Repeat-mediated deletions can be induced by a chromosomal break far from a repeat, but multiple pathways suppress such rearrangements

Mendez‐Dorantes, Carlos; Bhargava, Ragini; Stark, Jeremy M.

doi:10.1101/gad.311084.117

Cited by 42 publications

(93 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, when a single cleavage is made at L17, which generates a DSB about 400 kb away from the right repeat, very low RMD was observed (Fig E). These data are comparable to the previous observations from the Stark's lab (Mendez‐Dorantes et al ,) and also suggest that BIR/RMD can act over a long distance with substantial levels of RMD (~ 2%) when one repeat is 200 kb away from the break. These results support the BIR model in which the ssDNA strand from one repeat invades the duplex DNA of the other repeat to mediate RMD, and thus, the distance between the DSB and the second repeat can be large (Fig D, right).…”

Section: Resultssupporting

confidence: 90%

“…This is also different from observations in yeast that the kinetics of SSA product formation are governed largely by the distance of the DSB to the further repeat (Fishman‐Lobell & Haber, ; Sugawara & Haber, ; Vaze et al , ). However, this is in line with the observation in mouse embryonic stem (mES) cells that RMD frequency in not changed proportionally with the distance increase of the break to the further repeat when the distance is more than 3 kb (Mendez‐Dorantes et al , ).…”

Section: Resultssupporting

confidence: 85%

“…While cleavage at L17/R3.3k or L17/R28.4k readily induces RMD in the RMD‐GFP reporter containing identical repeats (0% mismatch), RMD is strongly suppressed when the repeats contain 1% or 3% mismatches (Fig A). Sequence divergence has been shown to suppress SSA in both yeast and mammalian cells (Sugawara et al , ; Mendez‐Dorantes et al , ), and our study suggests that the presence of mismatches also inhibits BIR/RMD.…”

Section: Resultssupporting

confidence: 70%

“…In the human genome, Alu‐associated RMD can occur over a substantial distance (Kolomietz et al , ; Pavlicek et al , ; Belancio et al , ). To study the mechanism involved in long‐range RMD, we used the RMD‐GFP reporter established in Dr. Stark's laboratory (Mendez‐Dorantes et al , ), which contains two 287 bp repeats separated by 0.4 Mb on mouse chromosome 17 (Fig A). RMD between these two repeats would generate a Cdkn1A‐GFP fusion gene, producing green cells.…”

Section: Resultsmentioning

confidence: 99%

“…In the human genome, most repetitive sequences such as Alu elements are not identical (Batzer & Deininger, ; White et al , ). To examine the role of BIR in RMD between divergent repeat sequences, we used previously established RMD‐GFP reporters that contain 1% or 3% divergence in repeats (Mendez‐Dorantes et al , ). While cleavage at L17/R3.3k or L17/R28.4k readily induces RMD in the RMD‐GFP reporter containing identical repeats (0% mismatch), RMD is strongly suppressed when the repeats contain 1% or 3% mismatches (Fig A).…”

Section: Resultsmentioning

confidence: 99%

See 4 more Smart Citations

Break‐induced replication plays a prominent role in long‐range repeat‐mediated deletion

Lü

Wang

et al. 2019

The EMBO Journal

View full text Add to dashboard Cite

Repetitive DNA sequences are often associated with chromosomal rearrangements in cancers. Conventionally, single‐strand annealing (SSA) is thought to mediate homology‐directed repair of double‐strand breaks (DSBs) between two repeats, causing repeat‐mediated deletion (RMD). In this report, we demonstrate that break‐induced replication (BIR) is used predominantly over SSA in mammalian cells for mediating RMD, especially when repeats are far apart. We show that SSA becomes inefficient in mammalian cells when the distance between the DSBs and the repeats is increased to the 1–2 kb range, while BIR‐mediated RMD (BIR/RMD) can act over a long distance (e.g., ~ 100–200 kb) when the DSB is close to one repeat. Importantly, oncogene expression potentiates BIR/RMD but not SSA, and BIR/RMD is used more frequently at single‐ended DSBs formed at collapsed replication forks than at double‐ended DSBs. In contrast to short‐range SSA, H2AX is required for long‐range BIR/RMD, and sequence divergence strongly suppresses BIR/RMD in a manner partially dependent on MSH2. Our finding that BIR/RMD has a more important role than SSA in mammalian cells has a significant impact on the understanding of repeat‐mediated rearrangements associated with oncogenesis.

