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  • 1
    In: Journal of Molecular Biology, Elsevier BV, Vol. 372, No. 4 ( 2007-09), p. 1070-1081
    Type of Medium: Online Resource
    ISSN: 0022-2836
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2007
    detail.hit.zdb_id: 1355192-9
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 43 ( 2020-10-27), p. 26876-26884
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 43 ( 2020-10-27), p. 26876-26884
    Abstract: Topoisomerase II (Top2) is an essential enzyme that resolves catenanes between sister chromatids as well as supercoils associated with the over- or under-winding of duplex DNA. Top2 alters DNA topology by making a double-strand break (DSB) in DNA and passing an intact duplex through the break. Each component monomer of the Top2 homodimer nicks one of the DNA strands and forms a covalent phosphotyrosyl bond with the 5′ end. Stabilization of this intermediate by chemotherapeutic drugs such as etoposide leads to persistent and potentially toxic DSBs. We describe the isolation of a yeast top2 mutant ( top2-F1025Y,R1128G ) the product of which generates a stabilized cleavage intermediate in vitro. In yeast cells, overexpression of the top2-F1025Y,R1128G allele is associated with a mutation signature that is characterized by de novo duplications of DNA sequence that depend on the nonhomologous end-joining pathway of DSB repair. Top2-associated duplications are promoted by the clean removal of the enzyme from DNA ends and are suppressed when the protein is removed as part of an oligonucleotide. TOP2 cells treated with etoposide exhibit the same mutation signature, as do cells that overexpress the wild-type protein. These results have implications for genome evolution and are relevant to the clinical use of chemotherapeutic drugs that target Top2.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Wiley ; 2021
    In:  Current Protocols Vol. 1, No. 10 ( 2021-10)
    In: Current Protocols, Wiley, Vol. 1, No. 10 ( 2021-10)
    Abstract: Topoisomerases are enzymes that play essential roles in DNA replication, transcription, chromosome segregation, and recombination. All cells have two major forms of DNA topoisomerases: type I enzymes, which make single‐stranded cuts in DNA, and type II enzymes, which cut and decatenate double‐stranded DNA. DNA topoisomerases are important targets of approved and experimental anti‐cancer agents. Provided in this article are protocols to assess activities of topoisomerases and their inhibitors. Included are an assay for topoisomerase I activity based on relaxation of supercoiled DNA; an assay for topoisomerase II based on the decatenation of double‐stranded DNA; and approaches for enriching and quantifying DNA‐protein covalent complexes formed as obligatory intermediates in the reactions of type I and II topoisomerases with DNA; and assays for measuring DNA cleavage in vitro . Topoisomerases are not the only proteins that form covalent adducts with DNA in living cells, and the approaches described here are likely to find use in characterizing other protein‐DNA adducts and exploring their utility as targets for therapy. © 2021 Wiley Periodicals LLC. Basic Protocol 1 : Assay of topoisomerase I activity Basic Protocol 2 : Assay of topoisomerase II activity Basic Protocol 3 : In vivo determination of topoisomerase covalent complexes using the in vivo complex of enzyme (ICE) assay Support Protocol 1 : Preparation of mouse tissue for determination of topoisomerase covalent complexes using the ICE assay Support Protocol 2 : Using recombinant topoisomerase standard for absolute quantification of cellular TOP2CC Basic Protocol 4 : Quantification of topoisomerase‐DNA covalent complexes by RADAR/ELISA: The rapid approach to DNA adduct recovery (RADAR) combined with the enzyme‐linked immunosorbent assay (ELISA) Basic Protocol 5 : Analysis of protein‐DNA covalent complexes by RADAR/Western Support Protocol 3 : Adduct‐Seq to characterize adducted DNA Support Protocol 4 : Nuclear fractionation and RNase treatment to reduce sample complexity Basic Protocol 6 : Determination of DNA cleavage by purified topoisomerase I Basic Protocol 7 : Determination of inhibitor effects on DNA cleavage by topoisomerase II using a plasmid linearization assay Alternate Protocol : Gel electrophoresis determination of topoisomerase II cleavage
    Type of Medium: Online Resource
    ISSN: 2691-1299 , 2691-1299
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 3059383-9
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  • 4
    In: Nature Neuroscience, Springer Science and Business Media LLC, Vol. 17, No. 6 ( 2014-6), p. 813-821
