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Belotserkovskii BP, Hanawalt PC. A model for transcription-dependent R-loop formation at double-stranded DNA breaks: Implications for their detection and biological effects. J Theor Biol 2024; 595:111962. [PMID: 39384064 DOI: 10.1016/j.jtbi.2024.111962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/20/2024] [Accepted: 10/04/2024] [Indexed: 10/11/2024]
Abstract
R-loops are structures containing an RNA-DNA duplex and an unpaired DNA strand. During R-loop formation an RNA strand invades the DNA duplex, displacing the homologous DNA strand and binding the complementary DNA strand. Here we analyze a model for transcription-dependent R-loop formation at double-stranded DNA breaks (DSBs). In this model, R-loop formation is preceded by detachment of the non-template DNA strand from the RNA polymerase (RNAP). Then, strand exchange is initiated between the nascent RNA and the non-template DNA strand. During that strand exchange the length of the R-loop could either increase, or decrease in a biased random-walk fashion, in which the bias would depend upon the DNA sequence. Eventually, the restoration of the DNA duplex would completely displace the RNA. However, as long as the RNAP remains bound to the template DNA strand it prevents that displacement. Thus, according to the model, RNAPs stalled at DSBs can increase the lifespan of R-loops, increasing their detectability in experiments, and perhaps enhancing their biological effects.
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2
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Maruta G, Maeoka H, Tsunoda T, Akiyoshi K, Takagi S, Shirasawa S, Ishikura S. RAD52-mediated repair of DNA double-stranded breaks at inactive centromeres leads to subsequent apoptotic cell death. Nucleic Acids Res 2024:gkae852. [PMID: 39360606 DOI: 10.1093/nar/gkae852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/12/2024] [Accepted: 09/18/2024] [Indexed: 10/04/2024] Open
Abstract
Centromeres, where the kinetochore complex binds, are susceptible to damages including DNA double-stranded breaks (DSBs). Here, we report the functional significance and the temporally and spatially distinct regulation of centromeric DSB repair via the three pathways of non-homologous end joining (NHEJ), homologous recombination (HR) and single-strand annealing (SSA). The SSA factor RAD52 is most frequently recruited to centromeric DSB sites compared with the HR factor RAD51 and the NHEJ factor DNA ligase IV (LIG4), indicating that SSA plays predominant roles in centromeric DSB repair. Upon centromeric DSB induction, LIG4 is recruited to both active centromeres, where kinetochore complex binds, and inactive centromeres. In contrast, RAD51 and RAD52 are recruited only to inactive centromeres. These results indicate that DSBs at active centromeres are repaired through NHEJ, whereas the three pathways of NHEJ, HR and SSA are involved in DSB repair at inactive centromeres. Furthermore, siRNA-mediated depletion of either LIG4 or RAD51 promotes cell death after centromeric DSB induction, whereas RAD52 depletion inhibits it, suggesting that HR and NHEJ are required for appropriate centromeric DSB repair, whereas SSA-mediated centromeric DSB repair leads to subsequent cell death. Thus, SSA-mediated DSB repair at inactive centromeres may cause centromere dysfunction through error-prone repair.
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Affiliation(s)
- Gen Maruta
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Department of Anesthesiology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Hisanori Maeoka
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Center for Advanced Molecular Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Kozaburo Akiyoshi
- Department of Anesthesiology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Satoshi Takagi
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Center for Advanced Molecular Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Center for Advanced Molecular Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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3
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Lee YJ, Lee SY, Kim S, Kim SH, Lee SH, Park S, Kim JJ, Kim DW, Kim H. REXO5 promotes genomic integrity through regulating R-loop using its exonuclease activity. Leukemia 2024; 38:2150-2161. [PMID: 39080354 PMCID: PMC11436357 DOI: 10.1038/s41375-024-02362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 09/29/2024]
Abstract
Chronic myeloid leukemia (CML), caused by BCR::ABL1 fusion gene, is known to regulate disease progression by altering the expression of genes. However, the molecular mechanisms underlying these changes are largely unknown. In this study, we identified RNA Exonuclease 5 (REXO5/LOC81691) as a novel gene with elevated mRNA expression levels in chronic myeloid leukemia (CML) patients. Additionally, using the REXO5 knockout (KO) K562 cell lines, we revealed a novel role for REXO5 in the DNA damage response (DDR). Compared to wild-type (WT) cells, REXO5 KO cells showed an accumulation of R-loops and increased DNA damage. We demonstrated that REXO5 translocates to sites of DNA damage through its RNA recognition motif (RRM) and selectively binds to R loops. Interestingly, we identified that REXO5 regulates R-loop levels by degrading mRNA within R-loop using its exonuclease domain. REXO5 KO showed ATR-CHK1 activation. Collectively, we demonstrated that REXO5 plays a key role in the physiological control of R-loops using its exonuclease domain. These findings may provide novel insights into how REXO5 expression changes contribute to CML pathogenesis.
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Affiliation(s)
- Ye Jin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Seo Yun Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea
| | - Soomi Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Soo-Hyun Kim
- Department of Hematology, Hematology Center, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu, South Korea
- Leukemia Omics Research Institute, Eulji University Uijeongbu Campus, Uijeongbu, South Korea
| | - Soo Hyeon Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea
| | - Sungho Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jae Jin Kim
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea.
| | - Dong-Wook Kim
- Department of Hematology, Hematology Center, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu, South Korea.
- Leukemia Omics Research Institute, Eulji University Uijeongbu Campus, Uijeongbu, South Korea.
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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4
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James CD, Youssef A, Prabhakar AT, Otoa R, Roe JD, Witt A, Lewis RL, Bristol ML, Wang X, Zhang K, Li R, Morgan IM. Human papillomavirus 16 replication converts SAMHD1 into a homologous recombination factor and promotes its recruitment to replicating viral DNA. J Virol 2024; 98:e0082624. [PMID: 39194246 PMCID: PMC11406955 DOI: 10.1128/jvi.00826-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024] Open
Abstract
We have demonstrated that SAMHD1 (sterile alpha motif and histidine-aspartic domain HD-containing protein 1) is a restriction factor for the human papillomavirus 16 (HPV16) life cycle. Here, we demonstrate that in HPV-negative cervical cancer C33a cells and human foreskin keratinocytes immortalized by HPV16 (HFK+HPV16), SAMHD1 is recruited to E1-E2 replicating DNA. Homologous recombination (HR) factors are required for HPV16 replication, and viral replication promotes phosphorylation of SAMHD1, which converts it from a dNTPase to an HR factor independent from E6/E7 expression. A SAMHD1 phospho-mimic (SAMHD1 T592D) reduces E1-E2-mediated DNA replication in C33a cells and has enhanced recruitment to the replicating DNA. In HFK+HPV16 cells, SAMHD1 T592D is recruited to the viral DNA and attenuates cellular growth, but does not attenuate growth in isogenic HFK cells immortalized by E6/E7 alone. SAMHD1 T592D also attenuates the development of viral replication foci following keratinocyte differentiation. The results indicated that enhanced SAMHD1 phosphorylation could be therapeutically beneficial in cells with HPV16 replicating genomes. Protein phosphatase 2A (PP2A) can dephosphorylate SAMHD1, and PP2A function can be inhibited by endothall. We demonstrate that endothall reduces E1-E2 replication and promotes SAMHD1 recruitment to E1-E2 replicating DNA, mimicking the SAMHD1 T592D phenotypes. Finally, we demonstrate that in head and neck cancer cell lines with HPV16 episomal genomes, endothall attenuates their growth and promotes recruitment of SAMHD1 to the viral genome. The results suggest that targeting cellular phosphatases has therapeutic potential for the treatment of HPV infections and cancers. IMPORTANCE Human papillomaviruses (HPVs) are causative agents in around 5% of all human cancers. The development of anti-viral therapeutics depends upon an increased understanding of the viral life cycle. Here, we demonstrate that HPV16 replication converts sterile alpha motif and histidine-aspartic domain HD-containing protein 1 (SAMHD1) into a homologous recombination (HR) factor via phosphorylation. This phosphorylation promotes recruitment of SAMHD1 to viral DNA to assist with replication. A SAMHD1 mutant that mimics phosphorylation is hyper-recruited to viral DNA and attenuates viral replication. Expression of this mutant in HPV16-immortalized cells attenuates the growth of these cells, but not cells immortalized by the viral oncogenes E6/E7 alone. Finally, we demonstrate that the phosphatase inhibitor endothall promotes hyper-recruitment of endogenous SAMHD1 to HPV16 replicating DNA and can attenuate the growth of both HPV16-immortalized human foreskin keratinocytes (HFKs) and HPV16-positive head and neck cancer cell lines. We propose that phosphatase inhibitors represent a novel tool for combating HPV infections and disease.
