Abstract

Double-strand break (DSB) repair is highly mutagenic compared to normal replication. In budding yeast, repair of an HO endonuclease-induced DSB at MAT can be repaired by using a transcriptionally silent HMR::Kl-URA3 donor. During repair, -1 deletions in homonucleotide runs are strongly favored over +1 insertions, whereas during replication, spontaneous +1 and -1 events are equal. Microhomology-bounded, repair-associated intragenic deletions (IDs) are recovered 12 times more frequently than tandem duplications (TDs). IDs have a mean length of 56 bp, while TDs average 22 bp. These data suggest a picture of the structure of the repair replication fork: IDs and TDs occur within the open structure of a migrating D-loop, where the 3' end of a partly copied new DNA strand can dissociate and anneal with a single-stranded region of microhomology that lies either ~80 bp ahead or ~40 bp behind the 3' end. Another major class of repair-associated mutations (~10%) are interchromosomal template switches (ICTS), even though the K. lactis URA3 sequence in HMR is only 72% identical (homeologous) with S. cerevisiae ura3-52. ICTS events begin and end at regions of short (~7 bp) microhomology; however, ICTS events are constrained to the middle of the copied sequence. Whereas microhomology usage in intragenic deletions is not influenced by adjacent homeology, we show that extensive pairing of adjacent homeology plays a critical role in ICTS. Thus, although by convention, structural variants are characterized by the precise base pairs at their junction, microhomology-mediated template switching actually requires alignment of extensive adjacent homeology.

Competing Interest Statement

The authors have declared no competing interest.

Details

Title
Mutations and structural variants arising during double-strand break repair
Author
Dalin, Simona; Webster, Sophie; Sugawara, Neal; Wu, Quiqin; Zhang, Shu; Macias, Carmen; Sapède, Elena; Cui, Tracy; Liang, Victoria; Tran, Laura; Beroukhim, Rameen; Haber, James E
University/institution
Cold Spring Harbor Laboratory Press
Section
New Results
Publication year
2025
Publication date
Mar 6, 2025
Publisher
Cold Spring Harbor Laboratory Press
ISSN
2692-8205
Source type
Working Paper
Language of publication
English
ProQuest document ID
3174600243
Copyright
© 2025. This article is published under http://creativecommons.org/licenses/by-nd/4.0/ (“the License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.