1
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D'Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. Nat Commun 2024; 15:5859. [PMID: 38997286 PMCID: PMC11245487 DOI: 10.1038/s41467-024-49905-7] [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: 11/05/2023] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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2
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Marshall S, Navarro MVAS, Ascenҫão CFR, Dibitetto D, Smolka MB. In-Depth Mapping of DNA-PKcs Signaling Uncovers Non-Canonical Features of Its Kinase Specificity. J Biol Chem 2024:107513. [PMID: 38945450 DOI: 10.1016/j.jbc.2024.107513] [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: 01/30/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024] Open
Abstract
DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via non-homologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation, and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a non-canonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Sequence and structural analyses of the DNA-PKcs substrate recognition pocket revealed unique features compared to closely related PIKK kinases that may explain its broader substrate preference. These findings expand the repertoire of DNA-PKcs and ATM substrates while establishing a novel preferential phosphorylation motif for DNA-PKcs.
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Affiliation(s)
- Shannon Marshall
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcos V A S Navarro
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; IFSC Institute of Physics of São Carlos, University of São Paulo, São Carlos - SP, 13566-590, Brazil.
| | - Carolline F R Ascenҫão
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Diego Dibitetto
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milan, Italy
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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3
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Manguso N, Kim M, Joshi N, Al Mahmud MR, Aldaco J, Suzuki R, Cortes-Ledesma F, Cui X, Yamada S, Takeda S, Giuliano A, You S, Tanaka H. TDP2 is a regulator of estrogen-responsive oncogene expression. NAR Cancer 2024; 6:zcae016. [PMID: 38596431 PMCID: PMC11000318 DOI: 10.1093/narcan/zcae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 02/19/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
With its ligand estrogen, the estrogen receptor (ER) initiates a global transcriptional program, promoting cell growth. This process involves topoisomerase 2 (TOP2), a key protein in resolving topological issues during transcription by cleaving a DNA duplex, passing another duplex through the break, and repairing the break. Recent studies revealed the involvement of various DNA repair proteins in the repair of TOP2-induced breaks, suggesting potential alternative repair pathways in cases where TOP2 is halted after cleavage. However, the contribution of these proteins in ER-induced transcriptional regulation remains unclear. We investigated the role of tyrosyl-DNA phosphodiesterase 2 (TDP2), an enzyme for the removal of halted TOP2 from the DNA ends, in the estrogen-induced transcriptome using both targeted and global transcription analyses. MYC activation by estrogen, a TOP2-dependent and transient event, became prolonged in the absence of TDP2 in both TDP2-deficient cells and mice. Bulk and single-cell RNA-seq analyses defined MYC and CCND1 as oncogenes whose estrogen response is tightly regulated by TDP2. These results suggest that TDP2 may inherently participate in the repair of estrogen-induced breaks at specific genomic loci, exerting precise control over oncogenic gene expression.
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Affiliation(s)
- Nicholas Manguso
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Minhyung Kim
- Department of Urology and Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Neeraj Joshi
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Md Rasel Al Mahmud
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Juan Aldaco
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Ryusuke Suzuki
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Felipe Cortes-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Xiaojiang Cui
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Shintaro Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Armando Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Sungyong You
- Department of Urology and Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
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4
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Guo X, Wang J, Wu Y, Zhu X, Xu L. Renal aging and mitochondrial quality control. Biogerontology 2024; 25:399-414. [PMID: 38349436 DOI: 10.1007/s10522-023-10091-6] [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: 11/08/2023] [Accepted: 12/29/2023] [Indexed: 06/01/2024]
Abstract
Mitochondria are dynamic organelles that participate in different cellular process that control metabolism, cell division, and survival, and the kidney is one of the most metabolically active organs that contains abundant mitochondria. Perturbations in mitochondrial homeostasis in the kidney can accelerate kidney aging, and maintaining mitochondrial homeostasis can effectively delay aging in the kidney. Kidney aging is a degenerative process linked to detrimental processes. The significance of aberrant mitochondrial homeostasis in renal aging has received increasing attention. However, the contribution of mitochondrial quality control (MQC) to renal aging has not been reviewed in detail. Here, we generalize the current factors contributing to renal aging, review the alterations in MQC during renal injury and aging, and analyze the relationship between mitochondria and intrinsic renal cells. We also introduce MQC in the context of renal aging, and discuss the study of mitochondria in the intrinsic cells of the kidney, which is the innovation of our paper. In addition, during kidney injury and repair, the specific functions and regulatory mechanisms of MQC systems in resident and circulating cell types remain unclear. Currently, most of the studies we reviewed are based on animal and cellular models, the relationship between renal tissue aging and mitochondria has not been adequately investigated in clinical studies, and there is still a long way to go.
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Affiliation(s)
- Xiuli Guo
- Department of Laboratory, The First Hospital of China Medical University, Shenyang, China
| | - Jiao Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yinjie Wu
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, China
| | - Xinwang Zhu
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Li Xu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524003, Guangdong, People's Republic of China.
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5
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Seasons GM, Pellow C, Kuipers HF, Pike GB. Ultrasound and neuroinflammation: immune modulation via the heat shock response. Theranostics 2024; 14:3150-3177. [PMID: 38855178 PMCID: PMC11155413 DOI: 10.7150/thno.96270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Current pharmacological therapeutic approaches targeting chronic inflammation exhibit transient efficacy, often with adverse effects, limiting their widespread use - especially in the context of neuroinflammation. Effective interventions require the consideration of homeostatic function, pathway dysregulation, and pleiotropic effects when evaluating therapeutic targets. Signalling molecules have multiple functions dependent on the immune context, and this complexity results in therapeutics targeting a single signalling molecule often failing in clinical translation. Additionally, the administration of non-physiologic levels of neurotrophic or anti-inflammatory factors can alter endogenous signalling, resulting in unanticipated effects. Exacerbating these challenges, the central nervous system (CNS) is isolated by the blood brain barrier (BBB), restricting the infiltration of many pharmaceutical compounds into the brain tissue. Consequently, there has been marked interest in therapeutic techniques capable of modulating the immune response in a pleiotropic manner; ultrasound remains on this frontier. While ultrasound has been used therapeutically in peripheral tissues - accelerating healing in wounds, bone fractures, and reducing inflammation - it is only recently that it has been applied to the CNS. The transcranial application of low intensity pulsed ultrasound (LIPUS) has successfully mitigated neuroinflammation in vivo, in models of neurodegenerative disease across a broad spectrum of ultrasound parameters. To date, the underlying biological effects and signalling pathways modulated by ultrasound are poorly understood, with a diverse array of reported molecules implicated. The distributed nature of the beneficial response to LIPUS implies the involvement of an, as yet, undetermined upstream signalling pathway, homologous to the protective effect of febrile range hyperthermia in chronic inflammation. As such, we review the heat shock response (HSR), a protective signalling pathway activated by thermal and mechanical stress, as the possible upstream regulator of the anti-inflammatory effects of ultrasound.
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Affiliation(s)
- Graham M. Seasons
- Hotchkiss Brain Institute, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
| | - Carly Pellow
- Hotchkiss Brain Institute, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Radiology, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
| | - Hedwich F. Kuipers
- Hotchkiss Brain Institute, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
- Department of Cell Biology & Anatomy, Hotchkiss Brain Institute and Snyder Institute for Chronic Diseases, University of Calgary, Alberta, T2N 1N4, Canada
| | - G. Bruce Pike
- Hotchkiss Brain Institute, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
- Department of Radiology, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
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6
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D’Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592422. [PMID: 38746145 PMCID: PMC11092767 DOI: 10.1101/2024.05.05.592422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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7
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Cao H, Deng B, Song T, Lian J, Xia L, Chu X, Zhang Y, Yang F, Wang C, Cai Y, Diao Y, Kapranov P. Genome-wide profiles of DNA damage represent highly accurate predictors of mammalian age. Aging Cell 2024; 23:e14122. [PMID: 38391092 PMCID: PMC11113270 DOI: 10.1111/acel.14122] [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: 10/29/2023] [Revised: 01/18/2024] [Accepted: 02/11/2024] [Indexed: 02/24/2024] Open
Abstract
The identification of novel age-related biomarkers represents an area of intense research interest. Despite multiple studies associating DNA damage with aging, there is a glaring paucity of DNA damage-based biomarkers of age, mainly due to the lack of precise methods for genome-wide surveys of different types of DNA damage. Recently, we developed two techniques for genome-wide mapping of the most prevalent types of DNA damage, single-strand breaks and abasic sites, with nucleotide-level resolution. Herein, we explored the potential of genomic patterns of DNA damage identified by these methods as a source of novel age-related biomarkers using mice as a model system. Strikingly, we found that models based on genomic patterns of either DNA lesion could accurately predict age with higher precision than the commonly used transcriptome analysis. Interestingly, the informative patterns were limited to relatively few genes and the DNA damage levels were positively or negatively correlated with age. These findings show that previously unexplored high-resolution genomic patterns of DNA damage contain useful information that can contribute significantly to both practical applications and basic science.