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Affiliation(s)
- Claire D James
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Aya Youssef
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Apurva T Prabhakar
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Raymonde Otoa
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Jenny D Roe
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Austin Witt
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Rachel L Lewis
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Molly L Bristol
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
- VCU Massey Cancer Center, Richmond, Virginia, USA
| | - Xu Wang
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Kun Zhang
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Renfeng Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Iain M Morgan
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
- VCU Massey Cancer Center, Richmond, Virginia, USA
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5
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Jalan M, Sharma A, Pei X, Weinhold N, Buechelmaier ES, Zhu Y, Ahmed-Seghir S, Ratnakumar A, Di Bona M, McDermott N, Gomez-Aguilar J, Anderson KS, Ng CKY, Selenica P, Bakhoum SF, Reis-Filho JS, Riaz N, Powell SN. RAD52 resolves transcription-replication conflicts to mitigate R-loop induced genome instability. Nat Commun 2024; 15:7776. [PMID: 39237529 PMCID: PMC11377823 DOI: 10.1038/s41467-024-51784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/15/2024] [Indexed: 09/07/2024] Open
Abstract
Collisions of the transcription and replication machineries on the same DNA strand can pose a significant threat to genomic stability. These collisions occur in part due to the formation of RNA-DNA hybrids termed R-loops, in which a newly transcribed RNA molecule hybridizes with the DNA template strand. This study investigated the role of RAD52, a known DNA repair factor, in preventing collisions by directing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Furthermore, RAD52's ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide evidence of an increased mutational burden from double-strand breaks at conserved R-loop sites in human tumor samples, which is increased in tumors with low RAD52 expression. In summary, this study underscores the importance of RAD52 in orchestrating the balance between replication and transcription processes to prevent collisions and maintain genome stability.
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Affiliation(s)
- Manisha Jalan
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA.
| | - Aman Sharma
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Xin Pei
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Nils Weinhold
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | | | - Yingjie Zhu
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
| | | | | | - Melody Di Bona
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
- Human Oncology and Pathogenesis, MSKCC, New York, NY, 10065, USA
| | - Niamh McDermott
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | | | - Kyrie S Anderson
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Bern, CH, 3008, Switzerland
- SIB, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
- Human Oncology and Pathogenesis, MSKCC, New York, NY, 10065, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
- AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA.
- Molecular Biology Program, MSKCC, New York, NY, 10065, USA.
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6
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McLaughlin E, Zavala Martinez MG, Dujeancourt-Henry A, Chaze T, Gianetto QG, Matondo M, Urbaniak MD, Glover L. Phosphoproteomic analysis of the response to DNA damage in Trypanosoma brucei. J Biol Chem 2024; 300:107657. [PMID: 39128729 PMCID: PMC11408851 DOI: 10.1016/j.jbc.2024.107657] [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: 07/02/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
Damage to the genetic material of the cell poses a universal threat to all forms of life. The DNA damage response is a coordinated cellular response to a DNA break, key to which is the phosphorylation signaling cascade. Identifying which proteins are phosphorylated is therefore crucial to understanding the mechanisms that underlie it. We have used stable isotopic labeling of amino acids in cell culture-based quantitative phosphoproteomics to profile changes in phosphorylation site abundance following double stranded DNA breaks, at two distinct loci in the genome of the single cell eukaryote Trypanosoma brucei. Here, we report on the T. brucei phosphoproteome following a single double-strand break at either a chromosome internal or subtelomeric locus, specifically the bloodstream form expression site. We detected >6500 phosphorylation sites, of which 211 form a core set of double-strand break responsive phosphorylation sites. Along with phosphorylation of canonical DNA damage factors, we have identified two novel phosphorylation events on histone H2A and found that in response to a chromosome internal break, proteins are predominantly phosphorylated, while a greater proportion of proteins dephosphorylated following a DNA break at a subtelomeric bloodstream form expression site. Our data represent the first DNA damage phosphoproteome and provides novel insights into repair at distinct chromosomal contexts in T. brucei.
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Affiliation(s)
- Emilia McLaughlin
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France; Sorbonne Université, Collège doctoral, Paris, France
| | - Monica Gabriela Zavala Martinez
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Annick Dujeancourt-Henry
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Thibault Chaze
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France; Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France
| | - Michael D Urbaniak
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Lucy Glover
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France.
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7
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Li S, Tian T, Zhang T, Lin Y, Cai X. A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure. Nat Protoc 2024:10.1038/s41596-024-01050-7. [PMID: 39215132 DOI: 10.1038/s41596-024-01050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 07/11/2024] [Indexed: 09/04/2024]
Abstract
As microRNAs (miRNA) regulate almost all physiopathological activities in the human body, miRNA therapeutics that deliver miRNA regulators have attracted considerable attention in the field of nucleic acid drug development. The use of tetrahedral DNA nanostructures to deliver miRNA regulators is promising because of their simple fabrication, enhanced cell entry, effective tissue penetration, biocompatibility and functional editability. This protocol extension builds on our previous protocol for the use of tetrahedral DNA nanostructures and was designed to establish an updated bioswitchable delivery system (BDS) for achieving controlled cargo loading and release. A ribonuclease H-sensitive sequence is designed as a bioswitchable apparatus for the targeted release of the miRNA regulator. The functional sequence of the miRNA regulator and minimal secondary structure formation tendency during annealing are two key points in cargo design. We provide two BDS design strategies; BDS-A comprises an intact DNA tetrahedron with the RNA cargo hanging outside, offering the merits of lower cost, simplicity, and more direct structural design. In the BDS-B design, the RNA regulators are embedded into the DNA tetrahedron, which is beneficial for dermal tissue permeation applications. Following sequence design in Oligo 7 and Tiamat, the BDS assembly is completed and then ribonuclease H achieves controlled release of the miRNA regulator by triggering the bioswitchable apparatus. This is verified via polyacrylamide and agarose gel electrophoresis or fluorophore modifications. Both BDSs show promising cellular membrane permeability, tissue permeability and target inhibition in vitro and in vivo. The assembly and characterization of the BDS can be completed in 4 d, and the validation time for biostability and biological applications will depend on the specific use.
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Affiliation(s)
- Songhang Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China.
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China.
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8
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Li Y, Liu C, Jia X, Bi L, Ren Z, Zhao Y, Zhang X, Guo L, Bao Y, Liu C, Li W, Sun B. RPA transforms RNase H1 to a bidirectional exoribonuclease for processive RNA-DNA hybrid cleavage. Nat Commun 2024; 15:7464. [PMID: 39198528 PMCID: PMC11358518 DOI: 10.1038/s41467-024-51984-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024] Open
Abstract
RNase H1 has been acknowledged as an endoribonuclease specializing in the internal degradation of the RNA moiety within RNA-DNA hybrids, and its ribonuclease activity is indispensable in multifaceted aspects of nucleic acid metabolism. However, the molecular mechanism underlying RNase H1-mediated hybrid cleavage remains inadequately elucidated. Herein, using single-molecule approaches, we probe the dynamics of the hybrid cleavage by Saccharomyces cerevisiae RNase H1. Remarkably, a single RNase H1 enzyme displays 3'-to-5' exoribonuclease activity. The directional RNA degradation proceeds processively and yet discretely, wherein unwinding approximately 6-bp hybrids as a prerequisite for two consecutive 3-nt RNA excisions limits the overall rate within each catalytic cycle. Moreover, Replication Protein A (RPA) reinforces RNase H1's 3'-to-5' nucleolytic rate and processivity and stimulates its 5'-to-3' exoribonuclease activity. This stimulation is primarily realized through the pre-separation of the hybrids and consequently transfers RNase H1 to a bidirectional exoribonuclease, further potentiating its cleavage efficiency. These findings unveil unprecedented characteristics of an RNase and provide a dynamic view of RPA-enhanced processive hybrid cleavage by RNase H1.
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Affiliation(s)
- Yanan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinshuo Jia
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhiyun Ren
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yilin Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xia Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lijuan Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yanling Bao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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9
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Chiang HC, Qi L, Mitra P, Huang Y, Hu Y, Li R. R-loop functions in Brca1-associated mammary tumorigenesis. Proc Natl Acad Sci U S A 2024; 121:e2403600121. [PMID: 39116124 PMCID: PMC11331088 DOI: 10.1073/pnas.2403600121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Deleterious accumulation of R-loops, a DNA-RNA hybrid structure, contributes to genome instability. They are associated with BRCA1 mutation-related breast cancer, an estrogen receptor α negative (ERα-) tumor type originating from luminal progenitor cells. However, a presumed causality of R-loops in tumorigenesis has not been established in vivo. Here, we overexpress mouse Rnaseh1 (Rh1-OE) in vivo to remove accumulated R-loops in Brca1-deficient mouse mammary epithelium (BKO). R-loop removal exacerbates DNA replication stress in proliferating BKO mammary epithelial cells, with little effect on homology-directed repair of double-strand breaks following ionizing radiation. Compared to their BKO counterparts, BKO-Rh1-OE mammary glands contain fewer luminal progenitor cells but more mature luminal cells. Despite a similar incidence of spontaneous mammary tumors in BKO and BKO-Rh1-OE mice, a significant percentage of BKO-Rh1-OE tumors express ERα and progesterone receptor. Our results suggest that rather than directly elevating the overall tumor incidence, R-loops influence the mammary tumor subtype by shaping the cell of origin for Brca1 tumors.
