1
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Bhachoo JS, Garvin AJ. SUMO and the DNA damage response. Biochem Soc Trans 2024; 52:773-792. [PMID: 38629643 PMCID: PMC11088926 DOI: 10.1042/bst20230862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
The preservation of genome integrity requires specialised DNA damage repair (DDR) signalling pathways to respond to each type of DNA damage. A key feature of DDR is the integration of numerous post-translational modification signals with DNA repair factors. These modifications influence DDR factor recruitment to damaged DNA, activity, protein-protein interactions, and ultimately eviction to enable access for subsequent repair factors or termination of DDR signalling. SUMO1-3 (small ubiquitin-like modifier 1-3) conjugation has gained much recent attention. The SUMO-modified proteome is enriched with DNA repair factors. Here we provide a snapshot of our current understanding of how SUMO signalling impacts the major DNA repair pathways in mammalian cells. We highlight repeating themes of SUMO signalling used throughout DNA repair pathways including the assembly of protein complexes, competition with ubiquitin to promote DDR factor stability and ubiquitin-dependent degradation or extraction of SUMOylated DDR factors. As SUMO 'addiction' in cancer cells is protective to genomic integrity, targeting components of the SUMO machinery to potentiate DNA damaging therapy or exacerbate existing DNA repair defects is a promising area of study.
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Affiliation(s)
- Jai S. Bhachoo
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
| | - Alexander J. Garvin
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
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2
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Chen L, Gai X, Yu X. Pre-rRNA facilitates the recruitment of RAD51AP1 to DNA double-strand breaks. J Biol Chem 2024; 300:107115. [PMID: 38403248 PMCID: PMC10959706 DOI: 10.1016/j.jbc.2024.107115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
RAD51-associated protein 1 (RAD51AP1) is known to promote homologous recombination (HR) repair. However, the precise mechanism of RAD51AP1 in HR repair is unclear. Here, we identify that RAD51AP1 associates with pre-rRNA. Both the N terminus and C terminus of RAD51AP1 recognize pre-rRNA. Pre-rRNA not only colocalizes with RAD51AP1 at double-strand breaks (DSBs) but also facilitates the recruitment of RAD51AP1 to DSBs. Consistently, transient inhibition of pre-rRNA synthesis by RNA polymerase I inhibitor suppresses the recruitment of RAD51AP1 as well as HR repair. Moreover, RAD51AP1 forms liquid-liquid phase separation in the presence of pre-rRNA in vitro, which may be the molecular mechanism of RAD51AP1 foci formation. Taken together, our results demonstrate that pre-rRNA mediates the relocation of RAD51AP1 to DSBs for HR repair.
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Affiliation(s)
- Linlin Chen
- School of Life Sciences, Fudan University, Shanghai, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaochen Gai
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
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3
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Simpson D, Ling J, Jing Y, Adamson B. Mapping the Genetic Interaction Network of PARP inhibitor Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553986. [PMID: 37645833 PMCID: PMC10462155 DOI: 10.1101/2023.08.19.553986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Genetic interactions have long informed our understanding of the coordinated proteins and pathways that respond to DNA damage in mammalian cells, but systematic interrogation of the genetic network underlying that system has yet to be achieved. Towards this goal, we measured 147,153 pairwise interactions among genes implicated in PARP inhibitor (PARPi) response. Evaluating genetic interactions at this scale, with and without exposure to PARPi, revealed hierarchical organization of the pathways and complexes that maintain genome stability during normal growth and defined changes that occur upon accumulation of DNA lesions due to cytotoxic doses of PARPi. We uncovered unexpected relationships among DNA repair genes, including context-specific buffering interactions between the minimally characterized AUNIP and BRCA1-A complex genes. Our work thus establishes a foundation for mapping differential genetic interactions in mammalian cells and provides a comprehensive resource for future studies of DNA repair and PARP inhibitors.
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Affiliation(s)
- Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jia Ling
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Yangwode Jing
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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4
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Liu W, Saito Y, Jackson J, Bhowmick R, Kanemaki MT, Vindigni A, Cortez D. RAD51 bypasses the CMG helicase to promote replication fork reversal. Science 2023; 380:382-387. [PMID: 37104614 PMCID: PMC10302453 DOI: 10.1126/science.add7328] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/25/2023] [Indexed: 04/29/2023]
Abstract
Replication fork reversal safeguards genome integrity as a replication stress response. DNA translocases and the RAD51 recombinase catalyze reversal. However, it remains unknown why RAD51 is required and what happens to the replication machinery during reversal. We find that RAD51 uses its strand exchange activity to circumvent the replicative helicase, which remains bound to the stalled fork. RAD51 is not required for fork reversal if the helicase is unloaded. Thus, we propose that RAD51 creates a parental DNA duplex behind the helicase that is used as a substrate by the DNA translocases for branch migration to create a reversed fork structure. Our data explain how fork reversal happens while maintaining the helicase in a position poised to restart DNA synthesis and complete genome duplication.
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Affiliation(s)
- Wenpeng Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rahul Bhowmick
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
| | - Masato T. Kanemaki
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
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5
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Lemonidis K, Rennie ML, Arkinson C, Chaugule VK, Clarke M, Streetley J, Walden H. Structural and biochemical basis of interdependent FANCI-FANCD2 ubiquitination. EMBO J 2023; 42:e111898. [PMID: 36385258 PMCID: PMC9890228 DOI: 10.15252/embj.2022111898] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/03/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022] Open
Abstract
Di-monoubiquitination of the FANCI-FANCD2 (ID2) complex is a central and crucial step for the repair of DNA interstrand crosslinks via the Fanconi anaemia pathway. While FANCD2 ubiquitination precedes FANCI ubiquitination, FANCD2 is also deubiquitinated at a faster rate than FANCI, which can result in a FANCI-ubiquitinated ID2 complex (IUb D2). Here, we present a 4.1 Å cryo-EM structure of IUb D2 complex bound to double-stranded DNA. We show that this complex, like ID2Ub and IUb D2Ub , is also in the closed ID2 conformation and clamps on DNA. The target lysine of FANCD2 (K561) becomes fully exposed in the IUb D2-DNA structure and is thus primed for ubiquitination. Similarly, FANCI's target lysine (K523) is also primed for ubiquitination in the ID2Ub -DNA complex. The IUb D2-DNA complex exhibits deubiquitination resistance, conferred by the presence of DNA and FANCD2. ID2Ub -DNA, on the other hand, can be efficiently deubiquitinated by USP1-UAF1, unless further ubiquitination on FANCI occurs. Therefore, FANCI ubiquitination effectively maintains FANCD2 ubiquitination in two ways: it prevents excessive FANCD2 deubiquitination within an IUb D2Ub -DNA complex, and it enables re-ubiquitination of FANCD2 within a transient, closed-on-DNA, IUb D2 complex.
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Affiliation(s)
- Kimon Lemonidis
- School of Molecular Biosciences, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Martin L Rennie
- School of Molecular Biosciences, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Connor Arkinson
- School of Molecular Biosciences, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
- Present address:
Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCAUSA
| | - Viduth K Chaugule
- School of Molecular Biosciences, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Mairi Clarke
- Scottish Centre for Macromolecular ImagingUniversity of GlasgowGlasgowUK
| | - James Streetley
- Scottish Centre for Macromolecular ImagingUniversity of GlasgowGlasgowUK
| | - Helen Walden
- School of Molecular Biosciences, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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6
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Kaminski N, Wondisford AR, Kwon Y, Lynskey ML, Bhargava R, Barroso-González J, García-Expósito L, He B, Xu M, Mellacheruvu D, Watkins SC, Modesti M, Miller KM, Nesvizhskii AI, Zhang H, Sung P, O'Sullivan RJ. RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA. Mol Cell 2022; 82:4001-4017.e7. [PMID: 36265488 PMCID: PMC9713952 DOI: 10.1016/j.molcel.2022.09.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/10/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a homology-directed repair (HDR) mechanism of telomere elongation that controls proliferation in subsets of aggressive cancer. Recent studies have revealed that telomere repeat-containing RNA (TERRA) promotes ALT-associated HDR (ALT-HDR). Here, we report that RAD51AP1, a crucial ALT factor, interacts with TERRA and utilizes it to generate D- and R-loop HR intermediates. We also show that RAD51AP1 binds to and might stabilize TERRA-containing R-loops as RAD51AP1 depletion reduces R-loop formation at telomere DNA breaks. Proteomic analyses uncover a role for RAD51AP1-mediated TERRA R-loop homeostasis in a mechanism of chromatin-directed suppression of TERRA and prevention of transcription-replication collisions (TRCs) during ALT-HDR. Intriguingly, we find that both TERRA binding and this non-canonical function of RAD51AP1 require its intrinsic SUMO-SIM regulatory axis. These findings provide insights into the multi-contextual functions of RAD51AP1 within the ALT mechanism and regulation of TERRA.
