scholarly journals Different DNA repair pathways are required following excision and integration of the DNA cut & paste transposon piggyBat in Saccharomyces cerevisiae.

2015 ◽  
Author(s):  
Weifeng She ◽  
Courtney Busch Cambouris ◽  
Nancy L. Craig
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Repair ◽  
Single Gene ◽  
Donor Site ◽  
Insertion Site ◽  
Strand Break ◽  
Host Factors ◽  
A Genome ◽  
Genes Encoding ◽  
Repair Pathways

The movement of transposable elements from place to place in a genome requires both element-encoded and host-encoded factors. In DNA cut & paste transposition, the element-encoded transposase performs the DNA breakage and joining reactions that excise the element from the donor site and integrate it into the new insertion site. Host factors can influence many aspects of transposition. Notably, host DNA repair factors mediate the regeneration of intact duplex DNA necessary after transposase action by repairing the double strand break in the broken donor backbone, from which the transposon has excised, and repairing the single strand gaps that flank the newly inserted transposon. We have exploited the ability of the mammalian transposon piggyBat, a member of the piggyBac superfamily, to transpose in Saccharomyces cerevisiae and used the yeast single gene deletion collection to screen for genes encoding host factors involved in piggyBat transposition. piggyBac transposition is distinguished by the fact that piggyBac elements insert into TTAA target sites and also that the donor backbone is restored to its pre-transposon sequence after transposon excision, that is, excision is precise. We have found that repair of the broken donor backbone requires the non-homologous end-joining repair pathway (NHEJ). By contrast, NHEJ is not required for DNA repair at the new insertion site. Thus multiple DNA repair pathways are required for piggyBac transposition.

scholarly journals BRCA1 Mediated Homologous Recombination and S Phase DNA Repair Pathways Restrict LINE-1 Retrotransposition in Human Cells

2019 ◽  
Author(s):  
Xiaoji Sun ◽  
Paolo Mita ◽  
David J. Kahler ◽  
Donghui Li ◽  
Aleksandra Wudzinska ◽  
...  
Keyword(s):  
Dna Repair ◽  
Homologous Recombination ◽  
Potential Role ◽  
Genome Instability ◽  
Protein Translation ◽  
Human Cells ◽  
Host Factors ◽  
Factors Affecting ◽  
A Genome ◽  
Repair Pathways

AbstractLong interspersed element-1 (LINE-1 or L1) is the only autonomous retrotransposon active in human cells. L1s DNA makes about 17% of the human genome and retrotransposition of a few active L1 copies has been detected in various tumors, underscoring the potential role of L1 in mediating or increasing genome instability during tumorigenic development. Different host factors have been shown to influence L1 mobility through several mechanisms. However, systematic analyses of host factors affecting L1 retrotransposition are limited. Here, we developed a high-throughput microscopy-based retrotransposition assay and coupled it to a genome-wide siRNA knockdown screen to study the cellular regulators of L1 retrotransposition in human cells. We showed that L1 insertion frequency was stimulated by knockdown of Double-Stranded Break (DSB) repair factors that are active in the S/G2 phase of the cell cycle including Homologous Recombination (HR), Fanconi Anemia (FA) and, to a less extent, microhomology-mediated end-joining (MMEJ) factors. In particular, we show that BRCA1, an E3 ubiquitin ligase with a key role in several DNA repair pathways, plays multiple roles in regulating L1; BRCA1 knockdown directly affects L1 retrotransposition frequency and structure and also plays a role in controlling L1 ORF2 protein translation through L1 mRNA binding. These results suggest the existence of a “battle” between HR factors and L1 retrotransposons, revealing a potential role for L1 in development of tumors characterized by BRCA1 and HR repair deficiencies.

scholarly journals DNA Repair Biosensor-Identified DNA Damage Activities of Endophyte Extracts from Garcinia cowa

Biomolecules ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1680
Author(s):  
Tassanee Lerksuthirat ◽  
Rakkreat Wikiniyadhanee ◽  
Sermsiri Chitphuk ◽  
Wasana Stitchantrakul ◽  
Somponnat Sampattavanich ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Fluorescent Proteins ◽  
Strand Break ◽  
Control Group ◽  
Focus Formation ◽  
Dna Damage And Repair ◽  
Biological Compounds ◽  
Repair Pathways ◽  
Garcinia Cowa

Recent developments in chemotherapy focus on target-specific mechanisms, which occur only in cancer cells and minimize the effects on normal cells. DNA damage and repair pathways are a promising target in the treatment of cancer. In order to identify novel compounds targeting DNA repair pathways, two key proteins, 53BP1 and RAD54L, were tagged with fluorescent proteins as indicators for two major double strand break (DSB) repair pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). The engineered biosensor cells exhibited the same DNA repair properties as the wild type. The biosensor cells were further used to investigate the DNA repair activities of natural biological compounds. An extract from Phyllosticta sp., the endophyte isolated from the medicinal plant Garcinia cowa Roxb. ex Choisy, was tested. The results showed that the crude extract induced DSB, as demonstrated by the increase in the DNA DSB marker γH2AX. The damaged DNA appeared to be repaired through NHEJ, as the 53BP1 focus formation in the treated fraction was higher than in the control group. In conclusion, DNA repair-based biosensors are useful for the preliminary screening of crude extracts and biological compounds for the identification of potential targeted therapeutic drugs.

scholarly journals Context-Dependent Strategies for Enhanced Genome Editing of Genodermatoses

Cells ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 112 ◽  
Author(s):  
Oliver Patrick March ◽  
Thomas Kocher ◽  
Ulrich Koller
Keyword(s):  
Genome Editing ◽  
Epidermolysis Bullosa ◽  
External Environment ◽  
Strand Break ◽  
Clinical Applications ◽  
Structural Proteins ◽  
Wound Management ◽  
Genes Encoding ◽  
Repair Pathways ◽  
Genetic Context