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Affiliation(s)
- Huai-Chin Chiang
- Department of Biochemistry and Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Leilei Qi
- Department of Anatomy and Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Payal Mitra
- Department of Biochemistry and Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Yimeng Huang
- Department of Biochemistry and Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Yanfen Hu
- Department of Anatomy and Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Rong Li
- Department of Biochemistry and Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
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10
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Ma J, Ross SR. Multifunctional role of DEAD-box helicase 41 in innate immunity, hematopoiesis and disease. Front Immunol 2024; 15:1451705. [PMID: 39185415 PMCID: PMC11341421 DOI: 10.3389/fimmu.2024.1451705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/18/2024] [Indexed: 08/27/2024] Open
Abstract
DEAD-box helicases are multifunctional proteins participating in many aspects of cellular RNA metabolism. DEAD-box helicase 41 (DDX41) in particular has pivotal roles in innate immune sensing and hematopoietic homeostasis. DDX41 recognizes foreign or self-nucleic acids generated during microbial infection, thereby initiating anti-pathogen responses. DDX41 also binds to RNA (R)-loops, structures consisting of DNA/RNA hybrids and a displaced strand of DNA that occur during transcription, thereby maintaining genome stability by preventing their accumulation. DDX41 deficiency leads to increased R-loop levels, resulting in inflammatory responses that likely influence hematopoietic stem and progenitor cell production and development. Beyond nucleic acid binding, DDX41 associates with proteins involved in RNA splicing as well as cellular proteins involved in innate immunity. DDX41 is also a tumor suppressor in familial and sporadic myelodysplastic syndrome/acute myelogenous leukemia (MDS/AML). In the present review, we summarize the functions of DDX helicases in critical biological processes, particularly focusing on DDX41's association with cellular molecules and the mechanisms underlying its roles in innate immunity, hematopoiesis and the development of myeloid malignancies.
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Affiliation(s)
| | - Susan R. Ross
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, IL, United States
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11
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Kawaguchi K, Satoh S, Obokata J. Transcription of damage-induced RNA in Arabidopsis was frequently initiated from DSB loci within the genic regions. Genes Cells 2024; 29:681-689. [PMID: 38845450 DOI: 10.1111/gtc.13133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 08/07/2024]
Abstract
DNA double-strand breaks (DSBs) are the most severe DNA lesions and need to be removed immediately to prevent loss of genomic information. Recently, it has been revealed that DSBs induce novel transcription from the cleavage sites in various species, resulting in RNAs being referred to as damage-induced RNAs (diRNAs). While diRNA synthesis is an early event in the DNA damage response and plays an essential role in DSB repair activation, the location where diRNAs are newly generated in plants remains unclear, as does their transcriptional mechanism. Here, we performed the sequencing of polyadenylated (polyA) diRNAs that emerged around all DSB loci in Arabidopsis thaliana under the expression of the exogenous restriction enzyme Sbf I and observed 88 diRNAs transcribed via RNA polymerase II in 360 DSB loci. Most of the detected diRNAs originated within active genes and were transcribed from DSBs in a bidirectional manner. Furthermore, we found that diRNA elongation tends to terminate at the boundary of an endogenous gene located near DSB loci. Our results provide reliable evidence for understanding the importance of new transcription at DSBs and show that diRNA is a crucial factor for successful DSB repair.
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Affiliation(s)
- Kohei Kawaguchi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
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12
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Choi SY. The roles of TonEBP in the DNA damage response: From DNA damage bypass to R-loop resolution. DNA Repair (Amst) 2024; 140:103697. [PMID: 38878563 DOI: 10.1016/j.dnarep.2024.103697] [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: 01/31/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 07/13/2024]
Abstract
Tonicity-responsive enhancer binding protein (TonEBP) is a stress-responsive protein that plays a critical role in the regulation of gene expression and cellular adaptation to stressful environments. Recent studies uncovered the novel role of TonEBP in the DNA damage response, which significantly impacts genomic stability. This review provides a comprehensive overview of the novel role of TonEBP in DNA damage repair, including its involvement in the DNA damage bypass pathway and the recognition and resolution of DNA damage-induced R-loop structures.
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Affiliation(s)
- Soo Youn Choi
- Department of Biology, Jeju National University, Jeju, the Republic of Korea.
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13
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Kalamara V, Garinis GA. The epitranscriptome: reshaping the DNA damage response. Trends Cell Biol 2024:S0962-8924(24)00122-3. [PMID: 39048401 DOI: 10.1016/j.tcb.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024]
Abstract
Genomic instability poses a formidable threat to cellular vitality and wellbeing, prompting cells to deploy an intricate DNA damage response (DDR) mechanism. Recent evidence has suggested that RNA is intricately linked to the DDR by serving as template, scaffold, or regulator during the repair of DNA damage. Additionally, RNA molecules undergo modifications, contributing to the epitranscriptome, a dynamic regulatory layer influencing cellular responses to genotoxic stress. The intricate interplay between RNA and the DDR sheds new light on how the RNA epigenome contributes to the maintenance of genomic integrity and ultimately shapes the fate of damaged cells.
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Affiliation(s)
- Vivian Kalamara
- Department of Biology, University of Crete, Heraklion, Crete, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013, Heraklion, Crete, Greece
| | - George A Garinis
- Department of Biology, University of Crete, Heraklion, Crete, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013, Heraklion, Crete, Greece.
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14
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Kannan A, Gangadharan Leela S, Branzei D, Gangwani L. Role of senataxin in R-loop-mediated neurodegeneration. Brain Commun 2024; 6:fcae239. [PMID: 39070547 PMCID: PMC11277865 DOI: 10.1093/braincomms/fcae239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/14/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
Senataxin is an RNA:DNA helicase that plays an important role in the resolution of RNA:DNA hybrids (R-loops) formed during transcription. R-loops are involved in the regulation of biological processes such as immunoglobulin class switching, gene expression and DNA repair. Excessive accumulation of R-loops results in DNA damage and loss of genomic integrity. Senataxin is critical for maintaining optimal levels of R-loops to prevent DNA damage and acts as a genome guardian. Within the nucleus, senataxin interacts with various RNA processing factors and DNA damage response and repair proteins. Senataxin interactors include survival motor neuron and zinc finger protein 1, with whom it co-localizes in sub-nuclear bodies. Despite its ubiquitous expression, mutations in senataxin specifically affect neurons and result in distinct neurodegenerative diseases such as amyotrophic lateral sclerosis type 4 and ataxia with oculomotor apraxia type 2, which are attributed to the gain-of-function and the loss-of-function mutations in senataxin, respectively. In addition, low levels of senataxin (loss-of-function) in spinal muscular atrophy result in the accumulation of R-loops causing DNA damage and motor neuron degeneration. Senataxin may play multiple functions in diverse cellular processes; however, its emerging role in R-loop resolution and maintenance of genomic integrity is gaining attention in the field of neurodegenerative diseases. In this review, we highlight the role of senataxin in R-loop resolution and its potential as a therapeutic target to treat neurodegenerative diseases.
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Affiliation(s)
| | - Shyni Gangadharan Leela
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Dana Branzei
- The AIRC Institute of Molecular Oncology Foundation, IFOM ETS, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia 27100, Italy
| | - Laxman Gangwani
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
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15
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Wulfridge P, Sarma K. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nat Cell Biol 2024; 26:1025-1036. [PMID: 38914786 DOI: 10.1038/s41556-024-01437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
R-loops are three-stranded nucleic acid structures that are abundant and widespread across the genome and that have important physiological roles in many nuclear processes. Their accumulation is observed in cancers and neurodegenerative disorders. Recent studies have implicated a function for R-loops and G-quadruplex (G4) structures, which can form on the displaced single strand of R-loops, in three-dimensional genome organization in both physiological and pathological contexts. Here we discuss the interconnected functions of DNA:RNA hybrids and G4s within R-loops, their impact on DNA repair and gene regulatory networks, and their emerging roles in genome organization during development and disease.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Lee H, Han DW, Yoo S, Kwon O, La H, Park C, Lee H, Kang K, Uhm SJ, Song H, Do JT, Choi Y, Hong K. RNA helicase DEAD-box-5 is involved in R-loop dynamics of preimplantation embryos. Anim Biosci 2024; 37:1021-1030. [PMID: 38419548 PMCID: PMC11065950 DOI: 10.5713/ab.23.0401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/09/2023] [Accepted: 12/07/2023] [Indexed: 03/02/2024] Open
Abstract
OBJECTIVE R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. METHODS In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. RESULTS We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. CONCLUSION These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.
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Affiliation(s)
- Hyeonji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Dong Wook Han
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020,
China
| | - Seonho Yoo
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Ohbeom Kwon
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Heeji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Kiye Kang
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Sang Jun Uhm
- Department of Animal Science, Sangji University, Wonju 26339,
Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
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17
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Liu Z, Ajit K, Wu Y, Zhu WG, Gullerova M. The GATAD2B-NuRD complex drives DNA:RNA hybrid-dependent chromatin boundary formation upon DNA damage. EMBO J 2024; 43:2453-2485. [PMID: 38719994 PMCID: PMC11183058 DOI: 10.1038/s44318-024-00111-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/19/2024] Open
Abstract
Double-strand breaks (DSBs) are the most lethal form of DNA damage. Transcriptional activity at DSBs, as well as transcriptional repression around DSBs, are both required for efficient DNA repair. The chromatin landscape defines and coordinates these two opposing events. However, how the open and condensed chromatin architecture is regulated remains unclear. Here, we show that the GATAD2B-NuRD complex associates with DSBs in a transcription- and DNA:RNA hybrid-dependent manner, to promote histone deacetylation and chromatin condensation. This activity establishes a spatio-temporal boundary between open and closed chromatin, which is necessary for the correct termination of DNA end resection. The lack of the GATAD2B-NuRD complex leads to chromatin hyperrelaxation and extended DNA end resection, resulting in homologous recombination (HR) repair failure. Our results suggest that the GATAD2B-NuRD complex is a key coordinator of the dynamic interplay between transcription and the chromatin landscape, underscoring its biological significance in the RNA-dependent DNA damage response.
