Helicase Q promotes homology-driven DNA double-strand break repair and prevents tandem duplications

J A Kamp,B B L G Lemmens,M Tijsterman,R J Romeijn,S C Changoer,R Van Schendel

doi:10.1038/s41467-021-27408-z

J A Kamp, B B L G Lemmens + Show 4 more

Open Access

https://doi.org/10.1038/s41467-021-27408-z

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Abstract

DNA double-strand breaks are a major threat to cellular survival and genetic integrity. In addition to high fidelity repair, three intrinsically mutagenic DNA break repair routes have been described, i.e. single-strand annealing (SSA), polymerase theta-mediated end-joining (TMEJ) and residual ill-defined microhomology-mediated end-joining (MMEJ) activity. Here, we identify C. elegans Helicase Q (HELQ-1) as being essential for MMEJ as well as for SSA. We also find HELQ-1 to be crucial for the synthesis-dependent strand annealing (SDSA) mode of homologous recombination (HR). Loss of HELQ-1 leads to increased genome instability: patchwork insertions arise at deletion junctions due to abortive rounds of polymerase theta activity, and tandem duplications spontaneously accumulate in genomes of helq-1 mutant animals as a result of TMEJ of abrogated HR intermediates. Our work thus implicates HELQ activity for all DSB repair modes guided by complementary base pairs and provides mechanistic insight into mutational signatures common in HR-defective cancers.

Highlights

DNA double-strand breaks are a major threat to cellular survival and genetic integrity
We have established that G4 motifs in the C. elegans genome provide a source for DNA breaks that depend on alternative end-joining for their repair[31,32]
Endogenous G4 motifs in dog-1 deficient C. elegans provide a unique model substrate to study theta-mediated end-joining (TMEJ) in vivo because their mutagenic consequences occur at well-defined genomic positions, with a frequency that can be measured with a variety of molecular techniques, including PCR, transgenic and endogenous reporters, and whole-genome sequencing[32,34,35]

Summary

Introduction

DNA double-strand breaks are a major threat to cellular survival and genetic integrity. Apart from mechanistic communalities in SDSA and SSA (e.g. the need for end resection and strand annealing), there are differences: because direct repeats that guide SSA will rarely be located precisely at the break ends, non-complementary 3′ protruding DNA flaps that inevitably arise upon annealing need to be removed in SSA, a biochemical activity attributed to the structure-specific endonuclease ERCC1/XPF13 Because of this necessity, ERCC1/XPF dependency is one frequently used criterium in defining SSA14, as well as a dependence on the ssDNA binding protein RAD52, which is able to stimulate base pairing of complementary sequences[15,16]. The underlying mechanism and the genetic requirements of this type of repair is unknown

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