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Affiliation(s)
- Huifen Cao
- Institute of Genomics, School of MedicineHuaqiao UniversityXiamenChina
| | - Bolin Deng
- Institute of Genomics, School of MedicineHuaqiao UniversityXiamenChina
| | - Tianrong Song
- Institute of Genomics, School of MedicineHuaqiao UniversityXiamenChina
| | - Jiabian Lian
- Department of Clinical Laboratorythe First Affiliated Hospital of Xiamen UniversityXiamenChina
| | - Lu Xia
- Xiamen Cell Therapy Research Centerthe First Affiliated Hospital of Xiamen UniversityXiamenChina
| | | | - Yufei Zhang
- Institute of Genomics, School of MedicineHuaqiao UniversityXiamenChina
| | - Fujian Yang
- Institute of Genomics, School of MedicineHuaqiao UniversityXiamenChina
| | - Chunlian Wang
- Institute of Genomics, School of MedicineHuaqiao UniversityXiamenChina
| | - Ye Cai
- Institute of Genomics, School of MedicineHuaqiao UniversityXiamenChina
| | - Yong Diao
- Institute of Genomics, School of MedicineHuaqiao UniversityXiamenChina
| | - Philipp Kapranov
- State Key Laboratory of Cellular Stress Biology, School of Life SciencesXiamen UniversityXiamenChina
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8
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Cao H, Zhang Y, Song T, Xia L, Cai Y, Kapranov P. Common occurrence of hotspots of single strand DNA breaks at transcriptional start sites. BMC Genomics 2024; 25:368. [PMID: 38622509 PMCID: PMC11017599 DOI: 10.1186/s12864-024-10284-4] [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: 12/28/2023] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND We recently developed two high-resolution methods for genome-wide mapping of two prominent types of DNA damage, single-strand DNA breaks (SSBs) and abasic (AP) sites and found highly complex and non-random patterns of these lesions in mammalian genomes. One salient feature of SSB and AP sites was the existence of single-nucleotide hotspots for both lesions. RESULTS In this work, we show that SSB hotspots are enriched in the immediate vicinity of transcriptional start sites (TSSs) in multiple normal mammalian tissues, however the magnitude of enrichment varies significantly with tissue type and appears to be limited to a subset of genes. SSB hotspots around TSSs are enriched on the template strand and associate with higher expression of the corresponding genes. Interestingly, SSB hotspots appear to be at least in part generated by the base-excision repair (BER) pathway from the AP sites. CONCLUSIONS Our results highlight complex relationship between DNA damage and regulation of gene expression and suggest an exciting possibility that SSBs at TSSs might function as sensors of DNA damage to activate genes important for DNA damage response.
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Affiliation(s)
- Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Yufei Zhang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Tianrong Song
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Lu Xia
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, 361000, Xiamen, China
| | - Ye Cai
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Philipp Kapranov
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, 361102, Xiamen, China.
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9
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Drake DM, Afsharian K, Or B, Shapiro AM, Lai ML, Miller L, Wells PG. BRCA1 protein dose-dependent risk for embryonic oxidative DNA damage, embryopathies and neurodevelopmental disorders with and without ethanol exposure. Redox Biol 2024; 70:103070. [PMID: 38359745 PMCID: PMC10877410 DOI: 10.1016/j.redox.2024.103070] [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: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Although widely known as a tumor suppressor, the breast cancer 1 susceptibility protein (BRCA1) is also important in development, where it regulates fetal DNA repair pathways that protect against DNA damage caused by physiological and drug-enhanced levels of reactive oxygen species (ROS). We previously showed that conditional heterozygous (+/-) knockout (cKO) mouse embryos with a minor 28% BRCA1 deficiency developed normally in culture, but when exposed to the ROS-initiating drug, alcohol (ethanol, EtOH), exhibited embryopathies not evident in wild-type (+/+) littermates. Herein, we characterized a directBrca1 +/- knockout (KO) model with a 2-fold greater (58%) reduction in BRCA1 protein vs. the cKO model. We also characterized and compared learning & memory deficits in both the cKO and KO models. Even saline-exposed Brca1 +/- vs. +/+ KO progeny exhibited enhanced oxidative DNA damage and embryopathies in embryo culture and learning & memory deficits in females in vivo, which were not observed in the cKO model, revealing the potential pathogenicity of physiological ROS levels. The embryopathic EtOH concentration for cultured direct KO embryos was half that for cKO embryos, and EtOH affected Brca1 +/+ embryos only in the direct KO model. The spectrum and severity of EtOH embryopathies in culture were greater in both Brca1 +/- vs. +/+ embryos, and direct KO vs. cKO +/- embryos. Motor coordination deficits were evident in both male and female Brca1 +/- KO progeny exposed in utero to EtOH. The results in our direct KO model with a greater BRCA1 deficiency vs. cKO mice provide the first evidence for BRCA1 protein dose-dependent susceptibility to developmental disorders caused by physiological and drug-enhanced oxidative stress.
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Affiliation(s)
- Danielle M Drake
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Kian Afsharian
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Or
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aaron M Shapiro
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Michelle L Lai
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lutfiya Miller
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Peter G Wells
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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10
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Jeong J, Kang BH, Ju S, Park NY, Kim D, Dinh NTB, Lee J, Rhee CY, Cho DH, Kim H, Chung DK, Bunch H. Lactiplantibacillus plantarum K8 lysates regulate hypoxia-induced gene expression. Sci Rep 2024; 14:6275. [PMID: 38491188 PMCID: PMC10943017 DOI: 10.1038/s41598-024-56958-7] [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: 07/19/2023] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
Hypoxic responses have been implicated in critical pathologies, including inflammation, immunity, and tumorigenesis. Recently, efforts to identify effective natural remedies and health supplements are increasing. Previous studies have reported that the cell lysates and the cell wall-bound lipoteichoic acids of Lactiplantibacillus plantarum K8 (K8) exert anti-inflammatory and immunomodulative effects. However, the effect of K8 on cellular hypoxic responses remains unknown. In this study, we found that K8 lysates had a potent suppressive effect on gene expression under hypoxia. K8 lysates markedly downregulated hypoxia-induced HIF1α accumulation in the human bone marrow and lung cancer cell lines, SH-SY5Y and H460. Consequently, the transcription of known HIF1α target genes, such as p21, GLUT1, and ALDOC, was notably suppressed in the K8 lysate supplement and purified lipoteichoic acids of K8, upon hypoxic induction. Intriguingly, K8 lysates decreased the expression of PHD2 and VHL proteins, which are responsible for HIF1α destabilization under normoxic conditions, suggesting that K8 may regulate HIF1α stability in a non-canonical pathway. Overall, our results suggest that K8 lysates desensitize the cells to hypoxic stresses and suppress HIF1α-mediated hypoxic gene activation.
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Affiliation(s)
- Jaehyeon Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Byeong-Hee Kang
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sangmin Ju
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Na Yeon Park
- School of Life Sciences, BK21 FOUR KNU Creative BioRearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Deukyeong Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ngoc Thi Bao Dinh
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jeongho Lee
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Chang Yun Rhee
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dong-Hyung Cho
- School of Life Sciences, BK21 FOUR KNU Creative BioRearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hangeun Kim
- Research and Development Center, Skin Biotechnology Center Co. Ltd., Yongin, 17104, Republic of Korea
| | - Dae Kyun Chung
- Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Heeyoun Bunch
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
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11
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Abugable AA, Antar S, El-Khamisy SF. Chromosomal single-strand break repair and neurological disease: Implications on transcription and emerging genomic tools. DNA Repair (Amst) 2024; 135:103629. [PMID: 38266593 DOI: 10.1016/j.dnarep.2024.103629] [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: 10/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Cells are constantly exposed to various sources of DNA damage that pose a threat to their genomic integrity. One of the most common types of DNA breaks are single-strand breaks (SSBs). Mutations in the repair proteins that are important for repairing SSBs have been reported in several neurological disorders. While several tools have been utilised to investigate SSBs in cells, it was only through recent advances in genomics that we are now beginning to understand the architecture of the non-random distribution of SSBs and their impact on key cellular processes such as transcription and epigenetic remodelling. Here, we discuss our current understanding of the genome-wide distribution of SSBs, their link to neurological disorders and summarise recent technologies to investigate SSBs at the genomic level.
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Affiliation(s)
- Arwa A Abugable
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Sarah Antar
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Sherif F El-Khamisy
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, UK.