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Affiliation(s)
- Zhichao Liu
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom
| | - Kamal Ajit
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom
| | - Yupei Wu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, 518055, Shenzhen, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, 518055, Shenzhen, China
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom.
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18
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Yang H, Lan L. Transcription-coupled DNA repair protects genome stability upon oxidative stress-derived DNA strand breaks. FEBS Lett 2024. [PMID: 38813713 DOI: 10.1002/1873-3468.14938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024]
Abstract
Elevated oxidative stress, which threatens genome stability, has been detected in almost all types of cancers. Cells employ various DNA repair pathways to cope with DNA damage induced by oxidative stress. Recently, a lot of studies have provided insights into DNA damage response upon oxidative stress, specifically in the context of transcriptionally active genomes. Here, we summarize recent studies to help understand how the transcription is regulated upon DNA double strand breaks (DSB) and how DNA repair pathways are selectively activated at the damage sites coupling with transcription. The role of RNA molecules, especially R-loops and RNA modifications during the DNA repair process, is critical for protecting genome stability. This review provides an update on how cells protect transcribed genome loci via transcription-coupled repair pathways.
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Affiliation(s)
- Haibo Yang
- Department of Urology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Li Lan
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
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19
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Xin BG, Huang LY, Yuan LG, Liu NN, Li HH, Ai X, Lei DS, Hou XM, Rety S, Xi XG. Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition. Nucleic Acids Res 2024; 52:3406-3418. [PMID: 38412313 PMCID: PMC11014265 DOI: 10.1093/nar/gkae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary structures and organizing ribonucleoprotein complexes. In our study, we conducted a systematic analysis of the helicase-related activities of Escherichia coli HrpA and presented the structures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP hydrolysis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core plays an essential role in unwinding RNA/RNA and RNA/DNA duplexes, the N-terminal extension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA/DNA duplex unwinding. Importantly, the APHB domain is implicated in binding to non-canonical DNA structures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase complex. This research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a foundation for further investigations into the recognition and functional implications of i-motif DNA structures in various biological processes.
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Affiliation(s)
- Ben-Ge Xin
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ling-Yun Huang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ling-Gang Yuan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hai-Hong Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xia Ai
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dong-Sheng Lei
- School of Physical Science and Technology, Electron Microscopy Centre of Lanzhou University, Lanzhou University, Lanzhou 730000, People's Republic of China
- Key Laboratory of Magnetism and Magnetic Materials of Ministry of Education, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Stephane Rety
- LBMC, ENS de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie F-69364 Lyon, France
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Laboratoirede de Biologie et Pharmacologie Appliquée(LBPA), CNRS UMR8113, ENS Paris-Saclay, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
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20
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Yang S, Zou Q, Liang Y, Zhang D, Peng L, Li W, Li W, Liu M, Tong Y, Chen L, Xu P, Yang Z, Zhou K, Xiao J, Wang H, Yu W. miR-1246 promotes osteosarcoma cell migration via NamiRNA-enhancer network dependent on Argonaute 2. MedComm (Beijing) 2024; 5:e543. [PMID: 38585233 PMCID: PMC10999177 DOI: 10.1002/mco2.543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
High metastatic propensity of osteosarcoma leads to its therapeutic failure and poor prognosis. Although nuclear activation miRNAs (NamiRNAs) are reported to activate gene transcription via targeting enhancer and further promote tumor metastasis, it remains uncertain whether NamiRNAs regulate osteosarcoma metastasis and their exact mechanism. Here, we found that extracellular vesicles of the malignant osteosarcoma cells (143B) remarkably increased the migratory abilities of MNNG cells representing the benign osteosarcoma cells by two folds, which attributed to their high miR-1246 levels. Specially, miR-1246 located in nucleus could activate the migration gene expression (such as MMP1) to accelerate MNNG cell migration through elevating the enhancer activities via increasing H3K27ac enrichment. Instead, MMP1 expression was dramatically inhibited after Argonaute 2 (AGO2) knockdown. Notably, in vitro assays demonstrated that AGO2 recognized the hybrids of miR-1246 and its enhancer DNA via PAZ domains to prevent their degradation from RNase H and these protective roles of AGO2 may favor the gene activation by miR-1246 in vivo. Collectively, our findings suggest that miR-1246 could facilitate osteosarcoma metastasis through interacting with enhancer to activate gene expression dependent on AGO2, highlighting the nuclear AGO2 as a guardian for NamiRNA-targeted gene activation and the potential of miR-1246 for osteosarcoma metastasis therapy.
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Affiliation(s)
- Shuai Yang
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qingping Zou
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Ying Liang
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Centre for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Lina Peng
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Wei Li
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Wenxuan Li
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Mengxing Liu
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Ying Tong
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Lu Chen
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Peng Xu
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhicong Yang
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Kaicheng Zhou
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Jianru Xiao
- Department of Orthopaedic OncologyChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Centre for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Wenqiang Yu
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
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21
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Di Tommaso E, Giunta S. Dynamic interplay between human alpha-satellite DNA structure and centromere functions. Semin Cell Dev Biol 2024; 156:130-140. [PMID: 37926668 DOI: 10.1016/j.semcdb.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Maintenance of genome stability relies on functional centromeres for correct chromosome segregation and faithful inheritance of the genetic information. The human centromere is the primary constriction within mitotic chromosomes made up of repetitive alpha-satellite DNA hierarchically organized in megabase-long arrays of near-identical higher order repeats (HORs). Centromeres are epigenetically specified by the presence of the centromere-specific histone H3 variant, CENP-A, which enables the assembly of the kinetochore for microtubule attachment. Notably, centromeric DNA is faithfully inherited as intact haplotypes from the parents to the offspring without intervening recombination, yet, outside of meiosis, centromeres are akin to common fragile sites (CFSs), manifesting crossing-overs and ongoing sequence instability. Consequences of DNA changes within the centromere are just starting to emerge, with unclear effects on intra- and inter-generational inheritance driven by centromere's essential role in kinetochore assembly. Here, we review evidence of meiotic selection operating to mitigate centromere drive, as well as recent reports on centromere damage, recombination and repair during the mitotic cell division. We propose an antagonistic pleiotropy interpretation to reconcile centromere DNA instability as both driver of aneuploidy that underlies degenerative diseases, while also potentially necessary for the maintenance of homogenized HORs for centromere function. We attempt to provide a framework for this conceptual leap taking into consideration the structural interface of centromere-kinetochore interaction and present case scenarios for its malfunctioning. Finally, we offer an integrated working model to connect DNA instability, chromatin, and structural changes with functional consequences on chromosome integrity.
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Affiliation(s)
- Elena Di Tommaso
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy.
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22
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley TF, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. Nat Commun 2024; 15:1943. [PMID: 38431617 PMCID: PMC10908796 DOI: 10.1038/s41467-024-45947-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
DNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes. RTF2, like RNase H2, is essential for mammalian development and maintains normal replication speed. However, persistent RTF2 and RNase H2 at stalled replication forks prevent efficient replication restart, which is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for RTF2-dependent regulation of replication-coupled ribonucleotide removal and reveal the existence of PRIM1-mediated direct replication restart in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas J Blobel
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Tom F Wiley
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics, The Rockefeller University, New York, NY, 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA.
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23
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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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24
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Zhang J, Chen F, Tang M, Xu W, Tian Y, Liu Z, Shu Y, Yang H, Zhu Q, Lu X, Peng B, Liu X, Xu X, Gullerova M, Zhu WG. The ARID1A-METTL3-m6A axis ensures effective RNase H1-mediated resolution of R-loops and genome stability. Cell Rep 2024; 43:113779. [PMID: 38358891 DOI: 10.1016/j.celrep.2024.113779] [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: 07/12/2023] [Revised: 12/02/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
R-loops are three-stranded structures that can pose threats to genome stability. RNase H1 precisely recognizes R-loops to drive their resolution within the genome, but the underlying mechanism is unclear. Here, we report that ARID1A recognizes R-loops with high affinity in an ATM-dependent manner. ARID1A recruits METTL3 and METTL14 to the R-loop, leading to the m6A methylation of R-loop RNA. This m6A modification facilitates the recruitment of RNase H1 to the R-loop, driving its resolution and promoting DNA end resection at DSBs, thereby ensuring genome stability. Depletion of ARID1A, METTL3, or METTL14 leads to R-loop accumulation and reduced cell survival upon exposure to cytotoxic agents. Therefore, ARID1A, METTL3, and METTL14 function in a coordinated, temporal order at DSB sites to recruit RNase H1 and to ensure efficient R-loop resolution. Given the association of high ARID1A levels with resistance to genotoxic therapies in patients, these findings open avenues for exploring potential therapeutic strategies for cancers with ARID1A abnormalities.
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Affiliation(s)
- Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Ming Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Zhichao Liu
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Yuxin Shu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Hui Yang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Bin Peng
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xingzhi Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China; Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518055, China; School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China; Department of Biochemistry and Molecular Biology, Peking University Health Science Centre, Beijing 100191, China.
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25
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Chiang HC, Qi L, Mitra P, Hu Y, Li R. R-Loop Functions in Brca1 -Associated Mammary Tumorigenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580374. [PMID: 38405919 PMCID: PMC10888925 DOI: 10.1101/2024.02.14.580374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Excessive R-loops, a DNA-RNA hybrid structure, are associated with genome instability and BRCA1 mutation-related breast cancer. Yet the causality of R-loops in tumorigenesis remains unclear. Here we show that R-loop removal by Rnaseh1 overexpression (Rh1-OE) in Brca1 -knockout (BKO) mouse mammary epithelium exacerbates DNA replication stress without affecting homology-directed DNA repair. R-loop removal also diminishes luminal progenitors, the cell of origin for estrogen receptor α (ERα)-negative BKO tumors. However, R-loop reduction does not dampen spontaneous BKO tumor incidence. Rather, it gives rise to a significant percentage of ERα-expressing BKO tumors. Thus, R-loops reshape mammary tumor subtype rather than promoting tumorigenesis.
