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  1. Article ; Online: Two independent DNA repair pathways cause mutagenesis in template switching deficient Saccharomyces cerevisiae.

    Jiang, Yangyang Kate / Medley, Eleanor A / Brown, Grant W

    Genetics

    2023  Volume 225, Issue 3

    Abstract: Upon DNA replication stress, cells utilize the postreplication repair pathway to repair single-stranded DNA and maintain genome integrity. Postreplication repair is divided into 2 branches: error-prone translesion synthesis, signaled by proliferating ... ...

    Abstract Upon DNA replication stress, cells utilize the postreplication repair pathway to repair single-stranded DNA and maintain genome integrity. Postreplication repair is divided into 2 branches: error-prone translesion synthesis, signaled by proliferating cell nuclear antigen (PCNA) monoubiquitination, and error-free template switching, signaled by PCNA polyubiquitination. In Saccharomyces cerevisiae, Rad5 is involved in both branches of repair during DNA replication stress. When the PCNA polyubiquitination function of Rad5 s disrupted, Rad5 recruits translesion synthesis polymerases to stalled replication forks, resulting in mutagenic repair. Details of how mutagenic repair is carried out, as well as the relationship between Rad5-mediated mutagenic repair and the canonical PCNA-mediated mutagenic repair, remain to be understood. We find that Rad5-mediated mutagenic repair requires the translesion synthesis polymerase ζ but does not require other yeast translesion polymerase activities. Furthermore, we show that Rad5-mediated mutagenic repair is independent of PCNA binding by Rev1 and so is separable from canonical mutagenic repair. In the absence of error-free template switching, both modes of mutagenic repair contribute additively to replication stress response in a replication timing-independent manner. Cellular contexts where error-free template switching is compromised are not simply laboratory phenomena, as we find that a natural variant in RAD5 is defective in PCNA polyubiquitination and therefore defective in error-free repair, resulting in Rad5- and PCNA-mediated mutagenic repair. Our results highlight the importance of Rad5 in regulating spontaneous mutagenesis and genetic diversity in S. cerevisiae through different modes of postreplication repair.
    MeSH term(s) Saccharomyces cerevisiae/metabolism ; Proliferating Cell Nuclear Antigen/genetics ; Proliferating Cell Nuclear Antigen/metabolism ; DNA Helicases/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; DNA Repair ; DNA Replication/genetics ; Mutagenesis ; DNA Damage
    Chemical Substances Proliferating Cell Nuclear Antigen ; DNA Helicases (EC 3.6.4.-) ; Saccharomyces cerevisiae Proteins ; RAD5 protein, S cerevisiae (EC 3.6.1.-)
    Language English
    Publishing date 2023-08-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1093/genetics/iyad153
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Setting molecular traps in yeast for identification of anticancer drug targets.

    Brown, Grant W / Andrews, Brenda

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 18

    MeSH term(s) Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; DNA Repair/drug effects ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; Drug Delivery Systems ; Flap Endonucleases/antagonists & inhibitors ; Flap Endonucleases/genetics ; Homologous Recombination/drug effects ; Humans ; Multiprotein Complexes/genetics ; Neoplasms/drug therapy ; Neoplasms/genetics ; Parthanatos/drug effects ; Poly (ADP-Ribose) Polymerase-1/genetics ; Saccharomyces cerevisiae/genetics ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology ; Synthetic Lethal Mutations/drug effects ; Synthetic Lethal Mutations/genetics
    Chemical Substances Antineoplastic Agents ; DNA-Binding Proteins ; Multiprotein Complexes ; Small Molecule Libraries ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30) ; Flap Endonucleases (EC 3.1.-) ; FEN1 protein, human (EC 3.1.11.-)
    Language English
    Publishing date 2021-04-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2105547118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Yeast goes viral: probing SARS-CoV-2 biology using

    Ho, Brandon / Loll-Krippleber, Raphael / Brown, Grant W

    Microbial cell (Graz, Austria)

    2022  Volume 9, Issue 4, Page(s) 80–83

    Abstract: The budding ... ...

    Abstract The budding yeast
    Language English
    Publishing date 2022-03-21
    Publishing country Austria
    Document type Journal Article ; Comment
    ZDB-ID 2814756-X
    ISSN 2311-2638
    ISSN 2311-2638
    DOI 10.15698/mic2022.04.774
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genetic screens in Saccharomyces cerevisiae identify a role for 40S ribosome recycling factors Tma20 and Tma22 in nonsense-mediated decay.

