multiple positions along the BIR track and that Pol ζ is responsible for the majority of both spontaneous and damage-induced base substitutions during BIR. We also report that BIR creates a potent substrate for APOBEC3A (A3A) cytidine deaminase that can promote formation of mutation clusters along the entire track of BIR. Finally, we demonstrate that uracil glycosylase initiates the bypass of DNA damage induced by A3A in the context of BIR without formation of base substitutions, but instead this pathway frequently leads to chromosomal rearrangements. Together, the expression of A3A during BIR in yeast recapitulates the main features of APOBEC-induced kataegis in human cancers, suggesting that BIR might represent an important source of these hyper-mutagenic events.

Highlights

DNA double strand DNA breaks (DSBs) are a dangerous type of DNA damage that if left unrepaired lead to cell death
SsDNA is a source of mutagenesis at multiple positions along the break-induced replication (BIR) track To analyze base substitution mutagenesis through the track of BIR, we used our yeast strain, disomic for chromosome III, that contains a galactose-inducible HO endonuclease that can create a DSB at the MATa locus of the truncated copy of chromosome III
We demonstrate in this work that BIR promotes accumulation of long regions of single-stranded DNA (ssDNA) throughout the synthesis tract of this DSB repair pathway

Summary

Introduction

DNA double strand DNA breaks (DSBs) are a dangerous type of DNA damage that if left unrepaired lead to cell death (reviewed in [1]). To avoid such consequences, cells employ multiple DSB repair pathways. One of these repair pathways, break-induced replication (BIR), is employed for repair of DSBs like those formed at collapsed replication forks or by telomere erosion; these types of damage possess only one DNA end capable of invading the homologous template (reviewed in [2,3]). BIR is responsible for the maintenance of telomeres in ∼10–15% of human cancers through a mechanism called alternative lengthening of telomeres (ALT) [12,13,14]

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Conclusion