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26
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Tetzlaff S, Hillebrand A, Drakoulis N, Gluhic Z, Maschmann S, Lyko P, Wicke S, Schmitz-Linneweber C. Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes. eLife 2024; 13:e95407. [PMID: 38363119 PMCID: PMC10948144 DOI: 10.7554/elife.95407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
The mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA from E. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexan Toxoplasma gondii to investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced the T. gondii mitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that the T. gondii genome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis that T. gondii's block-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.
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Affiliation(s)
| | | | | | - Zala Gluhic
- Molecular Genetics, Humboldt University BerlinBerlinGermany
| | | | - Peter Lyko
- Biodiversity and Evolution, Humboldt University BerlinBerlinGermany
| | - Susann Wicke
- Biodiversity and Evolution, Humboldt University BerlinBerlinGermany
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27
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Gómez-González B, Aguilera A. Break-induced RNA-DNA hybrids (BIRDHs) in homologous recombination: friend or foe? EMBO Rep 2023; 24:e57801. [PMID: 37818834 DOI: 10.15252/embr.202357801] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/29/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023] Open
Abstract
Double-strand breaks (DSBs) are the most harmful DNA lesions, with a strong impact on cell proliferation and genome integrity. Depending on cell cycle stage, DSBs are preferentially repaired by non-homologous end joining or homologous recombination (HR). In recent years, numerous reports have revealed that DSBs enhance DNA-RNA hybrid formation around the break site. We call these hybrids "break-induced RNA-DNA hybrids" (BIRDHs) to differentiate them from sporadic R-loops consisting of DNA-RNA hybrids and a displaced single-strand DNA occurring co-transcriptionally in intact DNA. Here, we review and discuss the most relevant data about BIRDHs, with a focus on two main questions raised: (i) whether BIRDHs form by de novo transcription after a DSB or by a pre-existing nascent RNA in DNA regions undergoing transcription and (ii) whether they have a positive role in HR or are just obstacles to HR accidentally generated as an intrinsic risk of transcription. We aim to provide a comprehensive view of the exciting and yet unresolved questions about the source and impact of BIRDHs in the cell.
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Affiliation(s)
- Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Seville, Spain
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28
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Heuzé J, Kemiha S, Barthe A, Vilarrubias AT, Aouadi E, Aiello U, Libri D, Lin Y, Lengronne A, Poli J, Pasero P. RNase H2 degrades toxic RNA:DNA hybrids behind stalled forks to promote replication restart. EMBO J 2023; 42:e113104. [PMID: 37855233 PMCID: PMC10690446 DOI: 10.15252/embj.2022113104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest, and restart in Saccharomyces cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate their chromosomes normally under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Treated cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative intermediate in resuming replication. Similar impairments in nascent DNA resection and ssDNA formation at HU-arrested forks were observed in human cells lacking RNase H2. However, fork resection was fully restored by addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H.
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Affiliation(s)
- Jonathan Heuzé
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Samira Kemiha
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Antoine Barthe
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Alba Torán Vilarrubias
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Elyès Aouadi
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Present address:
Institut de Génétique Moléculaire de MontpellierUniversité de Montpellier, CNRSMontpellierFrance
| | - Yea‐Lih Lin
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Armelle Lengronne
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Jérôme Poli
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Philippe Pasero
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
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29
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Girasol MJ, Krasilnikova M, Marques CA, Damasceno JD, Lapsley C, Lemgruber L, Burchmore R, Beraldi D, Carruthers R, Briggs EM, McCulloch R. RAD51-mediated R-loop formation acts to repair transcription-associated DNA breaks driving antigenic variation in Trypanosoma brucei. Proc Natl Acad Sci U S A 2023; 120:e2309306120. [PMID: 37988471 PMCID: PMC10691351 DOI: 10.1073/pnas.2309306120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/13/2023] [Indexed: 11/23/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of all genomes that intersect with many processes, including transcription, telomere homeostasis, and centromere function. Increasing evidence suggests that RNA-DNA hybrids can provide two conflicting roles in the maintenance and transmission of genomes: They can be the triggers of DNA damage, leading to genome change, or can aid the DNA repair processes needed to respond to DNA lesions. Evasion of host immunity by African trypanosomes, such as Trypanosoma brucei, relies on targeted recombination of silent Variant Surface Glycoprotein (VSG) genes into a specialized telomeric locus that directs transcription of just one VSG from thousands. How such VSG recombination is targeted and initiated is unclear. Here, we show that a key enzyme of T. brucei homologous recombination, RAD51, interacts with RNA-DNA hybrids. In addition, we show that RNA-DNA hybrids display a genome-wide colocalization with DNA breaks and that this relationship is impaired by mutation of RAD51. Finally, we show that RAD51 acts to repair highly abundant, localised DNA breaks at the single transcribed VSG and that mutation of RAD51 alters RNA-DNA hybrid abundance at 70 bp repeats both around the transcribed VSG and across the silent VSG archive. This work reveals a widespread, generalised role for RNA-DNA hybrids in directing RAD51 activity during recombination and uncovers a specialised application of this interplay during targeted DNA break repair needed for the critical T. brucei immune evasion reaction of antigenic variation.
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Affiliation(s)
- Mark John Girasol
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Faculty of the MD-PhD in Molecular Medicine Program, College of Medicine, University of the Philippines Manila, Manila1000, Philippines
| | - Marija Krasilnikova
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Catarina A. Marques
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Jeziel D. Damasceno
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Craig Lapsley
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Leandro Lemgruber
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Richard Burchmore
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Dario Beraldi
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Ross Carruthers
- College of Medical, Veterinary and Life Sciences, School of Cancer Sciences, University of Glasgow, GlasgowG12 0YN, United Kingdom
| | - Emma M. Briggs
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Richard McCulloch
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
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30
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James CD, Youssef A, Prabhakar AT, Otoa R, Witt A, Lewis RL, Bristol ML, Wang X, Zhang K, Li R, Morgan IM. Human Papillomavirus 16 replication converts SAMHD1 into a homologous recombination factor and promotes its recruitment to replicating viral DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566899. [PMID: 38014153 PMCID: PMC10680734 DOI: 10.1101/2023.11.13.566899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
We have demonstrated that SAMHD1 (sterile alpha motif and histidine-aspartic domain HD-containing protein 1) is a restriction factor for the HPV16 life cycle. Here we demonstrate that in HPV negative cervical cancer C33a cells and human foreskin keratinocytes immortalized by HPV16 (HFK+HPV16), SAMHD1 is recruited to E1-E2 replicating DNA. Homologous recombination (HR) factors are required for HPV16 replication and viral replication promotes phosphorylation of SAMHD1, which converts it from a dNTPase to an HR factor independent from E6/E7 expression. A SAMHD1 phosphor-mimic (SAMHD1 T592D) reduces E1-E2 mediated DNA replication in C33a cells and has enhanced recruitment to the replicating DNA. In HFK+HPV16 cells SAMHD1 T592D is recruited to the viral DNA and attenuates cellular growth, but does not attenuate growth in isogenic HFK cells immortalized by E6/E7 alone. SAMHD1 T592D also attenuates the development of viral replication foci following keratinocyte differentiation. The results indicated that enhanced SAMHD1 phosphorylation could be therapeutically beneficial in cells with HPV16 replicating genomes. Protein phosphatase 2A (PP2A) can dephosphorylate SAMHD1 and PP2A function can be inhibited by endothall. We demonstrate that endothall reduces E1-E2 replication and promotes SAMHD1 recruitment to E1-E2 replicating DNA, mimicking the SAMHD1 T592D phenotypes. Finally, we demonstrate that in head and neck cancer cell lines with HPV16 episomal genomes endothall attenuates their growth and promotes recruitment of SAMHD1 to the viral genome. The results suggest that targeting cellular phosphatases has therapeutic potential for the treatment of HPV infections and cancers. Importance Human papillomaviruses are causative agents in around 5% of all human cancers. The development of anti-viral therapeutics depends upon an increased understanding of the viral life cycle. Here we demonstrate that HPV16 replication converts SAMHD1 into an HR factor via phosphorylation. This phosphorylation promotes recruitment of SAMHD1 to viral DNA to assist with replication. A SAMHD1 mutant that mimics phosphorylation is hyper-recruited to viral DNA and attenuates viral replication. Expression of this mutant in HPV16 immortalized cells attenuates the growth of these cells, but not cells immortalized by the viral oncogenes E6/E7 alone. Finally, we demonstrate that the phosphatase inhibitor endothall promotes hyper-recruitment of endogenous SAMHD1 to HPV16 replicating DNA and can attenuate the growth of both HPV16 immortalized human foreskin keratinocytes and HPV16 positive head and neck cancer cell lines. We propose that phosphatase inhibitors represent a novel tool for combating HPV infections and disease.