    Type of Medium: Online Resource
    ISSN: 1097-6256 , 1546-1726
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2014
    detail.hit.zdb_id: 1494955-6
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Public Library of Science (PLoS) ; 2013
    In:  PLoS Genetics Vol. 9, No. 3 ( 2013-3-7), p. e1003370-
    In: PLoS Genetics, Public Library of Science (PLoS), Vol. 9, No. 3 ( 2013-3-7), p. e1003370-
    Type of Medium: Online Resource
    ISSN: 1553-7404
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2013
    detail.hit.zdb_id: 2186725-2
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  • 6
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 13_Supplement ( 2018-07-01), p. 4853-4853
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 4853-4853
    Abstract: DNA topoisomerases (topos) play an essential role in nuclear processes such as replication, transcription, and chromosome segregation. These enzymes regulate DNA topology by introducing transient breaks in DNA with formation of transient protein/DNA covalent complexes. These complexes can be trapped by aberrant DNA structures, and are also the basis for anti-cancer drugs that target topos. Since topos can be trapped on DNA, leading to strand breaks with protein adducts at the site of the breaks, cells require DNA repair pathways to process protein adducts. We have examined the repair of the type II topos (Top2) in yeast and mammalian cells. We developed a sensitive assay to detect ubiquitylation and other post-translational modifications (PTMs) of Top2 trapped on DNA in S. cerevisiae and have shown that the proteasome plays a key role in repair of Top2 damage induced by the anti-cancer drug etoposide. We demonstrated that sumoylation of Top2 is induced by etoposide, and that deletion of the SUMO ligase Siz2 prevents etoposide induced sumoylation. Deletion of either of the genes encoding the ubiquitin ligase Slx5/Slx8 led to decreased ubiquitylation of trapped Top2. The mammalian ortholog of Slx5/Slx8 is Rnf4, and it too plays a role in ubiquitylation and degradation of Top2 trapped by etoposide. A human cell line completely lacking Rnf4 is defective in ubiquitylation of Top2β, one of the two mammalian Top2 isoforms. Interestingly, repair of the Top2α isoform is unaffected in an Rnf4 knockout cell line. Proteolysis of trapped Top2 is also subject to negative regulation. The UBA domain protein UBAP2L, (also termed NICE4) is amplified in various cancers. Knockout of the UBAP2L increases proteolysis of trapped Top2. Levels of trapped Top2α and Top2β are decreased in the absence of UBAP2L, and the level of trapped Top2 returns to the wild type level when MG132 is added, indicating UBAP2L regulates the proteasome mediated degradation of Top2. UBAP2L physically interacts with Top2β as determined by co-immunoprecipitation, and the interaction is not seen in Rnf4 knockout cells. Finally, knockout of UBAP2L confers high level resistance to etoposide. Our results provide insights to the response of cancer cells to Top2 targeting agents. Citation Format: Yilun Sun, Karin C. Nitiss, John L. Nitiss. Regulation of proteolytic repair of Top2 covalent complexes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4853.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 7
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2010
    In:  Cell Research Vol. 20, No. 2 ( 2010-2), p. 122-123
    In: Cell Research, Springer Science and Business Media LLC, Vol. 20, No. 2 ( 2010-2), p. 122-123
    Type of Medium: Online Resource
    ISSN: 1001-0602 , 1748-7838
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2010
    detail.hit.zdb_id: 2082402-6
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2015
    In:  Cancer Research Vol. 75, No. 15_Supplement ( 2015-08-01), p. 1658-1658
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. 1658-1658
    Abstract: DNA topoisomerase II (Top2) is the target of several important anti-cancer agents, including doxorubicin and etoposide. Clinically active Top2 agents, termed Top2 poisons, act by blocking the enzyme reaction at a step where the protein is covalently bound to DNA. This leads to the accumulation of Top2/DNA complexes that act as DNA damaging agents that can trigger cell death. Surviving Top2-induced damage likely requires the repair of the enzyme induced damage and has been hypothesized to include pathways that proteolyze the protein bound to DNA followed by nucleolytic removal of the remaining peptide that is bound to DNA by a phosphotyrosyl linkage. This model of repair suggests that inhibition of proteolysis would lead to elevated levels of intact