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12
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Segev A, Heady L, Crewe M, Madabhushi R. Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome. Cell Rep 2024; 43:113809. [PMID: 38377005 PMCID: PMC11064056 DOI: 10.1016/j.celrep.2024.113809] [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: 03/20/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
We trapped catalytically engaged topoisomerase IIβ (TOP2B) in covalent DNA cleavage complexes (TOP2Bccs) and mapped their positions genome-wide in cultured mouse cortical neurons. We report that TOP2Bcc distribution varies with both nucleosome and compartmental chromosome organization. While TOP2Bccs in gene bodies correlate with their level of transcription, highly expressed genes that lack the usually associated chromatin marks, such as H3K36me3, show reduced TOP2Bccs, suggesting that histone posttranslational modifications regulate TOP2B activity. Promoters with high RNA polymerase II occupancy show elevated TOP2B chromatin immunoprecipitation sequencing signals but low TOP2Bccs, indicating that TOP2B catalytic engagement is curtailed at active promoters. Surprisingly, either poisoning or inhibiting TOP2B increases nascent transcription at most genes and enhancers but reduces transcription within long genes. These effects are independent of transcript length and instead correlate with the presence of intragenic enhancers. Together, these results clarify how cells modulate the catalytic engagement of topoisomerases to affect transcription.
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Affiliation(s)
- Amir Segev
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lance Heady
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Morgan Crewe
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ram Madabhushi
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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13
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Terrón-Bautista J, Martínez-Sánchez MDM, López-Hernández L, Vadusevan AA, García-Domínguez M, Williams RS, Aguilera A, Millán-Zambrano G, Cortés-Ledesma F. Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576640. [PMID: 38328138 PMCID: PMC10849543 DOI: 10.1101/2024.01.22.576640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Human type-II topoisomerases, TOP2A and TOP2B, remove transcription associated DNA supercoiling, thereby affecting gene-expression programs, and have recently been associated with 3D genome architecture. Here, we study the regulatory roles of TOP2 paralogs in response to estrogen, which triggers an acute transcriptional induction that involves rewiring of genome organization. We find that, whereas TOP2A facilitates transcription, as expected for a topoisomerase, TOP2B limits the estrogen response. Consistent with this, TOP2B activity is locally downregulated upon estrogen treatment to favor the establishment and stabilization of regulatory chromatin contacts, likely through an accumulation of DNA supercoiling. We show that estrogen-mediated inhibition of TOP2B requires estrogen receptor α (ERα), a non-catalytic function of TOP2A, and the action of the atypical SUMO-ligase ZATT. This mechanism of topological transcriptional-control, which may be shared by additional gene-expression circuits, highlights the relevance of DNA topoisomerases as central actors of genome dynamics.
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Affiliation(s)
- José Terrón-Bautista
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Topology and DNA Breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
| | | | - Laura López-Hernández
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Spain
| | - Ananda Ayyappan Vadusevan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario García-Domínguez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - R. Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Spain
| | - Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Spain
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Topology and DNA Breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
- Lead contact
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14
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Marshall S, Navarro MV, Ascenҫão CF, Smolka MB. IN-DEPTH MAPPING OF DNA-PKcs SIGNALING UNCOVERS CONSERVED FEATURES OF ITS KINASE SPECIFICITY. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576037. [PMID: 38293078 PMCID: PMC10827184 DOI: 10.1101/2024.01.17.576037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via non-homologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a non-canonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Cross-species analysis in mouse pre-B and human HCT116 cell lines revealed splicing factors and transcriptional regulators phosphorylated at this novel motif, several of which contain SAP domains. These findings expand the list of DNA-PKcs and ATM substrates and establish a novel preferential phosphorylation motif for DNA-PKcs that connects it to proteins involved in nucleotide processes and interactions.
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Affiliation(s)
- Shannon Marshall
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcos V.A.S. Navarro
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- 2. IFSC Institute of Physics of São Carlos, University of São Paulo, São Carlos - SP, 13566-590, Brazil
| | - Carolline F.R. Ascenҫão
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcus B. Smolka
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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15
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Jiao X, Di Sante G, Casimiro MC, Tantos A, Ashton AW, Li Z, Quach Y, Bhargava D, Di Rocco A, Pupo C, Crosariol M, Lazar T, Tompa P, Wang C, Yu Z, Zhang Z, Aldaaysi K, Vadlamudi R, Mann M, Skordalakes E, Kossenkov A, Du Y, Pestell RG. A cyclin D1 intrinsically disordered domain accesses modified histone motifs to govern gene transcription. Oncogenesis 2024; 13:4. [PMID: 38191593 PMCID: PMC10774418 DOI: 10.1038/s41389-023-00502-1] [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: 02/20/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
The essential G1-cyclin, CCND1, is frequently overexpressed in cancer, contributing to tumorigenesis by driving cell-cycle progression. D-type cyclins are rate-limiting regulators of G1-S progression in mammalian cells via their ability to bind and activate CDK4 and CDK6. In addition, cyclin D1 conveys kinase-independent transcriptional functions of cyclin D1. Here we report that cyclin D1 associates with H2BS14 via an intrinsically disordered domain (IDD). The same region of cyclin D1 was necessary for the induction of aneuploidy, induction of the DNA damage response, cyclin D1-mediated recruitment into chromatin, and CIN gene transcription. In response to DNA damage H2BS14 phosphorylation occurs, resulting in co-localization with γH2AX in DNA damage foci. Cyclin D1 ChIP seq and γH2AX ChIP seq revealed ~14% overlap. As the cyclin D1 IDD functioned independently of the CDK activity to drive CIN, the IDD domain may provide a rationale new target to complement CDK-extinction strategies.
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Affiliation(s)
- Xuanmao Jiao
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | | | - Mathew C Casimiro
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Department of Science and Mathematics, Abraham Baldwin Agricultural College, Tifton, GA, 31794, USA
| | - Agnes Tantos
- Institute of Enzymology, Hun-Ren Research Centre for Natural Sciences, Budapest, Hungary
| | - Anthony W Ashton
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Division of Cardiovascular Medicine, Lankenau Institute for Medical Research, Wynnewood, PA, 19003, USA
| | - Zhiping Li
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Yen Quach
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | | | | | - Claudia Pupo
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Marco Crosariol
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Peter Tompa
- Institute of Enzymology, Hun-Ren Research Centre for Natural Sciences, Budapest, Hungary
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Chenguang Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Zhao Zhang
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
| | - Kawthar Aldaaysi
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Ratna Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health Sciences Center, San Antonio, TX, 78229, USA
| | - Monica Mann
- Department of Obstetrics and Gynecology, University of Texas Health Sciences Center, San Antonio, TX, 78229, USA
| | | | | | - Yanming Du
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
| | - Richard G Pestell
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA.
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba.
- The Wistar Institute, Philadelphia, PA, 19107, USA.
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16
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Liu H, Fu H, Yu C, Zhang N, Huang C, Lv L, Hu C, Chen F, Xiao Z, Zhang Z, Lu H, Yuan K. Transcriptional pausing induced by ionizing radiation enables the acquisition of radioresistance in nasopharyngeal carcinoma. J Mol Cell Biol 2024; 15:mjad044. [PMID: 37407287 PMCID: PMC10960568 DOI: 10.1093/jmcb/mjad044] [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: 11/25/2022] [Revised: 03/24/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Lesions on the DNA template can impact transcription via distinct regulatory pathways. Ionizing radiation (IR) as the mainstay modality for many malignancies elicits most of the cytotoxicity by inducing a variety of DNA damages in the genome. How the IR treatment alters the transcription cycle and whether it contributes to the development of radioresistance remain poorly understood. Here, we report an increase in the paused RNA polymerase II (RNAPII), as indicated by the phosphorylation at serine 5 residue of its C-terminal domain, in recurrent nasopharyngeal carcinoma (NPC) patient samples after IR treatment and cultured NPC cells developing IR resistance. Reducing the pool of paused RNAPII by either inhibiting TFIIH-associated CDK7 or stimulating the positive transcription elongation factor b, a CDK9-CycT1 heterodimer, attenuates IR resistance of NPC cells. Interestingly, the poly(ADP-ribosyl)ation of CycT1, which disrupts its phase separation, is elevated in the IR-resistant cells. Mutation of the major poly(ADP-ribosyl)ation sites of CycT1 decreases RNAPII pausing and restores IR sensitivity. Genome-wide chromatin immunoprecipitation followed by sequencing analyses reveal that several genes involved in radiation response and cell cycle control are subject to the regulation imposed by the paused RNAPII. Particularly, we identify the NIMA-related kinase NEK7 under such regulation as a new radioresistance factor, whose downregulation results in the increased chromosome instability, enabling the development of IR resistance. Overall, our results highlight a novel link between the alteration in the transcription cycle and the acquisition of IR resistance, opening up new opportunities to increase the efficacy of radiotherapy and thwart radioresistance in NPC.