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Affiliation(s)
- Nicole Kaminski
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Boxue He
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA; Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Meng Xu
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Dattatreya Mellacheruvu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Simon C Watkins
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm UMR1068, Aix Marseille Université U105, Institut Paoli Calmettes, 27 Boulevard Lei Roure CS30059, 13273 Marseille Cedex 09, France
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Huaiying Zhang
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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7
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Kang Y, An S, Min D, Lee JY. Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying deoxyribonucleic acid damage repair. Front Bioeng Biotechnol 2022; 10:973314. [PMID: 36185427 PMCID: PMC9520083 DOI: 10.3389/fbioe.2022.973314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in single-molecule techniques have uncovered numerous biological secrets that cannot be disclosed by traditional methods. Among a variety of single-molecule methods, single-molecule fluorescence imaging techniques enable real-time visualization of biomolecular interactions and have allowed the accumulation of convincing evidence. These techniques have been broadly utilized for studying DNA metabolic events such as replication, transcription, and DNA repair, which are fundamental biological reactions. In particular, DNA repair has received much attention because it maintains genomic integrity and is associated with diverse human diseases. In this review, we introduce representative single-molecule fluorescence imaging techniques and survey how each technique has been employed for investigating the detailed mechanisms underlying DNA repair pathways. In addition, we briefly show how live-cell imaging at the single-molecule level contributes to understanding DNA repair processes inside cells.
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Affiliation(s)
- Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Soyeong An
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
- Center for Genomic Integrity, Institute of Basic Sciences, Ulsan, South Korea
- *Correspondence: Ja Yil Lee,
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8
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Petermann E, Lan L, Zou L. Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids. Nat Rev Mol Cell Biol 2022; 23:521-540. [PMID: 35459910 DOI: 10.1038/s41580-022-00474-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
RNA-DNA hybrids are generated during transcription, DNA replication and DNA repair and are crucial intermediates in these processes. When RNA-DNA hybrids are stably formed in double-stranded DNA, they displace one of the DNA strands and give rise to a three-stranded structure called an R-loop. R-loops are widespread in the genome and are enriched at active genes. R-loops have important roles in regulating gene expression and chromatin structure, but they also pose a threat to genomic stability, especially during DNA replication. To keep the genome stable, cells have evolved a slew of mechanisms to prevent aberrant R-loop accumulation. Although R-loops can cause DNA damage, they are also induced by DNA damage and act as key intermediates in DNA repair such as in transcription-coupled repair and RNA-templated DNA break repair. When the regulation of R-loops goes awry, pathological R-loops accumulate, which contributes to diseases such as neurodegeneration and cancer. In this Review, we discuss the current understanding of the sources of R-loops and RNA-DNA hybrids, mechanisms that suppress and resolve these structures, the impact of these structures on DNA repair and genome stability, and opportunities to therapeutically target pathological R-loops.
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Affiliation(s)
- Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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9
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Brickner JR, Garzon JL, Cimprich KA. Walking a tightrope: The complex balancing act of R-loops in genome stability. Mol Cell 2022; 82:2267-2297. [PMID: 35508167 DOI: 10.1016/j.molcel.2022.04.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 12/14/2022]
Abstract
Although transcription is an essential cellular process, it is paradoxically also a well-recognized cause of genomic instability. R-loops, non-B DNA structures formed when nascent RNA hybridizes to DNA to displace the non-template strand as single-stranded DNA (ssDNA), are partially responsible for this instability. Yet, recent work has begun to elucidate regulatory roles for R-loops in maintaining the genome. In this review, we discuss the cellular contexts in which R-loops contribute to genomic instability, particularly during DNA replication and double-strand break (DSB) repair. We also summarize the evidence that R-loops participate as an intermediate during repair and may influence pathway choice to preserve genomic integrity. Finally, we discuss the immunogenic potential of R-loops and highlight their links to disease should they become pathogenic.
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Affiliation(s)
- Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jada L Garzon
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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10
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Hariharasudhan G, Jeong SY, Kim MJ, Jung SM, Seo G, Moon JR, Lee S, Chang IY, Kee Y, You H, Lee JH. OUP accepted manuscript. Nucleic Acids Res 2022; 50:1501-1516. [PMID: 35061896 PMCID: PMC8860612 DOI: 10.1093/nar/gkac009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/23/2021] [Accepted: 01/13/2022] [Indexed: 11/24/2022] Open
Abstract
Homologous recombination (HR) is critical for error-free repair of DNA double-strand breaks. Chromatin loading of RAD51, a key protein that mediates the recombination, is a crucial step in the execution of the HR repair. Here, we present evidence that SUMOylation of RAD51 is crucial for the RAD51 recruitment to chromatin and HR repair. We found that topoisomerase 1-binding arginine/serine-rich protein (TOPORS) induces the SUMOylation of RAD51 at lysine residues 57 and 70 in response to DNA damaging agents. The SUMOylation was facilitated by an ATM-induced phosphorylation of TOPORS at threonine 515 upon DNA damage. Knockdown of TOPORS or expression of SUMOylation-deficient RAD51 mutants caused reduction in supporting normal RAD51 functions during the HR repair, suggesting the physiological importance of the modification. We found that the SUMOylation-deficient RAD51 reduces the association with its crucial binding partner BRCA2, explaining its deficiency in supporting the HR repair. These findings altogether demonstrate a crucial role for TOPORS-mediated RAD51 SUMOylation in promoting HR repair and genomic maintenance.
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Affiliation(s)
- Gurusamy Hariharasudhan
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Seo-Yeon Jeong
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Pharmacology, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Min-Ji Kim
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Sung Mi Jung
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Gwanwoo Seo
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Pharmacology, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Ju-Ran Moon
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Sumi Lee
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - In-Youb Chang
- Department of Anatomy, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Younghoon Kee
- Correspondence may also be addressed to Younghoon Kee. Tel: +82 53 785 1610;
| | - Ho Jin You
- Correspondence may also be addressed to Ho Jin You. Tel: +82 62 230 6337;
| | - Jung-Hee Lee
- To whom correspondence should be addressed. Tel: +82 62 230 6399;
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11
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Kong M, Greene EC. Mechanistic Insights From Single-Molecule Studies of Repair of Double Strand Breaks. Front Cell Dev Biol 2021; 9:745311. [PMID: 34869333 PMCID: PMC8636147 DOI: 10.3389/fcell.2021.745311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/28/2021] [Indexed: 01/01/2023] Open
Abstract
DNA double strand breaks (DSBs) are among some of the most deleterious forms of DNA damage. Left unrepaired, they are detrimental to genome stability, leading to high risk of cancer. Two major mechanisms are responsible for the repair of DSBs, homologous recombination (HR) and nonhomologous end joining (NHEJ). The complex nature of both pathways, involving a myriad of protein factors functioning in a highly coordinated manner at distinct stages of repair, lend themselves to detailed mechanistic studies using the latest single-molecule techniques. In avoiding ensemble averaging effects inherent to traditional biochemical or genetic methods, single-molecule studies have painted an increasingly detailed picture for every step of the DSB repair processes.