    Pacheco, Miguel / D'Orazio, Karole N / Lessen, Laura N / Veltri, Anthony J / Neiman, Zachary / Loll-Krippleber, Raphael / Brown, Grant W / Green, Rachel

    G3 (Bethesda, Md.)

    2024  Volume 14, Issue 3

    Abstract: The decay of messenger RNA with a premature termination codon by nonsense-mediated decay (NMD) is an important regulatory pathway for eukaryotes and an essential pathway in mammals. NMD is typically triggered by the ribosome terminating at a stop codon ... ...

    Abstract The decay of messenger RNA with a premature termination codon by nonsense-mediated decay (NMD) is an important regulatory pathway for eukaryotes and an essential pathway in mammals. NMD is typically triggered by the ribosome terminating at a stop codon that is aberrantly distant from the poly-A tail. Here, we use a fluorescence screen to identify factors involved in NMD in Saccharomyces cerevisiae. In addition to the known NMD factors, including the entire UPF family (UPF1, UPF2, and UPF3), as well as NMD4 and EBS1, we identify factors known to function in posttermination recycling and characterize their contribution to NMD. These observations in S. cerevisiae expand on data in mammals indicating that the 60S recycling factor ABCE1 is important for NMD by showing that perturbations in factors implicated in 40S recycling also correlate with a loss of NMD.
    MeSH term(s) Animals ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; RNA Helicases/metabolism ; Nonsense Mediated mRNA Decay ; Ribosomes/genetics ; Ribosomes/metabolism ; RNA, Messenger/genetics ; Mammals/genetics
    Chemical Substances RNA Helicases (EC 3.6.4.13) ; RNA, Messenger
    Language English
    Publishing date 2024-01-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkad295
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Exploiting DNA Replication Stress for Cancer Treatment.

    Ubhi, Tajinder / Brown, Grant W

    Cancer research

    2019  Volume 79, Issue 8, Page(s) 1730–1739

    Abstract: Complete and accurate DNA replication is fundamental to cellular proliferation and genome stability. Obstacles that delay, prevent, or terminate DNA replication cause the phenomena termed DNA replication stress. Cancer cells exhibit chronic replication ... ...

    Abstract Complete and accurate DNA replication is fundamental to cellular proliferation and genome stability. Obstacles that delay, prevent, or terminate DNA replication cause the phenomena termed DNA replication stress. Cancer cells exhibit chronic replication stress due to the loss of proteins that protect or repair stressed replication forks and due to the continuous proliferative signaling, providing an exploitable therapeutic vulnerability in tumors. Here, we outline current and pending therapeutic approaches leveraging tumor-specific replication stress as a target, in addition to the challenges associated with such therapies. We discuss how replication stress modulates the cell-intrinsic innate immune response and highlight the integration of replication stress with immunotherapies. Together, exploiting replication stress for cancer treatment seems to be a promising strategy as it provides a selective means of eliminating tumors, and with continuous advances in our knowledge of the replication stress response and lessons learned from current therapies in use, we are moving toward honing the potential of targeting replication stress in the clinic.
    MeSH term(s) Animals ; Antineoplastic Agents/therapeutic use ; DNA Damage/drug effects ; DNA Replication/drug effects ; Genomic Instability ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics
    Chemical Substances Antineoplastic Agents
    Language English
    Publishing date 2019-04-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1432-1
    ISSN 1538-7445 ; 0008-5472
    ISSN (online) 1538-7445
    ISSN 0008-5472
    DOI 10.1158/0008-5472.CAN-18-3631
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Post-replication repair: Rad5/HLTF regulation, activity on undamaged templates, and relationship to cancer.

    Gallo, David / Brown, Grant W

    Critical reviews in biochemistry and molecular biology

    2019  Volume 54, Issue 3, Page(s) 301–332

    Abstract: The eukaryotic post-replication repair (PRR) pathway allows completion of DNA replication when replication forks encounter lesions on the DNA template and are mediated by post-translational ubiquitination of the DNA sliding clamp proliferating cell ... ...