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Affiliation(s)
- Honglu Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Huanyi Fu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Chunhong Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Na Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Canhua Huang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Chunhong Hu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Zhiqiang Xiao
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhuohua Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- The Biobank of Xiangya Hospital, Central South University, Changsha 410008, China
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17
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Bunch H, Kim D, Naganuma M, Nakagawa R, Cong A, Jeong J, Ehara H, Vu H, Chang JH, Schellenberg MJ, Sekine SI. ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes. Nat Commun 2023; 14:8341. [PMID: 38097570 PMCID: PMC10721843 DOI: 10.1038/s41467-023-44089-y] [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: 09/14/2022] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
The function of the mitogen-activated protein kinase signaling pathway is required for the activation of immediate early genes (IEGs), including EGR1 and FOS, for cell growth and proliferation. Recent studies have identified topoisomerase II (TOP2) as one of the important regulators of the transcriptional activation of IEGs. However, the mechanism underlying transcriptional regulation involving TOP2 in IEG activation has remained unknown. Here, we demonstrate that ERK2, but not ERK1, is important for IEG transcriptional activation and report a critical ELK1 binding sequence for ERK2 function at the EGR1 gene. Our data indicate that both ERK1 and ERK2 extensively phosphorylate the C-terminal domain of TOP2B at mutual and distinctive residues. Although both ERK1 and ERK2 enhance the catalytic rate of TOP2B required to relax positive DNA supercoiling, ERK2 delays TOP2B catalysis of negative DNA supercoiling. In addition, ERK1 may relax DNA supercoiling by itself. ERK2 catalytic inhibition or knock-down interferes with transcription and deregulates TOP2B in IEGs. Furthermore, we present the first cryo-EM structure of the human cell-purified TOP2B and etoposide together with the EGR1 transcriptional start site (-30 to +20) that has the strongest affinity to TOP2B within -423 to +332. The structure shows TOP2B-mediated breakage and dramatic bending of the DNA. Transcription is activated by etoposide, while it is inhibited by ICRF193 at EGR1 and FOS, suggesting that TOP2B-mediated DNA break to favor transcriptional activation. Taken together, this study suggests that activated ERK2 phosphorylates TOP2B to regulate TOP2-DNA interactions and favor transcriptional activation in IEGs. We propose that TOP2B association, catalysis, and dissociation on its substrate DNA are important processes for regulating transcription and that ERK2-mediated TOP2B phosphorylation may be key for the catalysis and dissociation steps.
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Affiliation(s)
- Heeyoun Bunch
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- School of Applied Biosciences, College of Agriculture & Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Deukyeong Kim
- School of Applied Biosciences, College of Agriculture & Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Masahiro Naganuma
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Reiko Nakagawa
- RIKEN BDR Laboratory for Phyloinformatics, Hyogo, 650-0047, Japan
| | - Anh Cong
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jaehyeon Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Haruhiko Ehara
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hongha Vu
- Department of Biology Education, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Matthew J Schellenberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shun-Ichi Sekine
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
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18
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Drake DM, Zhen D, Kerrebijn I, Or B, Gao S, Afsharian K, Tran J, Bhatia S, Cheng A, Wells PG. Breast cancer 1 (BRCA1) protection in altered gene expression and neurodevelopmental disorders due to physiological and ethanol-enhanced reactive oxygen species formation. Free Radic Biol Med 2023; 208:272-284. [PMID: 37541454 DOI: 10.1016/j.freeradbiomed.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/08/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
The breast cancer 1 (Brca1) susceptibility gene regulates the repair of reactive oxygen species (ROS)-mediated DNA damage, which is implicated in neurodevelopmental disorders. Alcohol (ethanol, EtOH) exposure during pregnancy causes fetal alcohol spectrum disorders (FASD), including abnormal brain function, associated with enhanced ROS-initiated DNA damage. Herein, oxidative DNA damage in fetal brains and neurodevelopmental disorders were enhanced in saline-exposed +/- vs. +/+ Brca1 littermates. A single EtOH exposure during gestation further enhanced oxidative DNA damage, altered the expression of developmental/DNA damage response genes in fetal brains, and resulted in neurodevelopmental disorders, all of which were BRCA1-dependent. Pretreatment with the ROS inhibitor phenylbutylnitrone (PBN) blocked DNA damage and some neurodevelopmental disorders in both saline- and EtOH-exposed progeny, corroborating a ROS-dependent mechanism. Fetal BRCA1 protects against altered gene expression and neurodevelopmental disorders caused by both physiological and EtOH-enhanced levels of ROS formation. BRCA1 deficiencies may enhance the risk for FASD.
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Affiliation(s)
- Danielle M Drake
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Danlin Zhen
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Isabel Kerrebijn
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Or
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sophie Gao
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Kian Afsharian
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Jason Tran
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Shama Bhatia
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Ashley Cheng
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Peter G Wells
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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19
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Cowell IG, Casement JW, Austin CA. To Break or Not to Break: The Role of TOP2B in Transcription. Int J Mol Sci 2023; 24:14806. [PMID: 37834253 PMCID: PMC10573011 DOI: 10.3390/ijms241914806] [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: 09/08/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Transcription and its regulation pose challenges related to DNA torsion and supercoiling of the DNA template. RNA polymerase tracking the helical groove of the DNA introduces positive helical torsion and supercoiling upstream and negative torsion and supercoiling behind its direction of travel. This can inhibit transcriptional elongation and other processes essential to transcription. In addition, chromatin remodeling associated with gene activation can generate or be hindered by excess DNA torsional stress in gene regulatory regions. These topological challenges are solved by DNA topoisomerases via a strand-passage reaction which involves transiently breaking and re-joining of one (type I topoisomerases) or both (type II topoisomerases) strands of the phosphodiester backbone. This review will focus on one of the two mammalian type II DNA topoisomerase enzymes, DNA topoisomerase II beta (TOP2B), that have been implicated in correct execution of developmental transcriptional programs and in signal-induced transcription, including transcriptional activation by nuclear hormone ligands. Surprisingly, several lines of evidence indicate that TOP2B-mediated protein-free DNA double-strand breaks are involved in signal-induced transcription. We discuss the possible significance and origins of these DSBs along with a network of protein interaction data supporting a variety of roles for TOP2B in transcriptional regulation.
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Affiliation(s)
- Ian G. Cowell
- Biosciences Institute, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - John W. Casement
- Bioinformatics Support Unit, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Caroline A. Austin
- Biosciences Institute, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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20
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Deshpande RA, Marin-Gonzalez A, Barnes HK, Woolley PR, Ha T, Paull TT. Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. Nat Commun 2023; 14:5759. [PMID: 37717054 PMCID: PMC10505227 DOI: 10.1038/s41467-023-41544-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5' strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site-a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate sites of MRN-dependent processing by identifying sites of CtIP association and by sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated most efficiently when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that both complexes bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.
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Affiliation(s)
| | - Alberto Marin-Gonzalez
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Hannah K Barnes
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Phillip R Woolley
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Tanya T Paull
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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21
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Lim B, Djekidel MN, Matsui Y, Jung S, Yuan ZF, Wang X, Yang X, Pilehroud AS, Pan H, Wang F, Pruett-Miller S, Kavdia K, Pagala V, Fan Y, Peng J, Xu B, Peng JC. Phosphorylation of 53BP1 by ATM enforce neurodevelopmental programs in cortical organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539457. [PMID: 37205560 PMCID: PMC10187281 DOI: 10.1101/2023.05.04.539457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
53BP1 is a well-established DNA damage repair factor recently shown to regulate gene expression and critically influence tumor suppression and neural development. For gene regulation, how 53BP1 is regulated remains unclear. Here, we showed that 53BP1-serine 25 phosphorylation by ATM is required for neural progenitor cell proliferation and neuronal differentiation in cortical organoids. 53BP1-serine 25 phosphorylation dynamics controls 53BP1 target genes for neuronal differentiation and function, cellular response to stress, and apoptosis. Beyond 53BP1, ATM is required for phosphorylation of factors in neuronal differentiation, cytoskeleton, p53 regulation, and ATM, BNDF, and WNT signaling pathways for cortical organoid differentiation. Overall, our data suggest that 53BP1 and ATM control key genetic programs required for human cortical development.
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22
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Su S, Xue Y, Lee SK, Zhang Y, Fan J, De S, Sharov A, Wang W. A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation. Nucleic Acids Res 2023; 51:2415-2433. [PMID: 36794732 PMCID: PMC10018333 DOI: 10.1093/nar/gkad086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Topoisomerases are required to release topological stress generated by RNA polymerase II (RNAPII) during transcription. Here, we show that in response to starvation, the complex of topoisomerase 3b (TOP3B) and TDRD3 can enhance not only transcriptional activation, but also repression, which mimics other topoisomerases that can also alter transcription in both directions. The genes enhanced by TOP3B-TDRD3 are enriched with long and highly-expressed ones, which are also preferentially stimulated by other topoisomerases, suggesting that different topoisomerases may recognize their targets through a similar mechanism. Specifically, human HCT116 cells individually inactivated for TOP3B, TDRD3 or TOP3B topoisomerase activity, exhibit similarly disrupted transcription for both starvation-activated genes (SAGs) and starvation-repressed genes (SRGs). Responding to starvation, both TOP3B-TDRD3 and the elongating form of RNAPII exhibit concomitantly increased binding to TOP3B-dependent SAGs, at binding sites that overlap. Notably, TOP3B inactivation decreases the binding of elongating RNAPII to TOP3B-dependent SAGs while increased it to SRGs. Furthermore, TOP3B-ablated cells display reduced transcription of several autophagy-associated genes and autophagy per se. Our data suggest that TOP3B-TDRD3 can promote both transcriptional activation and repression by regulating RNAPII distribution. In addition, the findings that it can facilitate autophagy may account for the shortened lifespan of Top3b-KO mice.