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Affiliation(s)
| | - Eric C. Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, United States
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12
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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13
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Zhang Y, Xiang J, Tang L, Li J, Lu Q, Tian G, He BS, Yang J. Identifying Breast Cancer-Related Genes Based on a Novel Computational Framework Involving KEGG Pathways and PPI Network Modularity. Front Genet 2021; 12:596794. [PMID: 34484285 PMCID: PMC8415302 DOI: 10.3389/fgene.2021.596794] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/05/2021] [Indexed: 01/04/2023] Open
Abstract
Complex diseases, such as breast cancer, are often caused by mutations of multiple functional genes. Identifying disease-related genes is a critical and challenging task for unveiling the biological mechanisms behind these diseases. In this study, we develop a novel computational framework to analyze the network properties of the known breast cancer–associated genes, based on which we develop a random-walk-with-restart (RCRWR) algorithm to predict novel disease genes. Specifically, we first curated a set of breast cancer–associated genes from the Genome-Wide Association Studies catalog and Online Mendelian Inheritance in Man database and then studied the distribution of these genes on an integrated protein–protein interaction (PPI) network. We found that the breast cancer–associated genes are significantly closer to each other than random, which confirms the modularity property of disease genes in a PPI network as revealed by previous studies. We then retrieved PPI subnetworks spanning top breast cancer–associated KEGG pathways and found that the distribution of these genes on the subnetworks are non-random, suggesting that these KEGG pathways are activated non-uniformly. Taking advantage of the non-random distribution of breast cancer–associated genes, we developed an improved RCRWR algorithm to predict novel cancer genes, which integrates network reconstruction based on local random walk dynamics and subnetworks spanning KEGG pathways. Compared with the disease gene prediction without using the information from the KEGG pathways, this method has a better prediction performance on inferring breast cancer–associated genes, and the top predicted genes are better enriched on known breast cancer–associated gene ontologies. Finally, we performed a literature search on top predicted novel genes and found that most of them are supported by at least wet-lab experiments on cell lines. In summary, we propose a robust computational framework to prioritize novel breast cancer–associated genes, which could be used for further in vitro and in vivo experimental validation.
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Affiliation(s)
- Yan Zhang
- School of Computer Science and Engineering, Central South University, Changsha, China.,School of Information Science and Engineering, Changsha Medical University, Changsha, China.,Academician Workstation, Changsha Medical University, Changsha, China
| | - Ju Xiang
- School of Computer Science and Engineering, Central South University, Changsha, China.,Academician Workstation, Changsha Medical University, Changsha, China.,Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Liang Tang
- Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Jianming Li
- Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Qingqing Lu
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China.,Geneis Beijing Co., Ltd., Beijing, China
| | - Geng Tian
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China.,Geneis Beijing Co., Ltd., Beijing, China
| | - Bin-Sheng He
- Academician Workstation, Changsha Medical University, Changsha, China.,Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Jialiang Yang
- Academician Workstation, Changsha Medical University, Changsha, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China.,Geneis Beijing Co., Ltd., Beijing, China
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14
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Zhang Y, Xiang J, Tang L, Li J, Lu Q, Tian G, He BS, Yang J. Identifying Breast Cancer-Related Genes Based on a Novel Computational Framework Involving KEGG Pathways and PPI Network Modularity. Front Genet 2021; 12:596794. [PMID: 34484285 DOI: 10.3389/fgene.2021.596794/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/05/2021] [Indexed: 05/28/2023] Open
Abstract
Complex diseases, such as breast cancer, are often caused by mutations of multiple functional genes. Identifying disease-related genes is a critical and challenging task for unveiling the biological mechanisms behind these diseases. In this study, we develop a novel computational framework to analyze the network properties of the known breast cancer-associated genes, based on which we develop a random-walk-with-restart (RCRWR) algorithm to predict novel disease genes. Specifically, we first curated a set of breast cancer-associated genes from the Genome-Wide Association Studies catalog and Online Mendelian Inheritance in Man database and then studied the distribution of these genes on an integrated protein-protein interaction (PPI) network. We found that the breast cancer-associated genes are significantly closer to each other than random, which confirms the modularity property of disease genes in a PPI network as revealed by previous studies. We then retrieved PPI subnetworks spanning top breast cancer-associated KEGG pathways and found that the distribution of these genes on the subnetworks are non-random, suggesting that these KEGG pathways are activated non-uniformly. Taking advantage of the non-random distribution of breast cancer-associated genes, we developed an improved RCRWR algorithm to predict novel cancer genes, which integrates network reconstruction based on local random walk dynamics and subnetworks spanning KEGG pathways. Compared with the disease gene prediction without using the information from the KEGG pathways, this method has a better prediction performance on inferring breast cancer-associated genes, and the top predicted genes are better enriched on known breast cancer-associated gene ontologies. Finally, we performed a literature search on top predicted novel genes and found that most of them are supported by at least wet-lab experiments on cell lines. In summary, we propose a robust computational framework to prioritize novel breast cancer-associated genes, which could be used for further in vitro and in vivo experimental validation.
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Affiliation(s)
- Yan Zhang
- School of Computer Science and Engineering, Central South University, Changsha, China
- School of Information Science and Engineering, Changsha Medical University, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Ju Xiang
- School of Computer Science and Engineering, Central South University, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Liang Tang
- Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Jianming Li
- Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Qingqing Lu
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
- Geneis Beijing Co., Ltd., Beijing, China
| | - Geng Tian
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
- Geneis Beijing Co., Ltd., Beijing, China
| | - Bin-Sheng He
- Academician Workstation, Changsha Medical University, Changsha, China
- Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Jialiang Yang
- Academician Workstation, Changsha Medical University, Changsha, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
- Geneis Beijing Co., Ltd., Beijing, China
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15
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Xue C, Greene EC. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. Trends Genet 2021; 37:639-656. [PMID: 33896583 PMCID: PMC8187289 DOI: 10.1016/j.tig.2021.02.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Many clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based genome editing technologies take advantage of Cas nucleases to induce DNA double-strand breaks (DSBs) at desired locations within a genome. Further processing of the DSBs by the cellular DSB repair machinery is then necessary to introduce desired mutations, sequence insertions, or gene deletions. Thus, the accuracy and efficiency of genome editing are influenced by the cellular DSB repair pathways. DSBs are themselves highly genotoxic lesions and as such cells have evolved multiple mechanisms for their repair. These repair pathways include homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single-strand annealing (SSA). In this review, we briefly highlight CRISPR-Cas9 and then describe the mechanisms of DSB repair. Finally, we summarize recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced DSBs.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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16
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Wilde JJ, Aida T, Del Rosario RCH, Kaiser T, Qi P, Wienisch M, Zhang Q, Colvin S, Feng G. Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair. Cell 2021; 184:3267-3280.e18. [PMID: 34043941 PMCID: PMC8240950 DOI: 10.1016/j.cell.2021.04.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 03/03/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Searching for factors to improve knockin efficiency for therapeutic applications, biotechnology, and generation of non-human primate models of disease, we found that the strand exchange protein RAD51 can significantly increase Cas9-mediated homozygous knockin in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is a hallmark of meiosis but only occurs at low frequencies in somatic cells, and its occurrence in zygotes is controversial. Using multiple approaches, we provide evidence for an endogenous IHR mechanism in the early embryo that can be enhanced by RAD51. This process can be harnessed to generate homozygotes from wild-type zygotes using exogenous donors and to convert heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we identify additional IHR-promoting factors and describe features of IHR events. Together, our findings show conclusive evidence for IHR in mouse embryos and describe an efficient method for enhanced gene conversion.