    Abstract The eukaryotic post-replication repair (PRR) pathway allows completion of DNA replication when replication forks encounter lesions on the DNA template and are mediated by post-translational ubiquitination of the DNA sliding clamp proliferating cell nuclear antigen (PCNA). Monoubiquitinated PCNA recruits translesion synthesis (TLS) polymerases to replicate past DNA lesions in an error-prone manner while addition of K63-linked polyubiquitin chains signals for error-free template switching to the sister chromatid. Central to both branches is the E3 ubiquitin ligase and DNA helicase Rad5/helicase-like transcription factor (HLTF). Mutations in PRR pathway components lead to genomic rearrangements, cancer predisposition, and cancer progression. Recent studies have challenged the notion that the PRR pathway is involved only in DNA lesion tolerance and have shed new light on its roles in cancer progression. Molecular details of Rad5/HLTF recruitment and function at replication forks have emerged. Mounting evidence indicates that PRR is required during lesion-less replication stress, leading to TLS polymerase activity on undamaged templates. Analysis of PRR mutation status in human cancers and PRR function in cancer models indicates that down regulation of PRR activity is a viable strategy to inhibit cancer cell growth and reduce chemoresistance. Here, we review these findings, discuss how they change our views of current PRR models, and look forward to targeting the PRR pathway in the clinic.
    MeSH term(s) Acid Anhydride Hydrolases/genetics ; Acid Anhydride Hydrolases/metabolism ; Animals ; DNA Damage ; DNA Repair ; DNA Replication ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Humans ; Mutation ; Neoplasms/genetics ; Neoplasms/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Ubiquitination
    Chemical Substances DNA-Binding Proteins ; HLTF protein, human ; Transcription Factors ; Acid Anhydride Hydrolases (EC 3.6.-) ; RAD50 protein, human (EC 3.6.-)
    Language English
    Publishing date 2019-08-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1000977-2
    ISSN 1549-7798 ; 1381-3455 ; 1040-9238
    ISSN (online) 1549-7798
    ISSN 1381-3455 ; 1040-9238
    DOI 10.1080/10409238.2019.1651817
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  7. Article ; Online: Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes.

    Lamb, Natalie A / Bard, Jonathan E / Loll-Krippleber, Raphael / Brown, Grant W / Surtees, Jennifer A

    Genetics

    2022  Volume 221, Issue 4

    Abstract: Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of ... ...

    Abstract Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of free deoxyribonucleoside triphosphate pools by ribonucleotide reductase and repair of replication errors by the mismatch repair system. We identified genetic interactions between rnr1 alleles that skew and/or elevate deoxyribonucleoside triphosphate levels and mismatch repair gene deletions. These defects indicate that the rnr1 alleles lead to increased mutation loads that are normally acted upon by mismatch repair. We then utilized a targeted deep-sequencing approach to determine mutational profiles associated with mismatch repair pathway defects. By combining rnr1 and msh mutations to alter and/or increase deoxyribonucleoside triphosphate levels and alter the mutational load, we uncovered previously unreported specificities of Msh2-Msh3 and Msh2-Msh6. Msh2-Msh3 is uniquely able to direct the repair of G/C single-base deletions in GC runs, while Msh2-Msh6 specifically directs the repair of substitutions that occur at G/C dinucleotides. We also identified broader sequence contexts that influence variant profiles in different genetic backgrounds. Finally, we observed that the mutation profiles in double mutants were not necessarily an additive relationship of mutation profiles in single mutants. Our results have implications for interpreting mutation signatures from human tumors, particularly when mismatch repair is defective.
    MeSH term(s) Humans ; Deoxyribonucleosides ; DNA Mismatch Repair ; DNA Repair ; DNA-Binding Proteins/metabolism ; Mutation ; MutS Homolog 2 Protein/genetics ; MutS Homolog 2 Protein/metabolism ; MutS Proteins/genetics ; MutS Proteins/metabolism ; Ribonucleotide Reductases/genetics ; Ribonucleotide Reductases/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Substrate Specificity
    Chemical Substances Deoxyribonucleosides ; DNA-Binding Proteins ; MutS Homolog 2 Protein (EC 3.6.1.3) ; MutS Proteins (EC 3.6.1.3) ; Ribonucleotide Reductases (EC 1.17.4.-) ; Saccharomyces cerevisiae Proteins
    Language English
    Publishing date 2022-06-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1093/genetics/iyac092
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  8. Article ; Online: Mec1-independent activation of the Rad53 checkpoint kinase revealed by quantitative analysis of protein localization dynamics.