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Affiliation(s)
- Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jinshui Fan
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alexei Sharov
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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23
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Pollina EA, Gilliam DT, Landau AT, Lin C, Pajarillo N, Davis CP, Harmin DA, Yap EL, Vogel IR, Griffith EC, Nagy MA, Ling E, Duffy EE, Sabatini BL, Weitz CJ, Greenberg ME. A NPAS4-NuA4 complex couples synaptic activity to DNA repair. Nature 2023; 614:732-741. [PMID: 36792830 PMCID: PMC9946837 DOI: 10.1038/s41586-023-05711-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/05/2023] [Indexed: 02/17/2023]
Abstract
Neuronal activity is crucial for adaptive circuit remodelling but poses an inherent risk to the stability of the genome across the long lifespan of postmitotic neurons1-5. Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is unknown. Here we identify an activity-dependent DNA repair mechanism in which a new form of the NuA4-TIP60 chromatin modifier assembles in activated neurons around the inducible, neuronal-specific transcription factor NPAS4. We purify this complex from the brain and demonstrate its functions in eliciting activity-dependent changes to neuronal transcriptomes and circuitry. By characterizing the landscape of activity-induced DNA double-strand breaks in the brain, we show that NPAS4-NuA4 binds to recurrently damaged regulatory elements and recruits additional DNA repair machinery to stimulate their repair. Gene regulatory elements bound by NPAS4-NuA4 are partially protected against age-dependent accumulation of somatic mutations. Impaired NPAS4-NuA4 signalling leads to a cascade of cellular defects, including dysregulated activity-dependent transcriptional responses, loss of control over neuronal inhibition and genome instability, which all culminate to reduce organismal lifespan. In addition, mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental and autism spectrum disorders. Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation, the disruption of which may contribute to developmental disorders, neurodegeneration and ageing.
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Affiliation(s)
- Elizabeth A Pollina
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel T Gilliam
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Andrew T Landau
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Cindy Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Naomi Pajarillo
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - David A Harmin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ee-Lynn Yap
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ian R Vogel
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Eric C Griffith
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - M Aurel Nagy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Emi Ling
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Erin E Duffy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Bernardo L Sabatini
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Charles J Weitz
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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24
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ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen. Cell Rep 2023; 42:111909. [PMID: 36640339 PMCID: PMC10023214 DOI: 10.1016/j.celrep.2022.111909] [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: 07/27/2022] [Revised: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
ATM gene mutation carriers are predisposed to estrogen-receptor-positive breast cancer (BC). ATM prevents BC oncogenesis by activating p53 in every cell; however, much remains unknown about tissue-specific oncogenesis after ATM loss. Here, we report that ATM controls the early transcriptional response to estrogens. This response depends on topoisomerase II (TOP2), which generates TOP2-DNA double-strand break (DSB) complexes and rejoins the breaks. When TOP2-mediated ligation fails, ATM facilitates DSB repair. After estrogen exposure, TOP2-dependent DSBs arise at the c-MYC enhancer in human BC cells, and their defective repair changes the activation profile of enhancers and induces the overexpression of many genes, including the c-MYC oncogene. CRISPR/Cas9 cleavage at the enhancer also causes c-MYC overexpression, indicating that this DSB causes c-MYC overexpression. Estrogen treatment induced c-Myc protein overexpression in mammary epithelial cells of ATM-deficient mice. In conclusion, ATM suppresses the c-Myc-driven proliferative effects of estrogens, possibly explaining such tissue-specific oncogenesis.
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25
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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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26
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Taspase1 Facilitates Topoisomerase IIβ-Mediated DNA Double-Strand Breaks Driving Estrogen-Induced Transcription. Cells 2023; 12:cells12030363. [PMID: 36766705 PMCID: PMC9913075 DOI: 10.3390/cells12030363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
The human protease Taspase1 plays a pivotal role in developmental processes and cancerous diseases by processing critical regulators, such as the leukemia proto-oncoprotein MLL. Despite almost two decades of intense research, Taspase1's biology is, however, still poorly understood, and so far its cellular function was not assigned to a superordinate biological pathway or a specific signaling cascade. Our data, gained by methods such as co-immunoprecipitation, LC-MS/MS and Topoisomerase II DNA cleavage assays, now functionally link Taspase1 and hormone-induced, Topoisomerase IIβ-mediated transient DNA double-strand breaks, leading to active transcription. The specific interaction with Topoisomerase IIα enhances the formation of DNA double-strand breaks that are a key prerequisite for stimulus-driven gene transcription. Moreover, Taspase1 alters the H3K4 epigenetic signature upon estrogen-stimulation by cleaving the chromatin-modifying enzyme MLL. As estrogen-driven transcription and MLL-derived epigenetic labelling are reduced upon Taspase1 siRNA-mediated knockdown, we finally characterize Taspase1 as a multifunctional co-activator of estrogen-stimulated transcription.
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27
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Matias-Barrios VM, Dong X. The Implication of Topoisomerase II Inhibitors in Synthetic Lethality for Cancer Therapy. Pharmaceuticals (Basel) 2023; 16:ph16010094. [PMID: 36678591 PMCID: PMC9866718 DOI: 10.3390/ph16010094] [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: 11/10/2022] [Revised: 12/31/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
DNA topoisomerase II (Top2) is essential for all eukaryotic cells in the regulation of DNA topology through the generation of temporary double-strand breaks. Cancer cells acquire enhanced Top2 functions to cope with the stress generated by transcription and DNA replication during rapid cell division since cancer driver genes such as Myc and EZH2 hijack Top2 in order to realize their oncogenic transcriptomes for cell growth and tumor progression. Inhibitors of Top2 are therefore designed to target Top2 to trap it on DNA, subsequently causing protein-linked DNA breaks, a halt to the cell cycle, and ultimately cell death. Despite the effectiveness of these inhibitors, cancer cells can develop resistance to them, thereby limiting their therapeutic utility. To maximize the therapeutic potential of Top2 inhibitors, combination therapies to co-target Top2 with DNA damage repair (DDR) machinery and oncogenic pathways have been proposed to induce synthetic lethality for more thorough tumor suppression. In this review, we will discuss the mode of action of Top2 inhibitors and their potential applications in cancer treatments.
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Affiliation(s)
- Victor M. Matias-Barrios
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
- School of Medicine and Health Sciences, Tecnologico de Monterrey, Avenida Eugenio Garza Sada 2501, Monterrey 64849, Mexico
- Correspondence:
| | - Xuesen Dong
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
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28
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Bunch H. Studying RNA Polymerase II Promoter-Proximal Pausing by In Vitro Immobilized Template and Transcription Assays. Methods Mol Biol 2023; 2693:13-24. [PMID: 37540423 DOI: 10.1007/978-1-0716-3342-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The immobilized template assay is a versatile biochemical method for studying protein-nucleic acid interactions. Using this method, immobilized nucleic acid-associated or specific proteins can be identified and quantified by techniques such as mass spectrometry and immunoblotting. Here, a modified immobilized template assay combined with in vitro transcription assay to study the function of transcription factors and transcriptional activities at the human heat shock protein 70 (HSP70) gene is described. Notably, this method can be applied to study other important genes and transcription factors in vitro.
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Affiliation(s)
- Heeyoun Bunch
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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29
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Bunch H, Calderwood SK. Role of Heat Shock Factors in Stress-Induced Transcription: An Update. Methods Mol Biol 2023; 2693:25-38. [PMID: 37540424 DOI: 10.1007/978-1-0716-3342-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Heat shock proteins (HSP) are rapidly induced after proteotoxic stresses such as heat shock and accumulate at high concentrations in cells. HSP induction involves primarily a family of heat shock transcription factors (HSF) that bind the heat shock elements of the HSP genes and mediate transcription in trans. We discuss methods for the study of HSP binding to HSP promoters and the consequent increases in HSP gene expression in vitro and in vivo.
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Affiliation(s)
- Heyoun Bunch
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Stuart K Calderwood
- Molecular and Cellular Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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30
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Akter S, Shimba A, Ikuta K, Mahmud MRA, Yamada S, Sasanuma H, Tsuda M, Sone M, Ago Y, Murai K, Tanaka H, Takeda S. Physiological concentrations of glucocorticoids induce pathological DNA double-strand breaks. Genes Cells 2023; 28:53-67. [PMID: 36415926 DOI: 10.1111/gtc.12993] [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: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022]
Abstract
Steroid hormones induce the transcription of target genes by activating nuclear receptors. Early transcriptional response to various stimuli, including hormones, involves the active catalysis of topoisomerase II (TOP2) at transcription regulatory sequences. TOP2 untangles DNAs by transiently generating double-strand breaks (DSBs), where TOP2 covalently binds to DSB ends. When TOP2 fails to rejoin, called "abortive" catalysis, the resulting DSBs are repaired by tyrosyl-DNA phosphodiesterase 2 (TDP2) and non-homologous end-joining (NHEJ). A steroid, cortisol, is the most important glucocorticoid, and dexamethasone (Dex), a synthetic glucocorticoid, is widely used for suppressing inflammation in clinics. We here revealed that clinically relevant concentrations of Dex and physiological concentrations of cortisol efficiently induce DSBs in G1 phase cells deficient in TDP2 and NHEJ. The DSB induction depends on glucocorticoid receptor (GR) and TOP2. Considering the specific role of TDP2 in removing TOP2 adducts from DSB ends, induced DSBs most likely represent stalled TOP2-DSB complexes. Inhibition of RNA polymerase II suppressed the DSBs formation only modestly in the G1 phase. We propose that cortisol and Dex frequently generate DSBs through the abortive catalysis of TOP2 at transcriptional regulatory sequences, including promoters or enhancers, where active TOP2 catalysis occurs during early transcriptional response.