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Affiliation(s)
- Jonathan J Wilde
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
| | - Tomomi Aida
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Ricardo C H Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Kaiser
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Peimin Qi
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Martin Wienisch
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Steven Colvin
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Guoping Feng
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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17
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Ouyang J, Yadav T, Zhang JM, Yang H, Rheinbay E, Guo H, Haber DA, Lan L, Zou L. RNA transcripts stimulate homologous recombination by forming DR-loops. Nature 2021; 594:283-288. [PMID: 33981036 PMCID: PMC8855348 DOI: 10.1038/s41586-021-03538-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
Homologous recombination (HR) repairs DNA double-strand breaks (DSBs) in the S and G2 phases of the cell cycle1-3. Several HR proteins are preferentially recruited to DSBs at transcriptionally active loci4-10, but how transcription promotes HR is poorly understood. Here we develop an assay to assess the effect of local transcription on HR. Using this assay, we find that transcription stimulates HR to a substantial extent. Tethering RNA transcripts to the vicinity of DSBs recapitulates the effects of local transcription, which suggests that transcription enhances HR through RNA transcripts. Tethered RNA transcripts stimulate HR in a sequence- and orientation-dependent manner, indicating that they function by forming DNA-RNA hybrids. In contrast to most HR proteins, RAD51-associated protein 1 (RAD51AP1) only promotes HR when local transcription is active. RAD51AP1 drives the formation of R-loops in vitro and is required for tethered RNAs to stimulate HR in cells. Notably, RAD51AP1 is necessary for the DSB-induced formation of DNA-RNA hybrids in donor DNA, linking R-loops to D-loops. In vitro, RAD51AP1-generated R-loops enhance the RAD51-mediated formation of D-loops locally and give rise to intermediates that we term 'DR-loops', which contain both DNA-DNA and DNA-RNA hybrids and favour RAD51 function. Thus, at DSBs in transcribed regions, RAD51AP1 promotes the invasion of RNA transcripts into donor DNA, and stimulates HR through the formation of DR-loops.
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Affiliation(s)
- Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
| | - Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Jia-Min Zhang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Haibo Yang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Esther Rheinbay
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Hongshan Guo
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Charlestown, MA, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Charlestown, MA, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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18
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Pires E, Sharma N, Selemenakis P, Wu B, Huang Y, Alimbetov DS, Zhao W, Wiese C. RAD51AP1 mediates RAD51 activity through nucleosome interaction. J Biol Chem 2021; 297:100844. [PMID: 34058198 PMCID: PMC8233230 DOI: 10.1016/j.jbc.2021.100844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 10/31/2022] Open
Abstract
RAD51-associated protein 1 (RAD51AP1) is a key protein in the homologous recombination (HR) DNA repair pathway. Loss of RAD51AP1 leads to defective HR, genome instability, and telomere erosion. RAD51AP1 physically interacts with the RAD51 recombinase and promotes RAD51-mediated capture of donor DNA, synaptic complex assembly, and displacement-loop formation when tested with nucleosome-free DNA substrates. In cells, however, DNA is packaged into chromatin, posing an additional barrier to the complexities of the HR reaction. In this study, we show that RAD51AP1 binds to nucleosome core particles (NCPs), the minimum basic unit of chromatin in which approximately two superhelical turns of 147 bp double-stranded DNA are wrapped around one histone octamer with no free DNA ends remaining. We identified a C-terminal region in RAD51AP1, including its previously mapped DNA-binding domain, as critical for mediating the association between RAD51AP1 and both the NCP and the histone octamer. Using in vitro surrogate assays of HR activity, we show that RAD51AP1 is capable of promoting duplex DNA capture and initiating joint-molecule formation with the NCP and chromatinized template DNA, respectively. Together, our results suggest that RAD51AP1 directly assists in the RAD51-mediated search for donor DNA in chromatin. We present a model, in which RAD51AP1 anchors the DNA template through affinity for its nucleosomes to the RAD51-ssDNA nucleoprotein filament.
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Affiliation(s)
- Elena Pires
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA; Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Platon Selemenakis
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA; Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA
| | - Bo Wu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Yuxin Huang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Dauren S Alimbetov
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA.
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19
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Dharadhar S, van Dijk WJ, Scheffers S, Fish A, Sixma TK. Insert L1 is a central hub for allosteric regulation of USP1 activity. EMBO Rep 2021; 22:e51749. [PMID: 33619839 PMCID: PMC8024992 DOI: 10.15252/embr.202051749] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/22/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
During DNA replication, the deubiquitinating enzyme USP1 limits the recruitment of translesion polymerases by removing ubiquitin marks from PCNA to allow specific regulation of the translesion synthesis (TLS) pathway. USP1 activity depends on an allosteric activator, UAF1, and this is tightly controlled. In comparison to paralogs USP12 and USP46, USP1 contains three defined inserts and lacks the second WDR20-mediated activation step. Here we show how inserts L1 and L3 together limit intrinsic USP1 activity and how this is relieved by UAF1. Intriguingly, insert L1 also conveys substrate-dependent increase in USP1 activity through DNA and PCNA interactions, in a process that is independent of UAF1-mediated activation. This study establishes insert L1 as an important regulatory hub within USP1 necessary for both substrate-mediated activity enhancement and allosteric activation upon UAF1 binding.
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Affiliation(s)
- Shreya Dharadhar
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Serge Scheffers
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alexander Fish
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
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20
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The Greatwall kinase safeguards the genome integrity by affecting the kinome activity in mitosis. Oncogene 2020; 39:6816-6840. [PMID: 32978522 PMCID: PMC7605441 DOI: 10.1038/s41388-020-01470-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/21/2020] [Accepted: 09/10/2020] [Indexed: 12/19/2022]
Abstract
Progression through mitosis is balanced by the timely regulation of phosphorylation and dephosphorylation events ensuring the correct segregation of chromosomes before cytokinesis. This balance is regulated by the opposing actions of CDK1 and PP2A, as well as the Greatwall kinase/MASTL. MASTL is commonly overexpressed in cancer, which makes it a potential therapeutic anticancer target. Loss of Mastl induces multiple chromosomal errors that lead to the accumulation of micronuclei and multilobulated cells in mitosis. Our analyses revealed that loss of Mastl leads to chromosome breaks and abnormalities impairing correct segregation. Phospho-proteomic data for Mastl knockout cells revealed alterations in proteins implicated in multiple processes during mitosis including double-strand DNA damage repair. In silico prediction of the kinases with affected activity unveiled NEK2 to be regulated in the absence of Mastl. We uncovered that, RAD51AP1, involved in regulation of homologous recombination, is phosphorylated by NEK2 and CDK1 but also efficiently dephosphorylated by PP2A/B55. Our results suggest that MastlKO disturbs the equilibrium of the mitotic phosphoproteome that leads to the disruption of DNA damage repair and triggers an accumulation of chromosome breaks even in noncancerous cells.
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21
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Kim S, Kang N, Park SH, Wells J, Hwang T, Ryu E, Kim BG, Hwang S, Kim SJ, Kang S, Lee S, Stirling P, Myung K, Lee KY. ATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork. Nucleic Acids Res 2020; 48:7218-7238. [PMID: 32542338 PMCID: PMC7367208 DOI: 10.1093/nar/gkaa501] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/27/2022] Open
Abstract
R-loops are formed when replicative forks collide with the transcriptional machinery and can cause genomic instability. However, it is unclear how R-loops are regulated at transcription-replication conflict (TRC) sites and how replisome proteins are regulated to prevent R-loop formation or mediate R-loop tolerance. Here, we report that ATAD5, a PCNA unloader, plays dual functions to reduce R-loops both under normal and replication stress conditions. ATAD5 interacts with RNA helicases such as DDX1, DDX5, DDX21 and DHX9 and increases the abundance of these helicases at replication forks to facilitate R-loop resolution. Depletion of ATAD5 or ATAD5-interacting RNA helicases consistently increases R-loops during the S phase and reduces the replication rate, both of which are enhanced by replication stress. In addition to R-loop resolution, ATAD5 prevents the generation of new R-loops behind the replication forks by unloading PCNA which, otherwise, accumulates and persists on DNA, causing a collision with the transcription machinery. Depletion of ATAD5 reduces transcription rates due to PCNA accumulation. Consistent with the role of ATAD5 and RNA helicases in maintaining genomic integrity by regulating R-loops, the corresponding genes were mutated or downregulated in several human tumors.