The skin provides direct protection to the human body from assault by the harsh external environment. The crucial function of this organ is significantly disrupted in genodermatoses patients. Genodermatoses comprise a heterogeneous group of largely monogenetic skin disorders, typically involving mutations in genes encoding structural proteins. Therapeutic options for this debilitating group of diseases, including epidermolysis bullosa, primarily consist of wound management. Genome editing approaches co-opt double-strand break repair pathways to introduce desired sequence alterations at specific loci. Rapid advances in genome editing technologies have the potential to propel novel genetic therapies into the clinic. However, the associated phenotypes of many mutations may be treated via several genome editing strategies. Therefore, for potential clinical applications, implementation of efficient approaches based upon mutation, gene and disease context is necessary. Here, we describe current genome editing approaches for the treatment of genodermatoses, along with a discussion of the optimal strategy for each genetic context, in order to achieve enhanced genome editing approaches.

Targeting resistant prostate cancer with ATR and PARP inhibition (TRAP trial): A phase II study.

2020 ◽  
Vol 38 (6_suppl) ◽  
pp. TPS254-TPS254
Author(s):  
Zachery R. Reichert ◽  
Stephanie Daignault ◽  
Benjamin A. Teply ◽  
Michael Edward Devitt ◽  
Elisabeth I. Heath
Keyword(s):  
Prostate Cancer ◽  
Clinical Trial ◽  
Dna Repair ◽  
Homologous Recombination ◽  
Acquired Resistance ◽  
Progression Free Survival ◽  
Strand Break ◽  
Circulating Tumor Dna ◽  
Parp Inhibition ◽  
Genes Encoding

TPS254 Background: Inhibition of poly(ADP-ribose) polymerase (PARP) shows promise in prostate cancer, but is limited to the ~20% of men with defects in genes encoding for DNA repair proteins BRCA1, BRCA2 or ATM (homologous recombination defect positive, HRD+). The effect is modest for HRD+ patients with a progression free survival of ~7 months. Pharmacologically simulating genetic DNA repair defects may expand who benefits to homologous recombination defect negative (HRD-) patients and improve HRD+ response. The ataxia telangiectasia and Rad3-related protein (ATR) is ideal with its roles in cell cycle regulation, replication fork resolution and both single and double strand break repair. Preclinical studies on HRD-/HRD+ cell lines support this. We hypothesize co-inhibition of ATR and PARP will respond regardless of HRD status. Methods: TRAP is a prospective, multi-institutional, phase 2 clinical trial testing AZD6738 combined with olaparib in HRD+ and HRD- mCRPC patients. Primary endpoint is the response rate (RR) by RECIST radiographic response or PSA decline ≥50% in 35 HRD- patients, with a secondary objective of RR in 12 HRD+ patients. HRD+ is mono/biallelic loss of ATM or biallelic loss of BRCA1/2. Tissue based sequencing is done unless completed prior in mCRPC, known BRCA germline loss, treating provider deems biopsy unsafe or biopsy fails. Those unable or failing biopsy are designated as HRD-, but BRCA1/2 and ATM are tested via circulating tumor DNA in a commercial test. Eligible patients must progress after ≥1 line of mCRPC therapy. Progression on a second generation anti-androgen (e.g. apalutamide), abiraterone or within 6 months of docetaxel in hormone sensitive disease are eligible. Treatment entails 160 mg PO daily of AZD6738 on days 1-7 and 300 mg PO BID of olaparib on days 1-28 of a 28-day cycle. Statistical analysis will provide RR with 95% binomial confidence intervals. Analysis of tumor specimens, circulating tumor cells and DNA will be performed for predictors of response and acquired resistance. The study is at four sites in the US, participates in the Prostate Cancer Clinical Trials Consortium, LLC, is managed by the University of Michigan and funded by AstraZeneca. Clinical trial information: NCT03787680.

scholarly journals Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea

2021 ◽  
Vol 22 (24) ◽  
pp. 13296
Author(s):  
Mariarosaria De Falco ◽  
Mariarita De Felice
Keyword(s):  
Cell Cycle ◽  
Dna Repair ◽  
Genome Stability ◽  
Developmental Disorders ◽  
Strand Break ◽  
Human Diseases ◽  
Dna Damages ◽  
Dna Repair Mechanisms ◽  
Repair Mechanisms ◽  
Repair Pathways

All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.

scholarly journals Strand asymmetry influences mismatch repair during single-strand annealing

2019 ◽  
Author(s):  
Victoria O. Pokusaeva ◽  
Aránzazu Rosado Diez ◽  
Lorena Espinar ◽  
Guillaume J. Filion
Keyword(s):  
Dna Repair ◽  
Mismatch Repair ◽  
Tandem Repeats ◽  
Embryonic Stem ◽  
Intrinsic Property ◽  
Strand Break ◽  
Single Strand ◽  
A Genome ◽  
Single Strand Annealing ◽  
Strand Annealing

ABSTRACTBiases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. However, such biases have not yet been measured in chromatin for lack of technologies. Here we develop a genome-wide assay whereby the same DNA lesion is repaired in different chromatin contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated when the single strand annealing repair pathway is used. Surprisingly, the mismatch repair machinery favors the same strand 60-80% of the time. The location of the lesion in the genome and the type of mismatch have little influence on the repair bias in this context. Using machine learning, we further show that both the repair bias and the efficiency of the repair are independent of known chromatin features. These results suggest that some intrinsic property of the lesion can have a large influence on the outcome of DNA repair, irrespective of the surrounding chromatin context.

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