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Ou-Yang H, Yang SH, Chen W, Yang SH, Cidem A, Sung LY, Chen CM. Cruciform DNA Structures Act as Legible Templates for Accelerating Homologous Recombination in Transgenic Animals. Int J Mol Sci 2022; 23:3973. [PMID: 35409332 PMCID: PMC9000021 DOI: 10.3390/ijms23073973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Inverted repeat (IR) DNA sequences compose cruciform structures. Some genetic disorders are the result of genome inversion or translocation by cruciform DNA structures. The present study examined whether exogenous DNA integration into the chromosomes of transgenic animals was related to cruciform DNA structures. Large imperfect cruciform structures were frequently predicted around predestinated transgene integration sites in host genomes of microinjection-based transgenic (Tg) animals (αLA-LPH Tg goat, Akr1A1eGFP/eGFP Tg mouse, and NFκB-Luc Tg mouse) or CRISPR/Cas9 gene-editing (GE) animals (αLA-AP1 GE mouse). Transgene cassettes were imperfectly matched with their predestinated sequences. According to the analyzed data, we proposed a putative model in which the flexible cruciform DNA structures acted as a legible template for DNA integration into linear DNAs or double-strand break (DSB) alleles. To demonstrate this model, artificial inverted repeat knock-in (KI) reporter plasmids were created to analyze the KI rate using the CRISPR/Cas9 system in NIH3T3 cells. Notably, the KI rate of the 5′ homologous arm inverted repeat donor plasmid (5′IR) with the ROSA gRNA group (31.5%) was significantly higher than the knock-in reporter donor plasmid (KIR) with the ROSA gRNA group (21.3%, p < 0.05). However, the KI rate of the 3′ inverted terminal repeat/inverted repeat donor plasmid (3′ITRIR) group was not different from the KIR group (23.0% vs. 22.0%). These results demonstrated that the legibility of the sequence with the cruciform DNA existing in the transgene promoted homologous recombination (HR) with a higher KI rate. Our findings suggest that flexible cruciform DNAs folded by IR sequences improve the legibility and accelerate DNA 3′-overhang integration into the host genome via homologous recombination machinery.
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Affiliation(s)
- Huan Ou-Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Shiao-Hsuan Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Reproductive Medicine Center, Department of Gynecology, Changhua Christian Hospital, Changhua 515, Taiwan
| | - Wei Chen
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shang-Hsun Yang
- Department of Physiology, National Cheng Kung University, Tainan 701, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Abdulkadir Cidem
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25250, Turkey
| | - Li-Ying Sung
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chuan-Mu Chen
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Rong-Hsing Translational Medicine Research Center, Taichung Veterans General Hospital, Taichung 407, Taiwan
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Predicted Cellular Interactors of the Endogenous Retrovirus-K Integrase Enzyme. Microorganisms 2021; 9:microorganisms9071509. [PMID: 34361946 PMCID: PMC8303831 DOI: 10.3390/microorganisms9071509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
Integrase (IN) enzymes are found in all retroviruses and are crucial in the retroviral integration process. Many studies have revealed how exogenous IN enzymes, such as the human immunodeficiency virus (HIV) IN, contribute to altered cellular function. However, the same consideration has not been given to viral IN originating from symbionts within our own DNA. Endogenous retrovirus-K (ERVK) is pathologically associated with neurological and inflammatory diseases along with several cancers. The ERVK IN interactome is unknown, and the question of how conserved the ERVK IN protein-protein interaction motifs are as compared to other retroviral integrases is addressed in this paper. The ERVK IN protein sequence was analyzed using the Eukaryotic Linear Motif (ELM) database, and the results are compared to ELMs of other betaretroviral INs and similar eukaryotic INs. A list of putative ERVK IN cellular protein interactors was curated from the ELM list and submitted for STRING analysis to generate an ERVK IN interactome. KEGG analysis was used to identify key pathways potentially influenced by ERVK IN. It was determined that the ERVK IN potentially interacts with cellular proteins involved in the DNA damage response (DDR), cell cycle, immunity, inflammation, cell signaling, selective autophagy, and intracellular trafficking. The most prominent pathway identified was viral carcinogenesis, in addition to select cancers, neurological diseases, and diabetic complications. This potentiates the role of ERVK IN in these pathologies via protein-protein interactions facilitating alterations in key disease pathways.