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Affiliation(s)
- Sangin Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - James Wells
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada
| | - Taejoo Hwang
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Seong-Jung Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Semin Lee
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Peter Stirling
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
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22
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Mechanism and significance of chromosome damage repair by homologous recombination. Essays Biochem 2020; 64:779-790. [DOI: 10.1042/ebc20190093] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/29/2022]
Abstract
Abstract
Homologous recombination (HR) is a major, conserved pathway of chromosome damage repair. It not only fulfills key functions in the removal of deleterious lesions such as DNA double-strand breaks (DSBs) and interstrand cross-links (ICLs), but also in replication fork repair and protection. Several familial and acquired cancer predisposition syndromes stem from defects in HR. In particular, individuals with mutations in HR genes exhibit predisposition to breast, ovarian, pancreatic, and prostate cancers, and they also show signs of accelerated aging. However, aberrant and untimely HR events can lead to the loss of heterozygosity, genomic rearrangements, and cytotoxic nucleoprotein intermediates. Thus, it is critically important that HR be tightly regulated. In addition to DNA repair, HR is also involved in meiotic chromosome segregation and telomere maintenance in cells that lack telomerase. In this review, we focus on the role of HR in DSB repair (DSBR) and summarize the current state of the field.
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23
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Kim SJ, Wie M, Park SH, Kim TM, Park JH, Kim S, Myung K, Lee KY. ATAD5 suppresses centrosome over-duplication by regulating UAF1 and ID1. Cell Cycle 2020; 19:1952-1968. [PMID: 32594826 PMCID: PMC7469630 DOI: 10.1080/15384101.2020.1785724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Centrosomes are the primary microtubule-organizing centers that are important for mitotic spindle assembly. Centrosome amplification is commonly observed in human cancer cells and contributes to genomic instability. However, it is not clear how centrosome duplication is dysregulated in cancer cells. Here, we report that ATAD5, a replisome protein that unloads PCNA from chromatin as a replication factor C-like complex (RLC), plays an important role in regulating centrosome duplication. ATAD5 is present at the centrosome, specifically at the base of the mother and daughter centrioles that undergo duplication. UAF1, which interacts with ATAD5 and regulates PCNA deubiquitination as a complex with ubiquitin-specific protease 1, is also localized at the centrosome. Depletion of ATAD5 or UAF1 increases cells with over-duplicated centrosome whereas ATAD5 overexpression reduces such cells. Consistently, the proportion of cells showing the multipolar mode of chromosome segregation is increased among ATAD5-depleted cells. The localization and function of ATAD5 at the centrosomes do not require other RLC subunits. UAF1 interacts and co-localizes with ID1, a protein that increases centrosome amplification upon overexpression. ATAD5 depletion reduces interactions between UAF1 and ID1 and increases ID1 signal at the centrosome, providing a mechanistic framework for understanding the role of ATAD5 in centrosome duplication.
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Affiliation(s)
- Seong-Jung Kim
- Center for Genomic Integrity, Institute for Basic Science , Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology , Ulsan, Korea
| | - Minwoo Wie
- Center for Genomic Integrity, Institute for Basic Science , Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology , Ulsan, Korea
| | - Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science , Ulsan, Korea
| | - Tae Moon Kim
- Center for Genomic Integrity, Institute for Basic Science , Ulsan, Korea
| | - Jun Hong Park
- Center for Genomic Integrity, Institute for Basic Science , Ulsan, Korea.,Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine , Naju-si, Republic of Korea
| | - Shinseog Kim
- Center for Genomic Integrity, Institute for Basic Science , Ulsan, Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science , Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology , Ulsan, Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science , Ulsan, Korea
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24
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Liang F, Miller AS, Tang C, Maranon D, Williamson EA, Hromas R, Wiese C, Zhao W, Sung P, Kupfer GM. The DNA-binding activity of USP1-associated factor 1 is required for efficient RAD51-mediated homologous DNA pairing and homology-directed DNA repair. J Biol Chem 2020; 295:8186-8194. [PMID: 32350107 DOI: 10.1074/jbc.ra120.013714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/27/2020] [Indexed: 11/06/2022] Open
Abstract
USP1-associated factor 1 (UAF1) is an integral component of the RAD51-associated protein 1 (RAD51AP1)-UAF1-ubiquitin-specific peptidase 1 (USP1) trimeric deubiquitinase complex. This complex acts on DNA-bound, monoubiquitinated Fanconi anemia complementation group D2 (FANCD2) protein in the Fanconi anemia pathway of the DNA damage response. Moreover, RAD51AP1 and UAF1 cooperate to enhance homologous DNA pairing mediated by the recombinase RAD51 in DNA repair via the homologous recombination (HR) pathway. However, whereas the DNA-binding activity of RAD51AP1 has been shown to be important for RAD51-mediated homologous DNA pairing and HR-mediated DNA repair, the role of DNA binding by UAF1 in these processes is unclear. We have isolated mutant UAF1 variants that are impaired in DNA binding and tested them together with RAD51AP1 in RAD51-mediated HR. This biochemical analysis revealed that the DNA-binding activity of UAF1 is indispensable for enhanced RAD51 recombinase activity within the context of the UAF1-RAD51AP1 complex. In cells, DNA-binding deficiency of UAF1 increased DNA damage sensitivity and impaired HR efficiency, suggesting that UAF1 and RAD51AP1 have coordinated roles in DNA binding during HR and DNA damage repair. Our findings show that even though UAF1's DNA-binding activity is redundant with that of RAD51AP1 in FANCD2 deubiquitination, it is required for efficient HR-mediated chromosome damage repair.
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Affiliation(s)
- Fengshan Liang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Adam S Miller
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Caroline Tang
- Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - David Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Elizabeth A Williamson
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Gary M Kupfer
- Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, Connecticut, USA .,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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25
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Beyond reversal: ubiquitin and ubiquitin-like proteases and the orchestration of the DNA double strand break repair response. Biochem Soc Trans 2020; 47:1881-1893. [PMID: 31769469 PMCID: PMC6925521 DOI: 10.1042/bst20190534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022]
Abstract
The cellular response to genotoxic DNA double strand breaks (DSBs) uses a multitude of post-translational modifications to localise, modulate and ultimately clear DNA repair factors in a timely and accurate manner. Ubiquitination is well established as vital to the DSB response, with a carefully co-ordinated pathway of histone ubiquitination events being a central component of DSB signalling. Other ubiquitin-like modifiers (Ubl) including SUMO and NEDD8 have since been identified as playing important roles in DSB repair. In the last five years ∼20 additional Ub/Ubl proteases have been implicated in the DSB response. The number of proteases identified highlights the complexity of the Ub/Ubl signal present at DSBs. Ub/Ubl proteases regulate turnover, activity and protein-protein interactions of DSB repair factors both catalytically and non-catalytically. This not only ensures efficient repair of breaks but has a role in channelling repair into the correct DSB repair sub-pathways. Ultimately Ub/Ubl proteases have essential roles in maintaining genomic stability. Given that deficiencies in many Ub/Ubl proteases promotes sensitivity to DNA damaging chemotherapies, they could be attractive targets for cancer treatment.
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26
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Role of Rad51 and DNA repair in cancer: A molecular perspective. Pharmacol Ther 2020; 208:107492. [PMID: 32001312 DOI: 10.1016/j.pharmthera.2020.107492] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/13/2020] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of genome integrity is essential for any organism survival and for the inheritance of traits to offspring. To the purpose, cells have developed a complex DNA repair system to defend the genetic information against both endogenous and exogenous sources of damage. Accordingly, multiple repair pathways can be aroused from the diverse forms of DNA lesions, which can be effective per se or via crosstalk with others to complete the whole DNA repair process. Deficiencies in DNA healing resulting in faulty repair and/or prolonged DNA damage can lead to genes mutations, chromosome rearrangements, genomic instability, and finally carcinogenesis and/or cancer progression. Although it might seem paradoxical, at the same time such defects in DNA repair pathways may have therapeutic implications for potential clinical practice. Here we provide an overview of the main DNA repair pathways, with special focus on the role played by homologous repair and the RAD51 recombinase protein in the cellular DNA damage response. We next discuss the recombinase structure and function per se and in combination with all its principal mediators and regulators. Finally, we conclude with an analysis of the manifold roles that RAD51 plays in carcinogenesis, cancer progression and anticancer drug resistance, and conclude this work with a survey of the most promising therapeutic strategies aimed at targeting RAD51 in experimental oncology.