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Affiliation(s)
- Salma Akter
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihiro Shimba
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Md Rasel Al Mahmud
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shintaro Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masakatsu Sone
- Department of Metabolic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Metabolism and Endocrinology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Yukio Ago
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenichi Murai
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Shenzhen University School of Medicine, Shenzhen University, Shenzhen, Guangdong, China
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31
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Lu H, Yang M, Zhou Q. Reprogramming transcription after DNA damage: recognition, response, repair, and restart. Trends Cell Biol 2022:S0962-8924(22)00261-6. [PMID: 36513571 DOI: 10.1016/j.tcb.2022.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Genome integrity is constantly challenged by endogenous and exogenous insults that cause DNA damage. To cope with these threats, cells have a surveillance mechanism, known as the DNA damage response (DDR), to repair any lesions. Although transcription has long been implicated in DNA repair, how transcriptional reprogramming is coordinated with the DDR is just beginning to be understood. In this review, we highlight recent advances in elucidating the molecular mechanisms underlying major transcriptional events, including RNA polymerase (Pol) II stalling and transcriptional silencing and recovery, which occur in response to DNA damage. Furthermore, we discuss how such transcriptional adaptation contributes to sensing and eliminating damaged DNA and how it can jeopardize genome integrity when it goes awry.
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Affiliation(s)
- Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Min Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qiang Zhou
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong.
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32
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Uusküla-Reimand L, Wilson MD. Untangling the roles of TOP2A and TOP2B in transcription and cancer. SCIENCE ADVANCES 2022; 8:eadd4920. [PMID: 36322662 PMCID: PMC9629710 DOI: 10.1126/sciadv.add4920] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/12/2022] [Indexed: 06/09/2023]
Abstract
Type II topoisomerases (TOP2) are conserved regulators of chromatin topology that catalyze reversible DNA double-strand breaks (DSBs) and are essential for maintaining genomic integrity in diverse dynamic processes such as transcription, replication, and cell division. While controlled TOP2-mediated DSBs are an elegant solution to topological constraints of DNA, DSBs also contribute to the emergence of chromosomal translocations and mutations that drive cancer. The central importance of TOP2 enzymes as frontline chemotherapeutic targets is well known; however, their precise biological functions and impact in cancer development are still poorly understood. In this review, we provide an updated overview of TOP2A and TOP2B in the regulation of chromatin topology and transcription, and discuss the recent discoveries linking TOP2 activities with cancer pathogenesis.
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Affiliation(s)
- Liis Uusküla-Reimand
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D. Wilson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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33
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TRIM28 Is a Novel Regulator of CD133 Expression Associated with Cancer Stem Cell Phenotype. Int J Mol Sci 2022; 23:ijms23179874. [PMID: 36077272 PMCID: PMC9456468 DOI: 10.3390/ijms23179874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
CD133 is an extensively studied marker of the most malignant tumor cell population, designated as cancer stem cells (CSCs). However, the function of this glycoprotein and its involvement in cell regulatory cascades are still poorly understood. Here we show a positive correlation between the level of CD133 plasma membrane expression and the proliferative activity of cells of the Caco-2, HT-29, and HUH7 cancer cell lines. Despite a substantial difference in the proliferative activities of cell populations with different levels of CD133 expression, transcriptomic and proteomic profiling revealed only minor distinctions between them. Nonetheless, a further in silico assessment of the differentially expressed transcripts and proteins revealed 16 proteins that could be involved in the regulation of CD133 expression; these were assigned ranks reflecting the apparent extent of their involvement. Among them, the TRIM28 transcription factor had the highest rank. The prominent role of TRIM28 in CD133 expression modulation was confirmed experimentally in the Caco2 cell line clones: the knockout, though not the knockdown, of the TRIM28 gene downregulated CD133. These results for the first time highlight an important role of the TRIM28 transcription factor in the regulation of CD133-associated cancer cell heterogeneity.
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34
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Amatullah H, Fraschilla I, Digumarthi S, Huang J, Adiliaghdam F, Bonilla G, Wong LP, Rivard ME, Beauchamp C, Mercier V, Goyette P, Sadreyev RI, Anthony RM, Rioux JD, Jeffrey KL. Epigenetic reader SP140 loss of function drives Crohn's disease due to uncontrolled macrophage topoisomerases. Cell 2022; 185:3232-3247.e18. [PMID: 35952671 PMCID: PMC9442451 DOI: 10.1016/j.cell.2022.06.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/07/2022] [Accepted: 06/27/2022] [Indexed: 01/19/2023]
Abstract
How mis-regulated chromatin directly impacts human immune disorders is poorly understood. Speckled Protein 140 (SP140) is an immune-restricted PHD and bromodomain-containing epigenetic "reader," and SP140 loss-of-function mutations associate with Crohn's disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the relevance of these mutations and mechanisms underlying SP140-driven pathogenicity remains unexplored. Using a global proteomic strategy, we identified SP140 as a repressor of topoisomerases (TOPs) that maintains heterochromatin and macrophage fate. In humans and mice, SP140 loss resulted in unleashed TOP activity, de-repression of developmentally silenced genes, and ultimately defective microbe-inducible macrophage transcriptional programs and bacterial killing that drive intestinal pathology. Pharmacological inhibition of TOP1/2 rescued these defects. Furthermore, exacerbated colitis was restored with TOP1/2 inhibitors in Sp140-/- mice, but not wild-type mice, in vivo. Collectively, we identify SP140 as a TOP repressor and reveal repurposing of TOP inhibition to reverse immune diseases driven by SP140 loss.
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Affiliation(s)
- Hajera Amatullah
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Isabella Fraschilla
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Sreehaas Digumarthi
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA
| | - Julie Huang
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA
| | - Fatemeh Adiliaghdam
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Gracia Bonilla
- Department of Molecular Biology, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | | | | | | | | | - Ruslan I Sadreyev
- Department of Molecular Biology, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - John D Rioux
- Montreal Heart Institute, Montreal, QC H1T 1C8, Canada
| | - Kate L Jeffrey
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.
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Papapietro O, Nejentsev S. Topoisomerase 2β and DNA topology during B cell development. Front Immunol 2022; 13:982870. [PMID: 36045673 PMCID: PMC9423374 DOI: 10.3389/fimmu.2022.982870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Topoisomerase 2β (TOP2B) introduces transient double strand breaks in the DNA helix to remove supercoiling structures and unwind entangled DNA strains. Advances in genomic technologies have enabled the discovery of novel functions for TOP2B in processes such as releasing of the paused RNA polymerase II and maintaining the genome organization through DNA loop domains. Thus, TOP2B can regulate transcription directly by acting on transcription elongation and indirectly by controlling interactions between enhancer and promoter regions through genome folding. The identification of TOP2B mutations in humans unexpectedly revealed a unique role of TOP2B in B-cell progenitors. Here we discuss the functions of TOP2B and the mechanisms leading to the B-cell development defect in patients with TOP2B deficiency.
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Affiliation(s)
- Olivier Papapietro
- Molecular Cell Biology and Immunology, Amsterdam University Medical Centers (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- *Correspondence: Sergey Nejentsev, ; Olivier Papapietro,
| | - Sergey Nejentsev
- Molecular Cell Biology and Immunology, Amsterdam University Medical Centers (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Sergey Nejentsev, ; Olivier Papapietro,
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36
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Cao H, Zhang Y, Cai Y, Tang L, Gao F, Xu D, Kapranov P. Hotspots of single-strand DNA “breakome” are enriched at transcriptional start sites of genes. Front Mol Biosci 2022; 9:895795. [PMID: 36046604 PMCID: PMC9420937 DOI: 10.3389/fmolb.2022.895795] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
Single-strand breaks (SSBs) represent one of the most common types of DNA damage, yet not much is known about the genome landscapes of this type of DNA lesions in mammalian cells. Here, we found that SSBs are more likely to occur in certain positions of the human genome—SSB hotspots—in different cells of the same cell type and in different cell types. We hypothesize that the hotspots are likely to represent biologically relevant breaks. Furthermore, we found that the hotspots had a prominent tendency to be enriched in the immediate vicinity of transcriptional start sites (TSSs). We show that these hotspots are not likely to represent technical artifacts or be caused by common mechanisms previously found to cause DNA cleavage at promoters, such as apoptotic DNA fragmentation or topoisomerase type II (TOP2) activity. Therefore, such TSS-associated hotspots could potentially be generated using a novel mechanism that could involve preferential cleavage at cytosines, and their existence is consistent with recent studies suggesting a complex relationship between DNA damage and regulation of gene expression.