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31
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Huang Y, Liu B, Sinha SC, Amin S, Gan L. Mechanism and therapeutic potential of targeting cGAS-STING signaling in neurological disorders. Mol Neurodegener 2023; 18:79. [PMID: 37941028 PMCID: PMC10634099 DOI: 10.1186/s13024-023-00672-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023] Open
Abstract
DNA sensing is a pivotal component of the innate immune system that is responsible for detecting mislocalized DNA and triggering downstream inflammatory pathways. Among the DNA sensors, cyclic GMP-AMP synthase (cGAS) is a primary player in detecting cytosolic DNA, including foreign DNA from pathogens and self-DNA released during cellular damage, culminating in a type I interferon (IFN-I) response through stimulator of interferon genes (STING) activation. IFN-I cytokines are essential in mediating neuroinflammation, which is widely observed in CNS injury, neurodegeneration, and aging, suggesting an upstream role for the cGAS DNA sensing pathway. In this review, we summarize the latest developments on the cGAS-STING DNA-driven immune response in various neurological diseases and conditions. Our review covers the current understanding of the molecular mechanisms of cGAS activation and highlights cGAS-STING signaling in various cell types of central and peripheral nervous systems, such as resident brain immune cells, neurons, and glial cells. We then discuss the role of cGAS-STING signaling in different neurodegenerative conditions, including tauopathies, Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, as well as aging and senescence. Finally, we lay out the current advancements in research and development of cGAS inhibitors and assess the prospects of targeting cGAS and STING as therapeutic strategies for a wide spectrum of neurological diseases.
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Affiliation(s)
- Yige Huang
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Bangyan Liu
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Subhash C Sinha
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Sadaf Amin
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Li Gan
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
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Lim G, Hwang S, Yu K, Kang JY, Kang C, Hohng S. Translocating RNA polymerase generates R-loops at DNA double-strand breaks without any additional factors. Nucleic Acids Res 2023; 51:9838-9848. [PMID: 37638763 PMCID: PMC10570047 DOI: 10.1093/nar/gkad689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023] Open
Abstract
The R-loops forming around DNA double-strand breaks (DSBs) within actively transcribed genes play a critical role in the DSB repair process. However, the mechanisms underlying R-loop formation at DSBs remain poorly understood, with diverse proposed models involving protein factors associated with RNA polymerase (RNAP) loading, pausing/backtracking or preexisting transcript RNA invasion. In this single-molecule study using Escherichia coli RNAP, we discovered that transcribing RNAP alone acts as a highly effective DSB sensor, responsible for generation of R-loops upon encountering downstream DSBs, without requiring any additional factors. The R-loop formation efficiency is greatly influenced by DNA end structures, ranging here from 2.8% to 73%, and notably higher on sticky ends with 3' or 5' single-stranded overhangs compared to blunt ends without any overhangs. The R-loops extend unidirectionally upstream from the DSB sites and can reach the transcription start site, interfering with ongoing-round transcription. Furthermore, the extended R-loops can persist and maintain their structures, effectively preventing the efficient initiation of subsequent transcription rounds. Our results are consistent with the bubble extension model rather than the 5'-end invasion model or the middle insertion model. These discoveries provide valuable insights into the initiation of DSB repair on transcription templates across bacteria, archaea and eukaryotes.
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Affiliation(s)
- Gunhyoung Lim
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Seungha Hwang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Kilwon Yu
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Changwon Kang
- Department of Biological Sciences, and KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
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Wang J, Muste Sadurni M, Saponaro M. RNAPII response to transcription-blocking DNA lesions in mammalian cells. FEBS J 2023; 290:4382-4394. [PMID: 35731652 PMCID: PMC10952651 DOI: 10.1111/febs.16561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 09/21/2023]
Abstract
RNA polymerase II moves along genes to decode genetic information stored in the mammalian genome into messenger RNA and different forms of non-coding RNA. However, the transcription process is frequently challenged by DNA lesions caused by exogenous and endogenous insults, among which helix-distorting DNA lesions and double-stranded DNA breaks are particularly harmful for cell survival. In response to such DNA damage, RNA polymerase II transcription is regulated both locally and globally by multi-layer mechanisms, whereas transcription-blocking lesions are repaired before transcription can recover. Failure in DNA damage repair will cause genome instability and cell death. Although recent studies have expanded our understanding of RNA polymerase II regulation confronting DNA lesions, it is still not always clear what the direct contribution of RNA polymerase II is in the DNA damage repair processes. In this review, we focus on how RNA polymerase II and transcription are both repressed by transcription stalling lesions such as DNA-adducts and double strand breaks, as well as how they are actively regulated to support the cellular response to DNA damage and favour the repair of lesions.
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Affiliation(s)
- Jianming Wang
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Martina Muste Sadurni
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Marco Saponaro
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
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Liu C, Wang L, Li Y, Guo M, Hu J, Wang T, Li M, Yang Z, Lin R, Xu W, Chen Y, Luo M, Gao F, Chen JY, Sun Q, Liu H, Sun B, Li W. RNase H1 facilitates recombinase recruitment by degrading DNA-RNA hybrids during meiosis. Nucleic Acids Res 2023; 51:7357-7375. [PMID: 37378420 PMCID: PMC10415156 DOI: 10.1093/nar/gkad524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 05/29/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
DNA-RNA hybrids play various roles in many physiological progresses, but how this chromatin structure is dynamically regulated during spermatogenesis remains largely unknown. Here, we show that germ cell-specific knockout of Rnaseh1, a specialized enzyme that degrades the RNA within DNA-RNA hybrids, impairs spermatogenesis and causes male infertility. Notably, Rnaseh1 knockout results in incomplete DNA repair and meiotic prophase I arrest. These defects arise from the altered RAD51 and DMC1 recruitment in zygotene spermatocytes. Furthermore, single-molecule experiments show that RNase H1 promotes recombinase recruitment to DNA by degrading RNA within DNA-RNA hybrids and allows nucleoprotein filaments formation. Overall, we uncover a function of RNase H1 in meiotic recombination, during which it processes DNA-RNA hybrids and facilitates recombinase recruitment.
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Affiliation(s)
- Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing 100101, China
| | - Liying Wang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yanan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengmeng Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Teng Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengjing Li
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruoyao Lin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wei Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinghong Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengcheng Luo
- Department of Tissue and Embryology, School of Basic Medical Sciences, Wuhan University, Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430072, China
| | - Fei Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hongbin Liu
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Min J, Zhao J, Zagelbaum J, Lee J, Takahashi S, Cummings P, Schooley A, Dekker J, Gottesman ME, Rabadan R, Gautier J. Mechanisms of insertions at a DNA double-strand break. Mol Cell 2023; 83:2434-2448.e7. [PMID: 37402370 PMCID: PMC10527084 DOI: 10.1016/j.molcel.2023.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/06/2023] [Accepted: 06/08/2023] [Indexed: 07/06/2023]
Abstract
Insertions and deletions (indels) are common sources of structural variation, and insertions originating from spontaneous DNA lesions are frequent in cancer. We developed a highly sensitive assay called insertion and deletion sequencing (Indel-seq) to monitor rearrangements in human cells at the TRIM37 acceptor locus that reports indels stemming from experimentally induced and spontaneous genome instability. Templated insertions, which derive from sequences genome wide, require contact between donor and acceptor loci, require homologous recombination, and are stimulated by DNA end-processing. Insertions are facilitated by transcription and involve a DNA/RNA hybrid intermediate. Indel-seq reveals that insertions are generated via multiple pathways. The broken acceptor site anneals with a resected DNA break or invades the displaced strand of a transcription bubble or R-loop, followed by DNA synthesis, displacement, and then ligation by non-homologous end joining. Our studies identify transcription-coupled insertions as a critical source of spontaneous genome instability that is distinct from cut-and-paste events.
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Affiliation(s)
- Jaewon Min
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Junfei Zhao
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jina Lee
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sho Takahashi
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Portia Cummings
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Allana Schooley
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Max E Gottesman
- Department of Biochemistry and Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Raul Rabadan
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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36
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LaMarca EA, Saito A, Plaza-Jennings A, Espeso-Gil S, Hellmich A, Fernando MB, Javidfar B, Liao W, Estill M, Townsley K, Florio A, Ethridge JE, Do C, Tycko B, Shen L, Kamiya A, Tsankova NM, Brennand KJ, Akbarian S. R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549494. [PMID: 37503149 PMCID: PMC10370098 DOI: 10.1101/2023.07.18.549494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
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Affiliation(s)
- Elizabeth A LaMarca
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Amara Plaza-Jennings
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio Espeso-Gil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allyse Hellmich
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla Townsley
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Florio
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - James E Ethridge
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine Do
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Nadejda M Tsankova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Current affiliation: Department of Psychiatry, Yale University, New Haven, CT 06511, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Han W, Li Z, Guo Y, He K, Li W, Xu C, Ge L, He M, Yin X, Zhou J, Li C, Yao D, Bao J, Liang H. Efficient precise integration of large DNA sequences with 3'-overhang dsDNA donors using CRISPR/Cas9. Proc Natl Acad Sci U S A 2023; 120:e2221127120. [PMID: 37216515 PMCID: PMC10235934 DOI: 10.1073/pnas.2221127120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
CRISPR/Cas9 genome-editing tools have tremendously boosted our capability of manipulating the eukaryotic genomes in biomedical research and innovative biotechnologies. However, the current approaches that allow precise integration of gene-sized large DNA fragments generally suffer from low efficiency and high cost. Herein, we developed a versatile and efficient approach, termed LOCK (Long dsDNA with 3'-Overhangs mediated CRISPR Knock-in), by utilizing specially designed 3'-overhang double-stranded DNA (odsDNA) donors harboring 50-nt homology arm. The length of the 3'-overhangs of odsDNA is specified by the five consecutive phosphorothioate modifications. Compared with existing methods, LOCK allows highly efficient targeted insertion of kilobase-sized DNA fragments into the mammalian genomes with low cost and low off-target effects, yielding >fivefold higher knock-in frequencies than conventional homologous recombination-based approaches. This newly designed LOCK approach based on homology-directed repair is a powerful tool suitable for gene-sized fragment integration that is urgently needed for genetic engineering, gene therapies, and synthetic biology.