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Orhan E, Velazquez C, Tabet I, Sardet C, Theillet C. Regulation of RAD51 at the Transcriptional and Functional Levels: What Prospects for Cancer Therapy? Cancers (Basel) 2021; 13:2930. [PMID: 34208195 PMCID: PMC8230762 DOI: 10.3390/cancers13122930] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 01/07/2023] Open
Abstract
The RAD51 recombinase is a critical effector of Homologous Recombination (HR), which is an essential DNA repair mechanism for double-strand breaks. The RAD51 protein is recruited onto the DNA break by BRCA2 and forms homopolymeric filaments that invade the homologous chromatid and use it as a template for repair. RAD51 filaments are detectable by immunofluorescence as distinct foci in the cell nucleus, and their presence is a read out of HR proficiency. RAD51 is an essential gene, protecting cells from genetic instability. Its expression is low and tightly regulated in normal cells and, contrastingly, elevated in a large fraction of cancers, where its level of expression and activity have been linked with sensitivity to genotoxic treatment. In particular, BRCA-deficient tumors show reduced or obliterated RAD51 foci formation and increased sensitivity to platinum salt or PARP inhibitors. However, resistance to treatment sets in rapidly and is frequently based on a complete or partial restoration of RAD51 foci formation. Consequently, RAD51 could be a highly valuable therapeutic target. Here, we review the multiple levels of regulation that impact the transcription of the RAD51 gene, as well as the post-translational modifications that determine its expression level, recruitment on DNA damage sites and the efficient formation of homofilaments. Some of these regulation levels may be targeted and their impact on cancer cell survival discussed.
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Affiliation(s)
- Esin Orhan
- IRCM, Institut de Recherche en Cancérologie de Montpellier U1194 INSERM, Université de Montpellier, 34090 Montpellier, France; (E.O.); (I.T.); (C.S.)
| | | | - Imene Tabet
- IRCM, Institut de Recherche en Cancérologie de Montpellier U1194 INSERM, Université de Montpellier, 34090 Montpellier, France; (E.O.); (I.T.); (C.S.)
| | - Claude Sardet
- IRCM, Institut de Recherche en Cancérologie de Montpellier U1194 INSERM, Université de Montpellier, 34090 Montpellier, France; (E.O.); (I.T.); (C.S.)
| | - Charles Theillet
- IRCM, Institut de Recherche en Cancérologie de Montpellier U1194 INSERM, Université de Montpellier, 34090 Montpellier, France; (E.O.); (I.T.); (C.S.)
- ICM, Institut du Cancer de Montpellier, 34090 Montpellier, France;
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Jiang S, Lin T, Xie Q, Wang L. Network Analysis of RAD51 Proteins in Metazoa and the Evolutionary Relationships With Their Archaeal Homologs. Front Genet 2018; 9:383. [PMID: 30319685 PMCID: PMC6168637 DOI: 10.3389/fgene.2018.00383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/27/2018] [Indexed: 12/18/2022] Open
Abstract
The RAD51 (DNA repair protein RAD51) recombinases are essential for homologous recombination, DNA repair, and genome stability. Overexpression of RAD51 proteins has been observed in many cancer cells, such as thyroid carcinoma, breast cancer, pancreatic cancer, and others. In Metazoa, there are multiple members of RAD51 (RAD51, RAD51B, RAD51C, RAD51D, DMC1) (DNA meiotic recombinase 1), XRCC2 (X-ray repair cross-complementing 2), and XRCC3. In this study, we used a protein sequence similarity network (SSN) to analyze the evolutionary relationship within this protein family. The SSN based on the RAD51 proteins from Metazoa indicated that there are several proteins that have yet to be functionally defined. The SSN based on the distribution of the proteins supports the hypothesis that horizontal gene transfer plays an important role in the evolution of RAD51 proteins. Multiple sequence alignments with structural information revealed that the amino acid residues for ATP and Mg2+ are highly conserved. The seven RAD51 proteins in humans are under different selective pressure: RAD51 and DMC1 are under stringent negative selection, while other proteins are subject to relatively relaxed negative selection. Furthermore, the expression levels of the seven genes in different tissues showed that the genes in the same cluster in the phylogenetic tree showed similar expression profiles. Finally, the SSN based on the RAD51 proteins from both eukaryotes and prokaryotes suggested that the eukaryotic RAD51 recombinases share a common ancestor with the archaeal homologs, but XRCC2 may have a different origin. These findings expand the understanding of the evolution and diversity of RAD51 recombinases in Metazoa.
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Affiliation(s)
- Shan Jiang
- Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
| | - Ting Lin
- Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
| | - Qingji Xie
- Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
| | - Lijing Wang
- Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
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Kim H, Lee SY, Choi YM, Kim BJ. HBV polymerase-derived peptide exerts an anti-HIV-1 effect by inhibiting the acetylation of viral integrase. Biochem Biophys Res Commun 2018; 501:541-546. [PMID: 29752938 DOI: 10.1016/j.bbrc.2018.05.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/04/2018] [Indexed: 02/06/2023]
Abstract
Here, we found that a 6-mer peptide, Poly6, derived from the hepatitis B virus (HBV), which overlaps with a polymerase corresponding to a preS1 deletion reported to contribute to liver disease progression, can elicit an antiviral effect against human immunodeficiency virus (HIV)-1 by inhibiting HIV-1 integrase (IN) activity of infected cells. Mechanistic studies revealed that the anti-HIV-1 effects of Poly6 occurred via the inhibition of integration, which resulted from the inhibition of acetylation of HIV-1 IN possibly by downregulation of p300 histone acetyltransferase. Our data suggest the potential therapeutic use of a 6-mer HBV-derived peptide, Poly6, as an anti-HIV-1 agent to suppress HIV-1 infection via inhibiting integrase activity.