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37
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Weber Boutros S, Unni VK, Raber J. An Adaptive Role for DNA Double-Strand Breaks in Hippocampus-Dependent Learning and Memory. Int J Mol Sci 2022; 23:8352. [PMID: 35955487 PMCID: PMC9368779 DOI: 10.3390/ijms23158352] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
DNA double-strand breaks (DSBs), classified as the most harmful type of DNA damage based on the complexity of repair, lead to apoptosis or tumorigenesis. In aging, DNA damage increases and DNA repair decreases. This is exacerbated in disease, as post-mortem tissue from patients diagnosed with mild cognitive impairment (MCI) or Alzheimer's disease (AD) show increased DSBs. A novel role for DSBs in immediate early gene (IEG) expression, learning, and memory has been suggested. Inducing neuronal activity leads to increases in DSBs and upregulation of IEGs, while increasing DSBs and inhibiting DSB repair impairs long-term memory and alters IEG expression. Consistent with this pattern, mice carrying dominant AD mutations have increased baseline DSBs, and impaired DSB repair is observed. These data suggest an adaptive role for DSBs in the central nervous system and dysregulation of DSBs and/or repair might drive age-related cognitive decline (ACD), MCI, and AD. In this review, we discuss the adaptive role of DSBs in hippocampus-dependent learning, memory, and IEG expression. We summarize IEGs, the history of DSBs, and DSBs in synaptic plasticity, aging, and AD. DSBs likely have adaptive functions in the brain, and even subtle alterations in their formation and repair could alter IEGs, learning, and memory.
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Affiliation(s)
- Sydney Weber Boutros
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Vivek K. Unni
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA;
- Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR 97239, USA
- Oregon Health & Science University Parkinson Center, Portland, OR 97239, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA;
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA;
- Department of Radiation Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
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38
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Boutros SW, Kessler K, Unni VK, Raber J. Infusion of etoposide in the CA1 disrupts hippocampal immediate early gene expression and hippocampus-dependent learning. Sci Rep 2022; 12:12834. [PMID: 35896679 PMCID: PMC9329441 DOI: 10.1038/s41598-022-17052-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/20/2022] [Indexed: 11/21/2022] Open
Abstract
Tight regulation of immediate early gene (IEG) expression is important for synaptic plasticity, learning, and memory. Recent work has suggested that DNA double strand breaks (DSBs) may have an adaptive role in post-mitotic cells to induce IEG expression. Physiological activity in cultured neurons as well as behavioral training leads to increased DSBs and subsequent IEG expression. Additionally, infusion of etoposide-a common cancer treatment that induces DSBs-impairs trace fear memory. Here, we assessed the effects of hippocampal infusion of 60 ng of etoposide on IEG expression, learning, and memory in 3-4 month-old C57Bl/6J mice. Etoposide altered expression of the immediate early genes cFos and Arc in the hippocampus and impaired hippocampus-dependent contextual fear memory. These data add to the growing evidence that DSBs play an important role in IEG expression, learning, and memory, opening avenues for developing novel treatment strategies for memory-related disorders.
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Affiliation(s)
- Sydney Weber Boutros
- Department of Behavioral Neuroscience, OHSU, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - Kat Kessler
- Department of Behavioral Neuroscience, OHSU, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - Vivek K Unni
- Department of Neurology, OHSU, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA
- Jungers Center for Neurosciences Research, OHSU Parkinson Center, OHSU, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, OHSU, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
- Department of Neurology, OHSU, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
- Departments of Psychiatry and Radiation Medicine, OHSU, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
- Division of Neuroscience, ONPRC, 505 NW 185th Ave, Beaverton, OR, 97006, USA.
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Khazeem MM, Casement JW, Schlossmacher G, Kenneth NS, Sumbung NK, Chan JYT, McGow JF, Cowell IG, Austin CA. TOP2B Is Required to Maintain the Adrenergic Neural Phenotype and for ATRA-Induced Differentiation of SH-SY5Y Neuroblastoma Cells. Mol Neurobiol 2022; 59:5987-6008. [PMID: 35831557 PMCID: PMC9463316 DOI: 10.1007/s12035-022-02949-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/23/2022] [Indexed: 12/13/2022]
Abstract
The neuroblastoma cell line SH-SY5Y is widely used to study retinoic acid (RA)-induced gene expression and differentiation and as a tool to study neurodegenerative disorders. SH-SY5Y cells predominantly exhibit adrenergic neuronal properties, but they can also exist in an epigenetically interconvertible alternative state with more mesenchymal characteristics; as a result, these cells can be used to study gene regulation circuitry controlling neuroblastoma phenotype. Using a combination of pharmacological inhibition and targeted gene inactivation, we have probed the requirement for DNA topoisomerase IIB (TOP2B) in RA-induced gene expression and differentiation and in the balance between adrenergic neuronal versus mesenchymal transcription programmes. We found that expression of many, but not all genes that are rapidly induced by ATRA in SH-SY5Y cells was significantly reduced in the TOP2B null cells; these genes include BCL2, CYP26A1, CRABP2, and NTRK2. Comparing gene expression profiles in wild-type versus TOP2B null cells, we found that long genes and genes expressed at a high level in WT SH-SY5Y cells were disproportionately dependent on TOP2B. Notably, TOP2B null SH-SY5Y cells upregulated mesenchymal markers vimentin (VIM) and fibronectin (FN1) and components of the NOTCH signalling pathway. Enrichment analysis and comparison with the transcription profiles of other neuroblastoma-derived cell lines supported the conclusion that TOP2B is required to fully maintain the adrenergic neural-like transcriptional signature of SH-SY5Y cells and to suppress the alternative mesenchymal epithelial-like epigenetic state.
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Affiliation(s)
- Mushtaq M Khazeem
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,National Center of Hematology, Mustansiriyah University, Baghdad, Iraq
| | - John W Casement
- Bioinformatics Support Unit, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - George Schlossmacher
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Niall S Kenneth
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nielda K Sumbung
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Janice Yuen Tung Chan
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jade F McGow
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ian G Cowell
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Caroline A Austin
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Gaikwad M, Konkimalla VB, Salunke-Gawali S. Metal complexes as topoisomerase inhibitors. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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41
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Saayman X, Esashi F. Breaking the paradigm: early insights from mammalian DNA breakomes. FEBS J 2022; 289:2409-2428. [PMID: 33792193 PMCID: PMC9451923 DOI: 10.1111/febs.15849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) can result from both exogenous and endogenous sources and are potentially toxic lesions to the human genome. If improperly repaired, DSBs can threaten genome integrity and contribute to premature ageing, neurodegenerative disorders and carcinogenesis. Through decades of work on genome stability, it has become evident that certain regions of the genome are inherently more prone to breakage than others, known as genome instability hotspots. Recent advancements in sequencing-based technologies now enable the profiling of genome-wide distributions of DSBs, also known as breakomes, to systematically map these instability hotspots. Here, we review the application of these technologies and their implications for our current understanding of the genomic regions most likely to drive genome instability. These breakomes ultimately highlight both new and established breakage hotspots including actively transcribed regions, loop boundaries and early-replicating regions of the genome. Further, these breakomes challenge the paradigm that DNA breakage primarily occurs in hard-to-replicate regions. With these advancements, we begin to gain insights into the biological mechanisms both invoking and protecting against genome instability.
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Affiliation(s)
- Xanita Saayman
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, UK
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42
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PRKDC promotes hepatitis B virus transcription through enhancing the binding of RNA Pol II to cccDNA. Cell Death Dis 2022; 13:404. [PMID: 35468873 PMCID: PMC9038722 DOI: 10.1038/s41419-022-04852-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 12/21/2022]
Abstract
Hepatitis B virus infection remains a major health problem worldwide due to its high risk of liver failure and hepatocellular carcinoma. Covalently closed circular DNA (cccDNA), which is present as an individual minichromosome, serves as the template for transcription of all viral RNAs and pla ays critical role in viral persistence. Therefore, there is an urgent need to gain broader insight into the transcription regulation of cccDNA. Here, we combined a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) with an engineered ascorbate peroxidase 2 (APEX2) to identify cccDNA associated proteins systematically in living cells. By functional screening, we verified that protein kinase, DNA-activated, catalytic subunit (PRKDC) was an effective activator of HBV cccDNA transcription in HBV-infected HepG2-NTCP cells and primary human hepatocytes. Mechanismly, PRKDC interacted with POLR2A and POLR2B, the two largest subunits of RNA polymerase II (Pol II) and recruited Pol II to HBV cccDNA minichromosome in a kinase-dependent manner. PRKDC knockdown or inhibitor treatment significantly decreased the enrichment of POLR2A and POLR2B on cccDNA, as well as reducing the levels of cccDNA associated Pol II Ser5 and Ser2 phosphorylation, which eventually inhibited the HBV cccDNA activity. Collectively, these findings give us new insights into cccDNA transcription regulation, thus providing new potential targets for HBV treatment in patients.