show abstract

Section: Resultssupporting

confidence: 90%

Section: Resultssupporting

confidence: 85%

Section: Resultssupporting

confidence: 70%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 3 more Smart Citations

Break‐induced replication plays a prominent role in long‐range repeat‐mediated deletion

Lü

Wang

et al. 2019

The EMBO Journal

View full text Add to dashboard Cite

show abstract

The RAD52 S346X variant reduces risk of developing breast cancer in carriers of pathogenic germline BRCA2 mutations

et al. 2020

Self Cite

View full text Add to dashboard Cite

Women who carry pathogenic mutations in BRCA1 and BRCA2 have a lifetime risk of developing breast cancer of up to 80%. However, risk estimates vary in part due to genetic modifiers. We investigated the association of the RAD52 S346X variant as a modifier of the risk of developing breast and ovarian cancers in BRCA1 and BRCA2 mutation carriers from the Consortium of Investigators of Modifiers of BRCA1/2. The RAD52 S346X allele was associated with a reduced risk of developing breast cancer in BRCA2 carriers [per-allele hazard ratio (HR) = 0.69, 95% confidence interval (CI) 0.56-0.86; P = 0.0008] and to a lesser extent in BRCA1 carriers (per-allele HR = 0.78, 95% CI 0.64-0.97, P = 0.02). We examined how this variant affected DNA repair. Using a reporter system that measures repair of DNA double-strand breaks (DSBs) by single-strand annealing (SSA), expression of hRAD52 suppressed the loss of this repair in Rad52 À/À mouse embryonic stem cells. When hRAD52 S346X was expressed in these cells, there was a significantly reduced frequency of SSA. Interestingly, expression of hRAD52 S346X also reduced the stimulation of SSA observed upon depletion of BRCA2, demonstrating the reciprocal roles for RAD52 and BRCA2 in the control of DSB repair by SSA. From an immunofluorescence analysis, we observed little nuclear localization of the mutant protein as compared to the wild-type; it is likely that the reduced nuclear levels of RAD52 S346X explain the diminished DSB repair by SSA. Altogether, we identified a genetic modifier that protects against breast cancer in women who carry pathogenic mutations in BRCA2 (P = 0.0008) and to a lesser extent BRCA1 (P = 0.02). This RAD52 mutation causes a reduction in DSB repair by SSA, suggesting that defects in RAD52-dependent DSB repair are linked to reduced tumor risk in BRCA2-mutation carriers.Abbreviations CI, confidence interval; CIMBA, Consortium of Investigators of Modifiers of BRCA1/2; DSB, DNA double-strand break; GFP, green fluorescent protein; HDR, homology-directed repair; HR, hazard ratio; MAF, minor allele frequency; mESCs, mouse embryonic stem cells;

show abstract

Altered DNA repair creates novel Alu/Alu repeat‐mediated deletions

et al. 2021

View full text Add to dashboard Cite

Alu elements are the most abundant source of nonallelic homology that influences genetic instability in the human genome. When there is a DNA double-stranded break, the Alu element's high copy number, moderate length and distance and mismatch between elements uniquely influence recombination processes. We utilize a reporter-gene assay to show the complex influence of Alu mismatches on Alurelated repeat-mediated deletions (RMDs). The Alu/Alu heteroduplex intermediate can result in a nonallelic homologous recombination (HR). Alternatively, the heteroduplex can result in various DNA breaks around the Alu elements caused by competing nucleases. These breaks can undergo Alt-nonhomologous end joining to cause deletions focused around the Alu elements. Formation of these heteroduplex intermediates is largely RAD52 dependent. Cells with low ERCC1 levels utilize more of these alternatives resolutions, while cells with MSH2 defects tend to have more RMDs with a specific increase in the HR events. Therefore, Alu elements are expected to create different forms of deletions in various cancers depending on a number of these DNA repair defects.

show abstract

Repeat-mediated deletions can be induced by a chromosomal break far from a repeat, but multiple pathways suppress such rearrangements

Cited by 42 publications

References 56 publications

Break‐induced replication plays a prominent role in long‐range repeat‐mediated deletion

Break‐induced replication plays a prominent role in long‐range repeat‐mediated deletion

The RAD52 S346X variant reduces risk of developing breast cancer in carriers of pathogenic germline BRCA2 mutations

Altered DNA repair creates novel Alu/Alu repeat‐mediated deletions

Contact Info

Product

Resources

About