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Affiliation(s)
- Wenjie Han
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Zhigang Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Yijun Guo
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Kaining He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Wenqing Li
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Caoling Xu
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Lishuang Ge
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Miao He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Xue Yin
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Junxiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Chengxu Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Dongbao Yao
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Jianqiang Bao
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
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38
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Tschage L, Kowarz E, Marschalek R. Model System to Analyze RNA-Mediated DNA Repair in Mammalian Cells. CRISPR J 2023. [PMID: 37200486 DOI: 10.1089/crispr.2022.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
"RNA-templated/directed DNA repair" is a biological mechanism that has been experimentally demonstrated in bacteria, yeast, and mammalian cells. Recent study has shown that small noncoding RNAs (DDRNAs) and/or newly RNAPII transcribed RNAs (dilncRNAs) are orchestrating the initial steps of double-strand break (DSB) repair. In this study, we demonstrate that also pre-mRNA could be used as direct or indirect substrate for DSB repair. Our test system is based on (1) a stably integrated mutant reporter gene that produces constitutively a nonspliceable pre-mRNA, (2) a transiently expressed sgRNA-guided dCas13b::ADAR fusion protein to specifically RNA edit the nonspliceable pre-mRNA, and (3) transiently expressed I-SceI to create a DSB situation to study the effect of spliceable pre-mRNA on DNA repair. Based on our data, the RNA-edited pre-mRNA was used in cis for the DSB repair process, thereby converting the genomically encoded mutant reporter gene into an active reporter gene. Overexpression and knockdown of several cellular proteins were performed to delineate their role in this novel "RNA-mediated end joining" pathway.
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Affiliation(s)
- Lisa Tschage
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany
| | - Eric Kowarz
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany
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39
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Liu C, Xu W, Wang L, Yang Z, Li K, Hu J, Chen Y, Zhang R, Xiao S, Liu W, Wei H, Chen JY, Sun Q, Li W. Dual roles of R-loops in the formation and processing of programmed DNA double-strand breaks during meiosis. Cell Biosci 2023; 13:82. [PMID: 37170281 PMCID: PMC10173651 DOI: 10.1186/s13578-023-01026-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Meiotic recombination is initiated by Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions called hotspots; however, the factor(s) that specify the positions of meiotic DSB hotspots remain unclear. RESULTS Here, we examined the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, during budding yeast meiosis and found that the R-loops were changed dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage and found that these R-loops were associated with meiotic recombination during yeast meiosis. We show that transcription-replication head-on collisions could promote R-loop formation during meiotic DNA replication, and these R-loops are associated with Spo11. Furthermore, meiotic recombination hotspots can be eliminated by reversing the direction of transcription or replication, and reversing both of these directions can reconstitute the hotspots. CONCLUSIONS Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication.
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Affiliation(s)
- Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Liying Wang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yinghong Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruidan Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sai Xiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenwen Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huafang Wei
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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40
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Gong D, Wang L, Zhou H, Gao J, Zhang W, Zheng P. Long noncoding RNA Lnc530 localizes on R-loops and regulates R-loop formation and genomic stability in mouse embryonic stem cells. Stem Cell Reports 2023; 18:952-968. [PMID: 36931280 PMCID: PMC10147553 DOI: 10.1016/j.stemcr.2023.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023] Open
Abstract
Embryonic stem cells (ESCs) are superior to differentiated cells to maintain genome stability, but the underlying mechanisms remain largely elusive. R-loops are constantly formed during transcription and are inducers of DNA damage if not resolved. Here we report that mouse ESCs (mESCs) can efficiently prevent unscheduled R-loop formation, and a long noncoding RNA Lnc530 plays regulatory role. Lnc530 is expressed in mESCs and localizes on R-loops. Depletion of Lnc530 in mESCs causes R-loop accumulation and DNA damage, whereas forced expression of Lnc530 in differentiated cells suppresses the R-loop formation. Mechanistically, Lnc530 associates with DDX5 and TDP-43 in an inter-dependent manner on R-loops. Formation of Lnc530-DDX5-TDP-43 complex substantially increases the local protein levels of DDX5 and TDP-43, both of which play critical roles in R-loop regulation. This study uncovers an efficient strategy to prevent R-loop accumulation and preserve genomic stability in mESCs and possibly other stem cell types.
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Affiliation(s)
- Daohua Gong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; University of Chinese Academy of Sciences, Beijing 101408, China; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China.
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41
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Refaat AM, Nakata M, Husain A, Kosako H, Honjo T, Begum NA. HNRNPU facilitates antibody class-switch recombination through C-NHEJ promotion and R-loop suppression. Cell Rep 2023; 42:112284. [PMID: 36943867 DOI: 10.1016/j.celrep.2023.112284] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/23/2022] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
B cells generate functionally different classes of antibodies through class-switch recombination (CSR), which requires classical non-homologous end joining (C-NHEJ) to join the DNA breaks at the donor and acceptor switch (S) regions. We show that the RNA-binding protein HNRNPU promotes C-NHEJ-mediated S-S joining through the 53BP1-shieldin DNA-repair complex. Notably, HNRNPU binds to the S region RNA/DNA G-quadruplexes, contributing to regulating R-loop and single-stranded DNA (ssDNA) accumulation. HNRNPU is an intrinsically disordered protein that interacts with both C-NHEJ and R-loop complexes in an RNA-dependent manner. Strikingly, recruitment of HNRNPU and the C-NHEJ factors is highly sensitive to liquid-liquid phase separation inhibitors, suggestive of DNA-repair condensate formation. We propose that HNRNPU facilitates CSR by forming and stabilizing the C-NHEJ ribonucleoprotein complex and preventing excessive R-loop accumulation, which otherwise would cause persistent DNA breaks and aberrant DNA repair, leading to genomic instability.
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Affiliation(s)
- Ahmed M Refaat
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Mikiyo Nakata
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Afzal Husain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Hidetaka Kosako
- Division of Cell Signaling, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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42
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Pires VB, Lohner N, Wagner T, Wagner CB, Wilkens M, Hajikazemi M, Paeschke K, Butter F, Luke B. RNA-DNA hybrids prevent resection at dysfunctional telomeres. Cell Rep 2023; 42:112077. [PMID: 36729832 DOI: 10.1016/j.celrep.2023.112077] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/19/2022] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
At critically short telomeres, stabilized TERRA RNA-DNA hybrids drive homology-directed repair (HDR) to delay replicative senescence. However, even at long- and intermediate-length telomeres, not subject to HDR, transient TERRA RNA-DNA hybrids form, suggestive of additional roles. We report that telomeric RNA-DNA hybrids prevent Exo1-mediated resection when telomeres become non-functional. We used the well-characterized cdc13-1 allele, where telomere resection can be induced in a temperature-dependent manner, to demonstrate that ssDNA generation at telomeres is either prevented or augmented when RNA-DNA hybrids are stabilized or destabilized, respectively. The viability of cdc13-1 cells is affected by the presence or absence of hybrids accordingly. Telomeric hybrids do not affect the shortening rate of bulk telomeres. We suggest that TERRA hybrids require dynamic regulation to drive HDR at short telomeres; hybrid presence may initiate HDR through replication stress, whereby their removal allows strand resection.
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Affiliation(s)
- Vanessa Borges Pires
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal; Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Nina Lohner
- Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany; Faculty of Biology, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Tina Wagner
- Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Carolin B Wagner
- Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Maya Wilkens
- Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Mona Hajikazemi
- Clinic of Internal Medicine III, Oncology, Haematology, Rheumatology and Clinical Immunology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Clinic of Internal Medicine III, Oncology, Haematology, Rheumatology and Clinical Immunology, University Hospital Bonn, 53127 Bonn, Germany
| | - Falk Butter
- Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany; Faculty of Biology, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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43
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RNA:DNA hybrids from Okazaki fragments contribute to establish the Ku-mediated barrier to replication-fork degradation. Mol Cell 2023; 83:1061-1074.e6. [PMID: 36868227 DOI: 10.1016/j.molcel.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/09/2022] [Accepted: 02/04/2023] [Indexed: 03/05/2023]
Abstract
Nonhomologous end-joining (NHEJ) factors act in replication-fork protection, restart, and repair. Here, we identified a mechanism related to RNA:DNA hybrids to establish the NHEJ factor Ku-mediated barrier to nascent strand degradation in fission yeast. RNase H activities promote nascent strand degradation and replication restart, with a prominent role of RNase H2 in processing RNA:DNA hybrids to overcome the Ku barrier to nascent strand degradation. RNase H2 cooperates with the MRN-Ctp1 axis to sustain cell resistance to replication stress in a Ku-dependent manner. Mechanistically, the need of RNaseH2 in nascent strand degradation requires the primase activity that allows establishing the Ku barrier to Exo1, whereas impairing Okazaki fragment maturation reinforces the Ku barrier. Finally, replication stress induces Ku foci in a primase-dependent manner and favors Ku binding to RNA:DNA hybrids. We propose a function for the RNA:DNA hybrid originating from Okazaki fragments in controlling the Ku barrier specifying nuclease requirement to engage fork resection.