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27
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Park SH, Kang N, Song E, Wie M, Lee EA, Hwang S, Lee D, Ra JS, Park IB, Park J, Kang S, Park JH, Hohng S, Lee KY, Myung K. ATAD5 promotes replication restart by regulating RAD51 and PCNA in response to replication stress. Nat Commun 2019; 10:5718. [PMID: 31844045 PMCID: PMC6914801 DOI: 10.1038/s41467-019-13667-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022] Open
Abstract
Maintaining stability of replication forks is important for genomic integrity. However, it is not clear how replisome proteins contribute to fork stability under replication stress. Here, we report that ATAD5, a PCNA unloader, plays multiple functions at stalled forks including promoting its restart. ATAD5 depletion increases genomic instability upon hydroxyurea treatment in cultured cells and mice. ATAD5 recruits RAD51 to stalled forks in an ATR kinase-dependent manner by hydroxyurea-enhanced protein-protein interactions and timely removes PCNA from stalled forks for RAD51 recruitment. Consistent with the role of RAD51 in fork regression, ATAD5 depletion inhibits slowdown of fork progression and native 5-bromo-2'-deoxyuridine signal induced by hydroxyurea. Single-molecule FRET showed that PCNA itself acts as a mechanical barrier to fork regression. Consequently, DNA breaks required for fork restart are reduced by ATAD5 depletion. Collectively, our results suggest an important role of ATAD5 in maintaining genome integrity during replication stress.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Eunho Song
- Interdisciplinary Graduate Program in Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Republic of Korea.,Institute of Applied Physics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Minwoo Wie
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Eun A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Deokjae Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea.,Medytox Inc. 114, Yeongtong-gu, Suwon-si, Gyeonggi-do, Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - In Bae Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Jieun Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Jun Hong Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Sungchul Hohng
- Interdisciplinary Graduate Program in Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Republic of Korea.,Institute of Applied Physics, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea. .,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea.
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28
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Abstract
The homologous recombination (HR) machinery plays multiple roles in genome maintenance. Best studied in the context of DNA double-stranded break (DSB) repair, recombination enzymes can cleave, pair, and unwind DNA molecules, and collaborate with regulatory proteins to execute multiple DNA processing steps before generating specific repair products. HR proteins also help to cope with problems arising from DNA replication, modulating impaired replication forks or filling DNA gaps. Given these important roles, it is not surprising that each HR step is subject to complex regulation to adjust repair efficiency and outcomes as well as to limit toxic intermediates. Recent studies have revealed intricate regulation of all steps of HR by the protein modifier SUMO, which has been increasingly recognized for its broad influence in nuclear functions. This review aims to connect established roles of SUMO with its newly identified effects on recombinational repair and stimulate further thought on many unanswered questions.
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Affiliation(s)
- Nalini Dhingra
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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29
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Zhao L, Si CS, Yu Y, Lu JW, Zhuang Y. Depletion of DNA damage binding protein 2 sensitizes triple-negative breast cancer cells to poly ADP-ribose polymerase inhibition by destabilizing Rad51. Cancer Sci 2019; 110:3543-3552. [PMID: 31541611 PMCID: PMC6825009 DOI: 10.1111/cas.14201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022] Open
Abstract
Poly ADP‐ribose polymerase inhibitors (PARPi) have shown promising therapeutic efficacy in triple‐negative breast cancer (TNBC) patients. However, resistance ultimately develops, preventing a curative effect from being attained. Extensive investigations have indicated the diversity in the mechanisms underlying the PARPi sensitivity of breast cancer. In this study, we found that DNA damage binding protein 2 (DDB2), a DNA damage‐recognition factor, could protect TNBC cells from PARPi by regulating DNA double‐strand break repair through the homologous recombination pathway, whereas the depletion of DDB2 sensitizes TNBC cells to PARPi. Furthermore, we found that DDB2 was able to stabilize Rad51 by physical association and disrupting its ubiquitination pathway‐induced proteasomal degradation. These findings highlight an essential role of DDB2 in modulating homologous recombination pathway activity and suggest a promising therapeutic target for TNBC.
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Affiliation(s)
- Lin Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cheng-Shuai Si
- Department of General Surgery, Jiangsu Institute of Cancer Research, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jian-Wei Lu
- Department of Medical Oncology, Jiangsu Institute of Cancer Research, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Zhuang
- Department of Medical Oncology, Jiangsu Institute of Cancer Research, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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30
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Barroso-González J, García-Expósito L, Hoang SM, Lynskey ML, Roncaioli JL, Ghosh A, Wallace CT, de Vitis M, Modesti M, Bernstein KA, Sarkar SN, Watkins SC, O'Sullivan RJ. RAD51AP1 Is an Essential Mediator of Alternative Lengthening of Telomeres. Mol Cell 2019; 76:11-26.e7. [PMID: 31400850 PMCID: PMC6778027 DOI: 10.1016/j.molcel.2019.06.043] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/23/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a homology-directed repair (HDR) mechanism of telomere elongation that controls proliferation in aggressive cancers. We show that the disruption of RAD51-associated protein 1 (RAD51AP1) in ALT+ cancer cells leads to generational telomere shortening. This is due to RAD51AP1's involvement in RAD51-dependent homologous recombination (HR) and RAD52-POLD3-dependent break induced DNA synthesis. RAD51AP1 KO ALT+ cells exhibit telomere dysfunction and cytosolic telomeric DNA fragments that are sensed by cGAS. Intriguingly, they activate ULK1-ATG7-dependent autophagy as a survival mechanism to mitigate DNA damage and apoptosis. Importantly, RAD51AP1 protein levels are elevated in ALT+ cells due to MMS21 associated SUMOylation. Mutation of a single SUMO-targeted lysine residue perturbs telomere dynamics. These findings indicate that RAD51AP1 is an essential mediator of the ALT mechanism and is co-opted by post-translational mechanisms to maintain telomere length and ensure proliferation of ALT+ cancer cells.
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Affiliation(s)
- Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Song My Hoang
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Michelle L Lynskey
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Justin L Roncaioli
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Arundhati Ghosh
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Callen T Wallace
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Marco de Vitis
- Department of Science, University of Rome "ROMA TRE", 00146 Rome, Italy
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm UMR1068, Aix Marseille Université U105; Institut Paoli Calmettes, 27 Boulevard Lei Roure CS30059, 13273 Marseille, Cedex 09, France
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Saumendra N Sarkar
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA.
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31
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Ohsugi T, Yamaguchi K, Zhu C, Ikenoue T, Takane K, Shinozaki M, Tsurita G, Yano H, Furukawa Y. Anti-apoptotic effect by the suppression of IRF1 as a downstream of Wnt/β-catenin signaling in colorectal cancer cells. Oncogene 2019; 38:6051-6064. [PMID: 31292489 DOI: 10.1038/s41388-019-0856-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 02/27/2019] [Accepted: 04/16/2019] [Indexed: 12/29/2022]
Abstract
Impaired Wnt signaling pathway plays a crucial role in the development of colorectal cancer through activation of the β-catenin/TCF7L2 complex. Although genes upregulated by Wnt/β-catenin signaling have been intensively studied, the roles of downregulated genes are poorly understood. Previously, we reported that interferon-induced proteins with tetratricopeptide repeats 2 (IFIT2) was downregulated by the Wnt/β-catenin signaling, and that the suppressed expression of IFIT2 conferred antiapoptotic property to colorectal cancer (CRC) cells. However, the mechanisms underlying how Wnt/β-catenin signaling regulates IFIT2 remain to be elucidated. In this study, we have uncovered that the expression of IFIT2 is induced by IRF1, which is negatively regulated by the Wnt/β-catenin signaling. In addition, we found that downregulation of IRF1 is mediated by its degradation through the ubiquitination-proteasome pathway, and that decreased activity of a deubiquitinase complex containing USP1 and UAF1 is involved in the degradation of IRF1 by Wnt/β-catenin signaling. These data should provide better understanding of the Wnt signaling pathway and human carcinogenesis.