Top2/DNA complexes, and increased sensitivity to Top2 poisons such as etoposide. We have tested this model using the proteasome inhibitor carfilzomib in a pediatric rhabdomyosarcoma cell line (Rh30). We found that carfilzomib enhanced cell killing by etoposide, and that co-treatment of Rh30 cells with carfilzomib led to increases in both Top2 alpha and Top2 beta covalent complexes. These results suggest that proteasomal degradation of both Top2 isoforms is important for repairing DNA damage arising from etoposide. We are also interested in identifying the determinants of Top2 degradation following treatment with etoposide, especially proteins that recognize the trapped enzyme as DNA damage. We used a yeast genetic model system to address this question. We showed that the proteasome inhibitor MG132 greatly enhanced the sensitivity of yeast cells to etoposide, and that co-treatment of MG132 and etoposide led to elevated levels of Top2/DNA complexes compared to etoposide alone. We found that deletion of the human RNF4 homolog Slx5/Slx8 (a SUMO dependent ubiquitin ligase) also leads to an increase in Top2 covalent complexes induced by etoposide. We found that deletion of the genes encoding either Slx5 or Slx8 along with the repair protein Tdp1 led to much higher levels of cell killing compared to single deletions. These results suggest that there are at least two independent pathways for repairing Top2 damage, one dependent on Slx5/Slx8 dependent protein degradation and a second pathway dependent on nucleolytic removal of Top2. We suggest that Slx5/Slx8 plays a role in targeting Top2 for degradation following etoposide treatment. Our results also provide a rationale for the combination of a proteasome inhibitor with etoposide as an approach of increasing the efficacy of etoposide. Citation Format: Yilun Sun, Karin C. Nitiss, John L. Nitiss. Proteolytic processing pathways for topoisomerase covalent complexes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1658. doi:10.1158/1538-7445.AM2015-1658
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 9
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2010
    In:  Cancer Research Vol. 70, No. 8_Supplement ( 2010-04-15), p. 3500-3500
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 70, No. 8_Supplement ( 2010-04-15), p. 3500-3500
    Abstract: The generation of elevated levels of enzyme: DNA covalent complexes is the key event in cell killing by many drugs targeting DNA topoisomerases. These agents, termed topoisomerase poisons generate protein linked DNA strand that block transcription and replication, leading to cell death. A critical step in the repair of topoisomerase mediated DNA damage is the removal of protein that is covalently attached to DNA. Several specialized repair enzymes, including Tdp1 (tyrosyl DNA phosphodiesterase I) and TTRAP (TRAF and TNF receptor-associated protein) can hydrolyze phosphotyrosyl: DNA linkages. We previously reported that yeast Tdp1 could hydrolyze 5′ as well as 3′ phosphotyrosyl linkages. Human Tdp1 can also hydrolyze 5′ phosphotyrosyl linkages, although the efficiency of the reaction with the human enzyme is much less than that seen with the yeast enzyme. Interestingly, the human enzyme processes adducts bearing a seven amino acid peptide linked to an oligonucleotide with greater efficiency than a 5′ biotin linked oligonucleotide, suggesting that the nature of the adduct at DNA ends influences Tdp1 reaction kinetics. We also used substrates derived from Top2 trapped covalent complexes to assess the ability of other DNA repair enzymes to remove peptides covalently bound to DNA. We found that the heterodimeric nuclease Slx1/Slx4 is able to remove Top2 peptides that are covalently bound to DNA. This result is consistent with our genetic data from yeast that a mutation in the subunit that includes the nuclease (Slx1) is hypersensitive to Top2 poisons, but not sensitive to other DNA damaging agents. Our results indicate that there are multiple pathways for repairing Top2 covalent complexes and suggest that the Slx1/Slx4 dependent pathway may be particularly relevant to repairing topoisomerase mediated damage at replication forks. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3500.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2010
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 10
    In: Biochemical Pharmacology, Elsevier BV, Vol. 66, No. 4 ( 2003-08), p. 623-631
    Type of Medium: Online Resource
    ISSN: 0006-2952
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2003
    detail.hit.zdb_id: 1496199-4
    SSG: 15,3
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