    Ho, Brandon / Sanford, Ethan J / Loll-Krippleber, Raphael / Torres, Nikko P / Smolka, Marcus B / Brown, Grant W

    eLife

    2023  Volume 12

    Abstract: The replication checkpoint is essential for accurate DNA replication and repair, and maintenance of genomic integrity when a cell is challenged with genotoxic stress. Several studies have defined the complement of proteins that change subcellular ... ...

    Abstract The replication checkpoint is essential for accurate DNA replication and repair, and maintenance of genomic integrity when a cell is challenged with genotoxic stress. Several studies have defined the complement of proteins that change subcellular location in the budding yeast
    MeSH term(s) Protein Serine-Threonine Kinases/metabolism ; Cell Cycle Proteins/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Intracellular Signaling Peptides and Proteins/metabolism ; Checkpoint Kinase 2/genetics ; Checkpoint Kinase 2/metabolism ; Saccharomyces cerevisiae/metabolism ; Phosphorylation ; DNA Damage ; Methyl Methanesulfonate/pharmacology ; DNA Replication
    Chemical Substances Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Cell Cycle Proteins ; Saccharomyces cerevisiae Proteins ; Intracellular Signaling Peptides and Proteins ; Checkpoint Kinase 2 (EC 2.7.1.11) ; Methyl Methanesulfonate (AT5C31J09G)
    Language English
    Publishing date 2023-06-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.82483
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: FBXW7-loss Sensitizes Cells to ATR Inhibition Through Induced Mitotic Catastrophe.

    O'Brien, Siobhan / Ubhi, Tajinder / Wolf, Lucie / Gandhi, Krishna / Lin, Sichun / Chaudary, Naz / Dhani, Neesha C / Milosevic, Michael / Brown, Grant W / Angers, Stephane

    Cancer research communications

    2024  Volume 3, Issue 12, Page(s) 2596–2607

    Abstract: FBXW7 is a commonly mutated tumor suppressor gene that functions to regulate numerous oncogenes involved in cell-cycle regulation. Genome-wide CRISPR fitness screens identified a signature of DNA repair and DNA damage response genes as required for the ... ...

    Abstract FBXW7 is a commonly mutated tumor suppressor gene that functions to regulate numerous oncogenes involved in cell-cycle regulation. Genome-wide CRISPR fitness screens identified a signature of DNA repair and DNA damage response genes as required for the growth of FBXW7-knockout cells. Guided by these findings, we show that FBXW7-mutant cells have high levels of replication stress, which results in a genotype-specific vulnerability to inhibition of the ATR signaling pathway, as these mutant cells become heavily reliant on a robust S-G2 checkpoint. ATR inhibition induces an accelerated S-phase, leading to mitotic catastrophe and cell death caused by the high replication stress present in FBXW7-/- cells. In addition, we provide evidence in cell and organoid studies, and mining of publicly available high-throughput drug screening efforts, that this genotype-specific vulnerability extends to multiple types of cancer, providing a rational means of identifying responsive patients for targeted therapy.
    Significance: We have elucidated the synthetic lethal interactions between FBXW7 mutation and DNA damage response genes, and highlighted the potential of ATR inhibitors as targeted therapies for cancers harboring FBXW7 alterations.
    MeSH term(s) Humans ; F-Box-WD Repeat-Containing Protein 7/genetics ; Ataxia Telangiectasia Mutated Proteins/genetics ; DNA Repair ; Mutation ; Neoplasms/genetics ; Cell Death
    Chemical Substances F-Box-WD Repeat-Containing Protein 7 ; Ataxia Telangiectasia Mutated Proteins (EC 2.7.11.1) ; FBXW7 protein, human ; ATR protein, human (EC 2.7.11.1)
    Language English
    Publishing date 2024-01-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2767-9764
    ISSN (online) 2767-9764
    DOI 10.1158/2767-9764.CRC-23-0306
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  10. Article: A conserved function of corepressors is to nucleate assembly of the transcriptional preinitiation complex.

    Leydon, Alexander R / Downing, Benjamin / Sanchez, Janet Solano / Loll-Krippleber, Raphael / Belliveau, Nathan M / Rodriguez-Mias, Ricard A / Bauer, Andrew / Watson, Isabella J / Bae, Lena / Villén, Judit / Brown, Grant W / Nemhauser, Jennifer L

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast ... ...

    Abstract The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast model
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.01.587599
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