Biology subjects

Rothstein, R.

Publications and source records attributed to Rothstein, R..

5 recordsLinked to original sources

bioRxiv2026

A multi-species toolkit of TOP2 hypercleavage mutants for studying topoisomerase II-mediated DNA damage

DNA topoisomerase II (TOP2) generates transient DNA double-strand breaks that are trapped as TOP2-DNA covalent complexes (TOP2cc) by antibiotic and chemotherapy drugs. Here, we characterize tools for study of cellular responses to TOP2cc, exploiting a Saccharomyces cerevisiae TOP2 mutant (TOP2-F1025Y,R1128G) that generates spontaneous and inhibitor-induced covalent complexes at elevated frequencies. This Top2-hc (for "hypercleavage") mutant protein inhibits yeast cell growth when expressed alone or with endogenous Top2, and growth defects are exacerbated in DNA-repair-deficient genetic backgrounds and/or in the presence of low doses of the Top2 poison mAMSA. We generated analogous mutations in human and mouse TOP2A and TOP2B that gave increased TOP2cc, hypersensitization to topoisomerase poisons, increased DNA damage, and decreased cell survival in cultured cells. We further established knock-in mouse models with inducible, tissue-specific expression of each TOP2-hc isoform, demonstrating overt organismal toxicity and cellular markers of DNA damage responses. To illustrate the potential of these genetic tools, we carried out proof-of-principle screens in yeast and cultured human cells for sensitivity to TOP2-hc. The yeast screen revealed strong requirements for homologous recombination, moderate roles for sister chromatid cohesion and kinetochore function, and dependencies on vesicle and vacuolar functions. The pilot shRNA screen in human cells revealed shared requirements for resistance to expression of either TOP2A-hc or TOP2B-hc as well as examples of isoform specificity. These findings establish hypercleavage mutant proteins as effective tools for studying topoisomerase isoform-specific DNA damage and offer a foundation for exploring TOP2cc toxicity and tolerance in vivo. Significance statementDNA topoisomerase II enzymes untangle chromosomes by cutting DNA, but incomplete resealing creates toxic damage that is the basis of antibacterial and chemotherapy drugs. Here we describe toolkits in yeast, mammalian cells, and mice that take advantage of mutant topoisomerase II enzymes that trap on DNA without drugs, creating powerful genetic systems to better study how cells deal with this type of DNA damage. We provide benchmarking data to validate these tools and to illustrate how they can be used for screens in cultured cells or tissue-specific experiments in vivo. These toolkits overcome longstanding technical barriers and enable new ways to study topoisomerase II-mediated DNA damage.

genetics↗

bioRxiv2024

Strand asymmetry in the repair of replication dependent double-strand breaks

Single-strand breaks (SSBs) are one of the most common endogenous lesions and have the potential to give rise to cytotoxic double-strand breaks (DSBs) during DNA replication. To investigate the mechanism of replication fork collapse at SSBs and subsequent repair, we employed Cas9 nickase (nCas9) to generate site and strand-specific nicks in the budding yeast genome. We show that nCas9-induced nicks are converted to mostly double-ended DSBs during S-phase. We find that repair of replication-dependent DSBs requires homologous recombination (HR) and is independent of canonical non-homologous end joining. Consistent with a strong bias to repair these lesions using a sister chromatid template, we observe minimal induction of inter-chromosomal HR by nCas9. Using nCas9 and a gRNA to nick either the leading or lagging strand template, we carried out a genome-wide screen to identify factors necessary for the repair of replication-dependent DSBs. All the core HR genes were recovered in the screen with both gRNAs, but we recovered components of the replication-coupled nucleosome assembly (RCNA) pathway with only the gRNA targeting the leading strand template. By use of additional gRNAs, we find that the RCNA pathway is especially important to repair a leading strand fork collapse.

genetics↗

bioRxiv2022

Aberrant DNA repair is a vulnerability in histone H3.3-mutant brain tumors

Pediatric high-grade gliomas (pHGG) are devastating and incurable brain tumors with recurrent mutations in histone H3.3. These mutations promote oncogenesis by dysregulating gene expression through alterations of histone modifications. We identify aberrant DNA repair as an independent oncogenic mechanism, which fosters genome instability and tumor cell growth in H3.3 mutant pHGG, thus opening new therapeutic options. The two most frequent H3.3 mutations in pHGG, K27M and G34R, drive aberrant repair of replication-associated damage by non-homologous end joining (NHEJ). Aberrant NHEJ is mediated by the DNA repair enzyme Polynucleotide Kinase 3-Phosphatase (PNKP), which shows increased association with mutant H3.3 at damaged replication forks. PNKP sustains the proliferation of cells bearing H3.3 mutations, thus conferring a molecular vulnerability, specific to mutant cells, with potential for therapeutic targeting.

cancer biology↗

bioRxiv2022

Temporal coordination between chromosome mobility and homologous recombination

Homologous recombination (HR), a principal cellular pathway for double-strand break (DSB) repair, is linked to changes in chromosome movement. Although increased chromosome mobility in response to a DSB has been observed in a variety of species, its precise role in HR remains controversial. Here, we find that end resection, the recruitment of recombination proteins, increased chromosome mobility, the pairing of homologs and gene conversion are temporally linked in response to a DSB. In mre11{Delta} mutant cells, which exhibit a delay in the initial processing of a DSB, chromosome mobility and all subsequent recombination events are also delayed. Overexpression of the Dna2 nuclease suppresses the mre11{Delta} delay in end resection and restores the original timing of chromosome mobility and all subsequent downstream HR events. Thus, changing the timing of chromosome mobility results in a corresponding change in essential downstream HR events, reinforcing its mechanistic role in the DNA repair process.

cell biology↗

bioRxiv2018

Xrs2 and Tel1 independently contribute to MR-mediated DNA tethering and replisome stability

The yeast Mre11-Rad50-Xrs2 (MRX) complex has structural, signaling and catalytic functions in the cellular response to DNA damage. Xrs2, the eukaryotic-specific component of the complex, is required for nuclear import of Mre11 and Rad50, and to recruit the Tel1 kinase to damage sites. We show that nuclear-localized MR complex (Mre11-NLS) catalyzes homology-dependent repair without Xrs2, but MR cannot activate Tel1 and it fails to tether DSBs resulting in sensitivity to genotoxins, replisome instability and increased gross chromosome rearrangements (GCRs). Fusing the Tel1 interaction domain from Xrs2 to Mre11-NLS is sufficient to restore telomere elongation and Tel1 signaling to Xrs2-deficient cells. Furthermore, Tel1 stabilizes Mre11-DNA association, and this stabilization function becomes important for DNA damage resistance in the absence of Xrs2. Enforcing Tel1 recruitment to the nuclear MR complex fully rescues end tethering, stalled replication fork stability and suppresses GCRs, highlighting important roles for Xrs2 and Tel1 to ensure optimal MR activity.\n\nHighlightsO_LIXrs2 is required for recruitment but not for activation of Tel1 kinase\nC_LIO_LITel1 and Xrs2 function independently to optimize MR activity at DSBs and stalled replication forks\nC_LIO_LIStable association of Mre11 at DSBs is required to maintain end-to-end tethering\nC_LIO_LIMR-mediated DNA tethering promotes replisome stability and genome integrity\nC_LI

genetics↗