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Affiliation(s)
- Hong Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute, Cancer Research Institute and SNUMRC, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea
| | - So-Young Lee
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute, Cancer Research Institute and SNUMRC, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea
| | - Yu-Min Choi
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute, Cancer Research Institute and SNUMRC, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute, Cancer Research Institute and SNUMRC, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
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Matysiak J, Lesbats P, Mauro E, Lapaillerie D, Dupuy JW, Lopez AP, Benleulmi MS, Calmels C, Andreola ML, Ruff M, Llano M, Delelis O, Lavigne M, Parissi V. Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration. Retrovirology 2017; 14:39. [PMID: 28754126 PMCID: PMC5534098 DOI: 10.1186/s12977-017-0363-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/24/2017] [Indexed: 01/23/2023] Open
Abstract
Background Insertion of retroviral genome DNA occurs in the chromatin of the host cell. This step is modulated by chromatin structure as nucleosomes compaction was shown to prevent HIV-1 integration and chromatin remodeling has been reported to affect integration efficiency. LEDGF/p75-mediated targeting of the integration complex toward RNA polymerase II (polII) transcribed regions ensures optimal access to dynamic regions that are suitable for integration. Consequently, we have investigated the involvement of polII-associated factors in the regulation of HIV-1 integration. Results Using a pull down approach coupled with mass spectrometry, we have selected the FACT (FAcilitates Chromatin Transcription) complex as a new potential cofactor of HIV-1 integration. FACT is a histone chaperone complex associated with the polII transcription machinery and recently shown to bind LEDGF/p75. We report here that a tripartite complex can be formed between HIV-1 integrase, LEDGF/p75 and FACT in vitro and in cells. Biochemical analyzes show that FACT-dependent nucleosome disassembly promotes HIV-1 integration into chromatinized templates, and generates highly favored nucleosomal structures in vitro. This effect was found to be amplified by LEDGF/p75. Promotion of this FACT-mediated chromatin remodeling in cells both increases chromatin accessibility and stimulates HIV-1 infectivity and integration. Conclusions Altogether, our data indicate that FACT regulates HIV-1 integration by inducing local nucleosomes dissociation that modulates the functional association between the incoming intasome and the targeted nucleosome. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0363-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julien Matysiak
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Jean-William Dupuy
- Centre Génomique fonctionnelle Bordeaux, Plateforme Proteome, Université de Bordeaux, Bordeaux, France
| | - Angelica P Lopez
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Mohamed Salah Benleulmi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marie-Line Andreola
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marc Ruff
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch-Graffenstaden, France
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Olivier Delelis
- LBPA, UMR8113, CNRS, ENS-Cachan, Cachan, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marc Lavigne
- Department of Virology, UMR 3569, CNRS, Institut Pasteur, Paris, France.,Institut Cochin-INSERM U1016-CNRS UMR8104, Université Paris Descartes, Paris, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France. .,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France. .,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France.
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Bray S, Turnbull M, Hebert S, Douville RN. Insight into the ERVK Integrase - Propensity for DNA Damage. Front Microbiol 2016; 7:1941. [PMID: 27990140 PMCID: PMC5131560 DOI: 10.3389/fmicb.2016.01941] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/18/2016] [Indexed: 12/18/2022] Open
Abstract
Retroviruses create permanently integrated proviruses that exist in the host genome. Retroviral genomes encode for functionally conserved gag, pro, pol, and env regions, as well as integrase (IN), which is required for retroviral integration. IN mediates viral genome insertion through 3′ end processing of the viral DNA and the strand transfer reaction. This process requires the formation of a pre-integration complex, comprised of IN, viral DNA, and cellular proteins. Viral insertion causes DNA damage, leading to the requirement of host DNA repair mechanisms. Therefore, a failure of DNA repair pathways may result in genomic instability and potentially cause host cell death. Considering the numerous human diseases associated with genomic instability, the endogenous retrovirus-K (ERVK) IN should be considered as a putative contributor to DNA damage in human cells. Future research and drug discovery should focus on ERVK IN activity and its role in human conditions, such as neurological disease and cancers.
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Affiliation(s)
- Samantha Bray
- Douville Lab, Department of Biology, University of Winnipeg, Winnipeg MB, Canada
| | - Matthew Turnbull
- Douville Lab, Department of Biology, University of Winnipeg, Winnipeg MB, Canada
| | - Sherry Hebert
- Douville Lab, Department of Biology, University of Winnipeg, Winnipeg MB, Canada
| | - Renée N Douville
- Douville Lab, Department of Biology, University of Winnipeg, WinnipegMB, Canada; Department of Immunology, University of Manitoba, WinnipegMB, Canada
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Koito A, Ishizaka Y. Retroviruses, retroelements and their restrictions. Front Microbiol 2013; 4:197. [PMID: 23874330 PMCID: PMC3710956 DOI: 10.3389/fmicb.2013.00197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 06/24/2013] [Indexed: 12/13/2022] Open
Affiliation(s)
- Atsushi Koito
- Department of Retrovirology and Self-Defense, Kumamoto University Kumamoto, Japan
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