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44
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Eghbalsaied S, Kues WA. CRISPR/Cas9-mediated targeted knock-in of large constructs using nocodazole and RNase HII. Sci Rep 2023; 13:2690. [PMID: 36792645 PMCID: PMC9931768 DOI: 10.1038/s41598-023-29789-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
On-target integration of large cassettes via homology-directed repair (HDR) has several applications. However, the HDR-mediated targeted knock-in suffered from low efficiency. In this study, we made several large plasmids (12.1-13.4 kb) which included the CRISPR/Cas9 system along with a puromycin transgene as part of the large DNA donor (5.3-7.1 kb insertion cassettes) and used them to evaluate their targeted integration efficiency into a transgenic murine embryonic fibroblast (MEF) cell line carrying a single copy of a Venus transgene. We established a detection assay by which HDR events could be discriminated from the error-prone non-homologous end-joining (NHEJ) events. Improving the plasmid quality could considerably leverage the cell toxicity impediment of large plasmids. The use of the TILD (targeted integration with linearized dsDNA) cassettes did not improve the HDR rate compared to the circular plasmids. However, the direct inclusion of nocodazole into the electroporation solution significantly improved the HDR rate. Also, simultaneous delivery of RNase HII and the donor plasmids into the electroporated cells considerably improved the HDR events. In conclusion, the results of this study showed that using cell synchronization reagents in the electroporation medium can efficiently induce HDR rate in the mammalian genome.
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Affiliation(s)
- Shahin Eghbalsaied
- grid.417834.dBiotechnology/Stem Cell Physiology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Höltystr. 10, 31535 Neustadt, Germany ,grid.411463.50000 0001 0706 2472Department of Animal Science, Isfahan (Khorasgan) Branch, Islamic Azad University, Tehran, Iran ,grid.1008.90000 0001 2179 088XSchool of Biosciences, Royal Parade, The University of Melbourne, Melbourne, VIC Australia
| | - Wilfried A. Kues
- grid.417834.dBiotechnology/Stem Cell Physiology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Höltystr. 10, 31535 Neustadt, Germany
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45
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MDC1 maintains active elongation complexes of RNA polymerase II. Cell Rep 2023; 42:111979. [PMID: 36640322 DOI: 10.1016/j.celrep.2022.111979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 10/04/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
The role of MDC1 in the DNA damage response has been extensively studied; however, its impact on other cellular processes is not well understood. Here, we describe the role of MDC1 in transcription as a regulator of RNA polymerase II (RNAPII). Depletion of MDC1 causes a genome-wide reduction in the abundance of actively engaged RNAPII elongation complexes throughout the gene body of protein-encoding genes under unperturbed conditions. Decreased engaged RNAPII subsequently alters the assembly of the spliceosome complex on chromatin, leading to changes in pre-mRNA splicing. Mechanistically, the S/TQ domain of MDC1 modulates RNAPII-mediated transcription. Upon genotoxic stress, MDC1 promotes the abundance of engaged RNAPII complexes at DNA breaks, thereby stimulating nascent transcription at the damaged sites. Of clinical relevance, cancer cells lacking MDC1 display hypersensitivity to RNAPII inhibitors. Overall, we unveil a role of MDC1 in RNAPII-mediated transcription with potential implications for cancer treatment.
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46
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Emerging role for R-loop formation in hepatocellular carcinoma. Genes Genomics 2023; 45:543-551. [PMID: 36635460 DOI: 10.1007/s13258-022-01360-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
The pathophysiological characteristics of hepatocellular carcinoma (HCC) is closely associated with genomic instability. Genomic instability has long been considered to be a hallmark of both human genetic disease and cancers. It is now well accepted that regulating R-loop formation to minimized levels is one of critical modulation to maintain genome integrity, and that improper regulation of R-loop metabolism causes genomic instability via DNA breakage, ultimately resulting in replicative senescence and even tumorigenesis. Given that R-loop is natural by-product formed during normal transcription condition, and that several types of cancer have defense mechanism against the genomic instability resulted from R-loop formation, modulating functional implication of proteins involved in the intrinsic and specific mechanisms of abnormal R-loop formation in cancers therefore could play an important part in appropriated therapeutic strategies for HCC cohorts. In this review, we highlight the latest understanding on how R-loops promote genomic instability and address how alterations in these pathways link to human HCC.
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47
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Jia X, Li Y, Wang T, Bi L, Guo L, Chen Z, Zhang X, Ye S, Chen J, Yang B, Sun B. Discrete RNA-DNA hybrid cleavage by the EXD2 exonuclease pinpoints two rate-limiting steps. EMBO J 2023; 42:e111703. [PMID: 36326837 PMCID: PMC9811613 DOI: 10.15252/embj.2022111703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
EXD2 is a recently identified exonuclease that cleaves RNA and DNA in double-stranded (ds) forms. It thus serves as a model system for investigating the similarities and discrepancies between exoribonuclease and exodeoxyribonuclease activities and for understanding the nucleic acid (NA) unwinding-degradation coordination of an exonuclease. Here, using a single-molecule fluorescence resonance energy transfer (smFRET) approach, we show that despite stable binding to both substrates, EXD2 barely cleaves dsDNA and yet displays both exoribonuclease and exodeoxyribonuclease activities toward RNA-DNA hybrids with a cleavage preference for RNA. Unexpectedly, EXD2-mediated hybrid cleavage proceeds in a discrete stepwise pattern, wherein a sudden 4-bp duplex unwinding increment and the subsequent dwell constitute a complete hydrolysis cycle. The relatively weak exodeoxyribonuclease activity of EXD2 partially originates from frequent hybrid rewinding. Importantly, kinetic analysis and comparison of the dwell times under varied conditions reveal two rate-limiting steps of hybrid unwinding and nucleotide excision. Overall, our findings help better understand the cellular functions of EXD2, and the cyclic coupling between duplex unwinding and exonucleolytic degradation may be generalizable to other exonucleases.
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Affiliation(s)
- Xinshuo Jia
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yanan Li
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Teng Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Ziting Chen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Shasha Ye
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Present address:
ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Jia Chen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Bei Yang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghaiChina
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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48
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Sharma R, Patelli AS, Bruin LD, Maddocks JH. cgNA+web : A visual interface to the cgNA+ sequence-dependent statistical mechanics model of double-stranded nucleic acids. J Mol Biol 2023. [DOI: 10.1016/j.jmb.2023.167978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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49
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Hodson C, van Twest S, Dylewska M, O'Rourke JJ, Tan W, Murphy VJ, Walia M, Abbouche L, Nieminuszczy J, Dunn E, Bythell-Douglas R, Heierhorst J, Niedzwiedz W, Deans AJ. Branchpoint translocation by fork remodelers as a general mechanism of R-loop removal. Cell Rep 2022; 41:111749. [PMID: 36476850 DOI: 10.1016/j.celrep.2022.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Co-transcriptional R loops arise from stalling of RNA polymerase, leading to the formation of stable DNA:RNA hybrids. Unresolved R loops promote genome instability but are counteracted by helicases and nucleases. Here, we show that branchpoint translocases are a third class of R-loop-displacing enzyme in vitro. In cells, deficiency in the Fanconi-anemia-associated branchpoint translocase FANCM causes R-loop accumulation, particularly after treatment with DNA:RNA-hybrid-stabilizing agents. This correlates with FANCM localization at R-loop-prone regions of the genome. Moreover, other branchpoint translocases associated with human disease, such as SMARCAL1 and ZRANB3, and those from lower organisms can also remove R loops in vitro. Branchpoint translocases are more potent than helicases in resolving R loops, indicating their evolutionary important role in R-loop suppression. In human cells, FANCM, SMARCAL1, and ZRANB3 depletion causes additive effects on R-loop accumulation and DNA damage. Our work reveals a mechanistic basis for R-loop displacement that is linked to genome stability.
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Affiliation(s)
- Charlotte Hodson
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Julienne J O'Rourke
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Winnie Tan
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Mannu Walia
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Lara Abbouche
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Elyse Dunn
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Jörg Heierhorst
- Department of Medicine (St Vincent's Health), University of Melbourne, Fitzroy, VIC 3065, Australia; Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine (St Vincent's Health), University of Melbourne, Fitzroy, VIC 3065, Australia.
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50
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Zhou J, Zhang W, Sun Q. R-loop: The new genome regulatory element in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2275-2289. [PMID: 36223078 DOI: 10.1111/jipb.13383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
An R-loop is a three-stranded chromatin structure that consists of a displaced single strand of DNA and an RNA:DNA hybrid duplex, which was thought to be a rare by-product of transcription. However, recent genome-wide data have shown that R-loops are widespread and pervasive in a variety of genomes, and a growing body of experimental evidence indicates that R-loops have both beneficial and harmful effects on an organism. To maximize benefit and avoid harm, organisms have evolved several means by which they tightly regulate R-loop levels. Here, we summarize our current understanding of the biogenesis and effects of R-loops, the mechanisms that regulate them, and methods of R-loop profiling, reviewing recent research advances on R-loops in plants. Furthermore, we provide perspectives on future research directions for R-loop biology in plants, which might lead to a more comprehensive understanding of R-loop functions in plant genome regulation and contribute to future agricultural improvements.
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Affiliation(s)
- Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
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