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Affiliation(s)
- Tomoyuki Ohsugi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Chi Zhu
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Tsuneo Ikenoue
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Kiyoko Takane
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Masaru Shinozaki
- Department of Surgery, IMSUT Hospital, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Giichiro Tsurita
- Department of Surgery, IMSUT Hospital, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Hideaki Yano
- Department of Surgery, Center Hospital of the National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan.
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32
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Liang F, Miller AS, Longerich S, Tang C, Maranon D, Williamson EA, Hromas R, Wiese C, Kupfer GM, Sung P. DNA requirement in FANCD2 deubiquitination by USP1-UAF1-RAD51AP1 in the Fanconi anemia DNA damage response. Nat Commun 2019; 10:2849. [PMID: 31253762 PMCID: PMC6599204 DOI: 10.1038/s41467-019-10408-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/08/2019] [Indexed: 02/02/2023] Open
Abstract
Fanconi anemia (FA) is a multigenic disease of bone marrow failure and cancer susceptibility stemming from a failure to remove DNA crosslinks and other chromosomal lesions. Within the FA DNA damage response pathway, DNA-dependent monoubiquitinaton of FANCD2 licenses downstream events, while timely FANCD2 deubiquitination serves to extinguish the response. Here, we show with reconstituted biochemical systems, which we developed, that efficient FANCD2 deubiquitination by the USP1-UAF1 complex is dependent on DNA and DNA binding by UAF1. Surprisingly, we find that the DNA binding activity of the UAF1-associated protein RAD51AP1 can substitute for that of UAF1 in FANCD2 deubiquitination in our biochemical system. We also reveal the importance of DNA binding by UAF1 and RAD51AP1 in FANCD2 deubiquitination in the cellular setting. Our results provide insights into a key step in the FA pathway and help define the multifaceted role of the USP1-UAF1-RAD51AP1 complex in DNA damage tolerance and genome repair. In the Fanconi anemia pathway, deubiquitination of FANCD2 is a fundamental regulatory step. Here, the authors have developed a set of biochemical tools to reconstitute FANCD2 deubiquitination by recombinant USP1-UAF1-RAD51AP1 and reveal critical mechanistic details of the process.
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Affiliation(s)
- Fengshan Liang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA.,Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Adam S Miller
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Simonne Longerich
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Caroline Tang
- Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - David Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Elizabeth A Williamson
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Gary M Kupfer
- Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA. .,Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA. .,Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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33
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Zhao W, Wiese C, Kwon Y, Hromas R, Sung P. The BRCA Tumor Suppressor Network in Chromosome Damage Repair by Homologous Recombination. Annu Rev Biochem 2019; 88:221-245. [PMID: 30917004 DOI: 10.1146/annurev-biochem-013118-111058] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mutations in the BRCA1 and BRCA2 genes predispose afflicted individuals to breast, ovarian, and other cancers. The BRCA-encoded products form complexes with other tumor suppressor proteins and with the recombinase enzyme RAD51 to mediate chromosome damage repair by homologous recombination and also to protect stressed DNA replication forks against spurious nucleolytic attrition. Understanding how the BRCA tumor suppressor network executes its biological functions would provide the foundation for developing targeted cancer therapeutics, but progress in this area has been greatly hampered by the challenge of obtaining purified BRCA complexes for mechanistic studies. In this article, we review how recent effort begins to overcome this technical challenge, leading to functional and structural insights into the biochemical attributes of these complexes and the multifaceted roles that they fulfill in genome maintenance. We also highlight the major mechanistic questions that remain.
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Affiliation(s)
- Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA; ,
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA; ,
| | - Robert Hromas
- Department of Medicine, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA; ,
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34
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Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira-da-Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. MICROBIAL CELL 2019; 6:65-101. [PMID: 30652106 PMCID: PMC6334232 DOI: 10.15698/mic2019.01.665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L Klein
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Kenny K H Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Yi-Hsuan Chang
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Michael J Morten
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Sucheta Mukherjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Elizabeth S Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - João P Vieira-da-Rocha
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Shuang Wang
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Julie S Biteen
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France.,Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Eli Rothenberg
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
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35
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Suan Lim K, Li H, Roberts EA, Gaudiano EF, Clairmont C, Sambel L, Ponnienselvan K, Liu JC, Yang C, Kozono D, Parmar K, Yusufzai T, Zheng N, D’Andrea AD. USP1 Is Required for Replication Fork Protection in BRCA1-Deficient Tumors. Mol Cell 2018; 72:925-941.e4. [PMID: 30576655 PMCID: PMC6390489 DOI: 10.1016/j.molcel.2018.10.045] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 08/23/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
Abstract
BRCA1-deficient tumor cells have defects in homologous-recombination repair and replication fork stability, resulting in PARP inhibitor sensitivity. Here, we demonstrate that a deubiquitinase, USP1, is upregulated in tumors with mutations in BRCA1. Knockdown or inhibition of USP1 resulted in replication fork destabilization and decreased viability of BRCA1-deficient cells, revealing a synthetic lethal relationship. USP1 binds to and is stimulated by fork DNA. A truncated form of USP1, lacking its DNA-binding region, was not stimulated by DNA and failed to localize and protect replication forks. Persistence of monoubiquitinated PCNA at the replication fork was the mechanism of cell death in the absence of USP1. Taken together, USP1 exhibits DNA-mediated activation at the replication fork, protects the fork, and promotes survival in BRCA1-deficient cells. Inhibition of USP1 may be a useful treatment for a subset of PARP-inhibitor-resistant BRCA1-deficient tumors with acquired replication fork stabilization.
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Affiliation(s)
- Kah Suan Lim
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Heng Li
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Emma A. Roberts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Emily F. Gaudiano
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Larissa Sambel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Jessica C. Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Chunyu Yang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kalindi Parmar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA,Howard Hughes Medical Institute, Box 357280, Seattle, WA
| | - Alan D. D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
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36
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Nonstructural Protein 5A Impairs DNA Damage Repair: Implications for Hepatitis C Virus-Mediated Hepatocarcinogenesis. J Virol 2018; 92:JVI.00178-18. [PMID: 29563287 DOI: 10.1128/jvi.00178-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/11/2018] [Indexed: 01/01/2023] Open
Abstract
RAD51-associated protein 1 (RAD51AP1) is a member of the multiprotein complexes postulated to carry out RAD51-mediated homologous recombination and DNA repair in mammalian cells. In the present study, we showed that hepatitis C virus (HCV) NS5A directly bound RAD51AP1 and increased the protein level of RAD51AP1 through modulation of the ubiquitin-proteasome pathway. We also demonstrated that RAD51AP1 protein levels were increased in the liver tissues of HCV-infected patients and NS5A-transgenic mice. Importantly, NS5A impaired DNA repair by disrupting the RAD51/RAD51AP1/UAF1 complex and rendered HCV-infected cells more sensitive to DNA damage. Silencing of RAD51AP1 expression resulted in a decrease of viral propagation. We further demonstrated that RAD51AP1 was involved in the assembly step of the HCV life cycle by protecting viral RNA. These data suggest that HCV exploits RAD51AP1 to promote viral propagation and thus that host DNA repair is compromised in HCV-infected cells. Overall, our findings provide mechanistic insight into the pathogenesis of HCV infection.IMPORTANCE Chronic infection with HCV is the leading cause of hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying HCV-induced HCC are not fully understood. Here we demonstrate that the HCV NS5A protein physically interacts with RAD51AP1 and increases the RAD51AP1 protein level through modulation of the ubiquitin-proteasome pathway. HCV coopts host RAD51AP1 to protect viral RNA at an assembly step of the HCV life cycle. Note that the RAD51 protein accumulates in the cytoplasm of HCV-infected cells, and thus the RAD51/RAD51AP1/UAF1-mediated DNA damage repair system in the nucleus is compromised in HCV-infected cells. Our data may provide new insight into the molecular mechanisms of HCV-induced pathogenesis.
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37
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Morris JR, Garvin AJ. SUMO in the DNA Double-Stranded Break Response: Similarities, Differences, and Cooperation with Ubiquitin. J Mol Biol 2017; 429:3376-3387. [PMID: 28527786 DOI: 10.1016/j.jmb.2017.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 10/19/2022]
Abstract
In recent years, our knowledge of the varied role that ubiquitination plays in promoting signal amplification, novel protein interactions, and protein turnover has progressed rapidly. This is particularly remarkable in the examination of how DNA double-stranded breaks (DSBs) are repaired, with many components of the ubiquitin (Ub) conjugation, de-conjugation, and recognition machinery now identified as key factors in DSB repair. In addition, a member of the Ub-like family, small Ub-like modifier (SUMO), has also been recognised as integral for efficient repair. Here, we summarise our emerging understanding of SUMOylation both as a distinct modification and as a cooperative modification with Ub, using the cellular response to DNA DSBs as the primary setting to compare these modifications.
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Affiliation(s)
- Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomics, Medical and Dental School, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomics, Medical and Dental School, University of Birmingham, Edgbaston, B15 2TT, UK
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38
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Pires E, Sung P, Wiese C. Role of RAD51AP1 in homologous recombination DNA repair and carcinogenesis. DNA Repair (Amst) 2017; 59:76-81. [PMID: 28963981 PMCID: PMC5643253 DOI: 10.1016/j.dnarep.2017.09.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 12/11/2022]
Abstract
Homologous recombination (HR) serves to repair DNA double-strand breaks and damaged replication forks and is essential for maintaining genome stability and tumor suppression. HR capacity also determines the efficacy of anticancer therapy. Hence, there is an urgent need to better understand all HR proteins and sub-pathways. An emerging protein that is critical for RAD51-mediated HR is RAD51-associated protein 1 (RAD51AP1). Although much has been learned about its biochemical attributes, the precise molecular role of RAD51AP1 in the HR reaction is not yet fully understood. The available literature also suggests that RAD51AP1 expression may be relevant for cancer development and progression. Here, we review the efforts that led to the discovery of RAD51AP1 and elaborate on our current understanding of its biochemical profile and biological function. We also discuss how RAD51AP1 may help to promote cancer development and why it could potentially represent a promising new target for therapeutic intervention.
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Affiliation(s)
- Elena Pires
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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39
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Garvin AJ, Morris JR. SUMO, a small, but powerful, regulator of double-strand break repair. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160281. [PMID: 28847818 PMCID: PMC5577459 DOI: 10.1098/rstb.2016.0281] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
The response to a DNA double-stranded break in mammalian cells is a process of sensing and signalling the lesion. It results in halting the cell cycle and local transcription and in the mediation of the DNA repair process itself. The response is launched through a series of post-translational modification signalling events coordinated by phosphorylation and ubiquitination. More recently modifications of proteins by Small Ubiquitin-like MOdifier (SUMO) isoforms have also been found to be key to coordination of the response (Morris et al. 2009 Nature462, 886-890 (doi:10.1038/nature08593); Galanty et al. 2009 Nature462, 935-939 (doi:10.1038/nature08657)). However our understanding of the role of SUMOylation is slight compared with our growing knowledge of how ubiquitin drives signal amplification and key chromatin interactions. In this review we consider our current knowledge of how SUMO isoforms, SUMO conjugation machinery, SUMO proteases and SUMO-interacting proteins contribute to directing altered chromatin states and to repair-protein kinetics at a double-stranded DNA lesion in mammalian cells. We also consider the gaps in our understanding.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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40
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Xie Z, Pang D, Wang K, Li M, Guo N, Yuan H, Li J, Zou X, Jiao H, Ouyang H, Li Z, Tang X. Optimization of a CRISPR/Cas9-mediated Knock-in Strategy at the Porcine Rosa26 Locus in Porcine Foetal Fibroblasts. Sci Rep 2017; 7:3036. [PMID: 28596588 PMCID: PMC5465212 DOI: 10.1038/s41598-017-02785-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/19/2017] [Indexed: 01/22/2023] Open
Abstract
Genetically modified pigs have important roles in agriculture and biomedicine. However, genome-specific knock-in techniques in pigs are still in their infancy and optimal strategies have not been extensively investigated. In this study, we performed electroporation to introduce a targeting donor vector (a non-linearized vector that did not contain a promoter or selectable marker) into Porcine Foetal Fibroblasts (PFFs) along with a CRISPR/Cas9 vector. After optimization, the efficiency of the EGFP site-specific knock-in could reach up to 29.6% at the pRosa26 locus in PFFs. Next, we used the EGFP reporter PFFs to address two key conditions in the process of achieving transgenic pigs, the limiting dilution method and the strategy to evaluate the safety and feasibility of the knock-in locus. This study demonstrates that we establish an efficient procedures for the exogenous gene knock-in technique and creates a platform to efficiently generate promoter-less and selectable marker-free transgenic PFFs through the CRISPR/Cas9 system. This study should contribute to the generation of promoter-less and selectable marker-free transgenic pigs and it may provide insights into sophisticated site-specific genome engineering techniques for additional species.
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Affiliation(s)
- Zicong Xie
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Daxin Pang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Kankan Wang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Mengjing Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Nannan Guo
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Hongming Yuan
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Jianing Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Xiaodong Zou
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Huping Jiao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Hongsheng Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Xiaochun Tang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China.
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41
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Affiliation(s)
- Karissa L Paquin
- a Department of Cell and Molecular Biology , University of Rhode Island , Kingston , RI , USA
| | - David A Vierra
- a Department of Cell and Molecular Biology , University of Rhode Island , Kingston , RI , USA
| | - Niall G Howlett
- a Department of Cell and Molecular Biology , University of Rhode Island , Kingston , RI , USA
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42
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Cukras S, Lee E, Palumbo E, Benavidez P, Moldovan GL, Kee Y. The USP1-UAF1 complex interacts with RAD51AP1 to promote homologous recombination repair. Cell Cycle 2016; 15:2636-2646. [PMID: 27463890 DOI: 10.1080/15384101.2016.1209613] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
USP1 deubiquitinating enzyme and its stoichiometric binding partner UAF1 play an essential role in promoting DNA homologous recombination (HR) repair in response to various types of DNA damaging agents. Deubiquitination of FANCD2 may be attributed to the key role of USP1-UAF1 complex in regulating HR repair, however whether USP1-UAF1 promotes HR repair independently of FANCD2 deubiquitination is not known. Here we show evidence that the USP1-UAF1 complex has a FANCD2-independent function in promoting HR repair. Proteomic search of UAF1-interacting proteins revealed that UAF1 associates with RAD51AP1, a RAD51-interacting protein implicated in HR repair. We show that UAF1 mediates the interaction between USP1 and RAD51AP1, and that depletion of USP1 or UAF1 led to a decreased stability of RAD51AP1. Protein interaction mapping analysis identified some key residues within RAD51AP1 required for interacting with the USP1-UAF1 complex. Cells expressing the UAF1 interaction-deficient mutant of RAD51AP1 show increased chromosomal aberrations in response to Mitomycin C treatment. Moreover, similar to the RAD51AP1 depleted cells, the cells expressing UAF1-interaction deficient RAD51AP1 display persistent RAD51 foci following DNA damage exposure, indicating that these factors regulate a later step during the HR repair. These data altogether suggest that the USP1-UAF1 complex promotes HR repair via multiple mechanisms: through FANCD2 deubiquitination, as well as by interacting with RAD51AP1.
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Affiliation(s)
- Scott Cukras
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Euiho Lee
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Emily Palumbo
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Pamela Benavidez
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - George-Lucian Moldovan
- b Department of Biochemistry and Molecular Biology , Pennsylvania State University College of Medicine , Hershey , PA , USA
| | - Younghoon Kee
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
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