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43
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Provasek VE, Mitra J, Malojirao VH, Hegde ML. DNA Double-Strand Breaks as Pathogenic Lesions in Neurological Disorders. Int J Mol Sci 2022; 23:ijms23094653. [PMID: 35563044 PMCID: PMC9099445 DOI: 10.3390/ijms23094653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
The damage and repair of DNA is a continuous process required to maintain genomic integrity. DNA double-strand breaks (DSBs) are the most lethal type of DNA damage and require timely repair by dedicated machinery. DSB repair is uniquely important to nondividing, post-mitotic cells of the central nervous system (CNS). These long-lived cells must rely on the intact genome for a lifetime while maintaining high metabolic activity. When these mechanisms fail, the loss of certain neuronal populations upset delicate neural networks required for higher cognition and disrupt vital motor functions. Mammalian cells engage with several different strategies to recognize and repair chromosomal DSBs based on the cellular context and cell cycle phase, including homologous recombination (HR)/homology-directed repair (HDR), microhomology-mediated end-joining (MMEJ), and the classic non-homologous end-joining (NHEJ). In addition to these repair pathways, a growing body of evidence has emphasized the importance of DNA damage response (DDR) signaling, and the involvement of heterogeneous nuclear ribonucleoprotein (hnRNP) family proteins in the repair of neuronal DSBs, many of which are linked to age-associated neurological disorders. In this review, we describe contemporary research characterizing the mechanistic roles of these non-canonical proteins in neuronal DSB repair, as well as their contributions to the etiopathogenesis of selected common neurological diseases.
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Affiliation(s)
- Vincent E. Provasek
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (V.H.M.)
- College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Joy Mitra
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (V.H.M.)
- Correspondence: (J.M.); (M.L.H.)
| | - Vikas H. Malojirao
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (V.H.M.)
| | - Muralidhar L. Hegde
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (V.H.M.)
- College of Medicine, Texas A&M University, College Station, TX 77843, USA
- Department of Neurosciences, Weill Cornell Medical College, New York, NY 11021, USA
- Correspondence: (J.M.); (M.L.H.)
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44
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Pommier Y, Nussenzweig A, Takeda S, Austin C. Human topoisomerases and their roles in genome stability and organization. Nat Rev Mol Cell Biol 2022; 23:407-427. [PMID: 35228717 PMCID: PMC8883456 DOI: 10.1038/s41580-022-00452-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA–protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer. Topoisomerases have essential roles in transcription, DNA replication, chromatin remodelling and, as recently revealed, 3D genome organization. However, topoisomerases also generate DNA–protein crosslinks coupled with DNA breaks, which are increasingly recognized as a source of disease-causing genomic damage.
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45
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Randolph K, Hyder U, D’Orso I. KAP1/TRIM28: Transcriptional Activator and/or Repressor of Viral and Cellular Programs? Front Cell Infect Microbiol 2022; 12:834636. [PMID: 35281453 PMCID: PMC8904932 DOI: 10.3389/fcimb.2022.834636] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 01/01/2023] Open
Abstract
Several transcriptional and epigenetic regulators have been functionally linked to the control of viral and cellular gene expression programs. One such regulator is Krüppel-associated box (KRAB)-associated protein 1 (KAP1: also named TRIM28 or TIF1β), which has been extensively studied in the past three decades. Here we offer an up-to date review of its various functions in a diversity of contexts. We first summarize the discovery of KAP1 repression of endogenous retroviruses during development. We then deliberate evidence in the literature suggesting KAP1 is both an activator and repressor of HIV-1 transcription and discuss experimental differences and limitations of previous studies. Finally, we discuss KAP1 regulation of DNA and RNA viruses, and then expand on KAP1 control of cellular responses and immune functions. While KAP1 positive and negative regulation of viral and cellular transcriptional programs is vastly documented, our mechanistic understanding remains narrow. We thus propose that precision genetic tools to reveal direct KAP1 functions in gene regulation will be required to not only illuminate new biology but also provide the foundation to translate the basic discoveries from the bench to the clinics.
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46
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Sabino JC, de Almeida MR, Abreu PL, Ferreira AM, Caldas P, Domingues MM, Santos NC, Azzalin CM, Grosso AR, de Almeida SF. Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops. eLife 2022; 11:69476. [PMID: 35191837 PMCID: PMC8896830 DOI: 10.7554/elife.69476] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
DNA oxidation by ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming. The conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) initiates developmental and cell-type-specific transcriptional programs through mechanisms that include changes in the chromatin structure. Here, we show that the presence of 5hmC in the transcribed gene promotes the annealing of the nascent RNA to the template DNA strand, leading to the formation of an R-loop. Depletion of TET enzymes reduced global R-loops in absence of gene expression changes, whereas CRISPR-mediated tethering of TET to an active gene promoted the formation of R-loops. The genome-wide distribution of 5hmC and R-loops show a positive correlation in mouse and human stem cells and overlap in half of all active genes. Moreover, R-loop resolution leads to differential expression of a subset of genes that are involved in crucial events during stem cell proliferation. Altogether, our data reveal that epigenetic reprogramming via TET activity promotes co-transcriptional R-loop formation, disclosing new mechanisms of gene expression regulation.
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Affiliation(s)
- João C Sabino
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Madalena R de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Patrícia L Abreu
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ana M Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Paulo Caldas
- Institute for Health and Bioeconomy, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Marco M Domingues
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Claus M Azzalin
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Rita Grosso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sérgio Fernandes de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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47
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HIF-1 Interacts with TRIM28 and DNA-PK to release paused RNA polymerase II and activate target gene transcription in response to hypoxia. Nat Commun 2022; 13:316. [PMID: 35031618 PMCID: PMC8760265 DOI: 10.1038/s41467-021-27944-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022] Open
Abstract
Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that acts as a regulator of oxygen (O2) homeostasis in metazoan species by binding to hypoxia response elements (HREs) and activating the transcription of hundreds of genes in response to reduced O2 availability. RNA polymerase II (Pol II) initiates transcription of many HIF target genes under non-hypoxic conditions but pauses after approximately 30–60 nucleotides and requires HIF-1 binding for release. Here we report that in hypoxic breast cancer cells, HIF-1 recruits TRIM28 and DNA-dependent protein kinase (DNA-PK) to HREs to release paused Pol II. We show that HIF-1α and TRIM28 assemble the catalytically-active DNA-PK heterotrimer, which phosphorylates TRIM28 at serine-824, enabling recruitment of CDK9, which phosphorylates serine-2 of the Pol II large subunit C-terminal domain as well as the negative elongation factor to release paused Pol II, thereby stimulating productive transcriptional elongation. Our studies reveal a molecular mechanism by which HIF-1 stimulates gene transcription and reveal that the anticancer effects of drugs targeting DNA-PK in breast cancer may be due in part to their inhibition of HIF-dependent transcription. Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that modulates target gene expression in response to changes in oxygen availability. Here the authors show that HIF-1 forms a complex with TRIM28 and DNA-dependent protein kinase (DNA-PK) that phosphorylates TRIM28. This leads to CDK9 recruitment, which stimulates RNA polymerase II (RNAPII) pause release and transcriptional elongation.
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Kaiser C, Bradu A, Gamble N, Caldwell JA, Koh AS. AIRE in context: Leveraging chromatin plasticity to trigger ectopic gene expression. Immunol Rev 2022; 305:59-76. [PMID: 34545959 PMCID: PMC9250823 DOI: 10.1111/imr.13026] [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: 08/15/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022]
Abstract
The emergence of antigen receptor diversity in clonotypic lymphocytes drove the evolution of a novel gene, Aire, that enabled the adaptive immune system to discriminate foreign invaders from self-constituents. AIRE functions in the epithelial cells of the thymus to express genes highly restricted to alternative cell lineages. This somatic plasticity facilitates the selection of a balanced repertoire of T cells that protects the host from harmful self-reactive clones, yet maintains a wide range of affinities for virtually any foreign antigen. Here, we review the latest understanding of AIRE's molecular actions with a focus on its interplay with chromatin. We argue that AIRE is a multi-valent chromatin effector that acts late in the transcription cycle to modulate the activity of previously poised non-coding regulatory elements of tissue-specific genes. We postulate a role for chromatin instability-caused in part by ATP-dependent chromatin remodeling-that variably sets the scope of the accessible landscape on which AIRE can act. We highlight AIRE's intrinsic repressive function and its relevance in providing feedback control. We synthesize these recent advances into a putative model for the mechanistic modes by which AIRE triggers ectopic transcription for immune repertoire selection.
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Affiliation(s)
- Caroline Kaiser
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Alexandra Bradu
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Noah Gamble
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jason A. Caldwell
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Andrew S. Koh
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
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Feng W, Smith CM, Simpson DA, Gupta GP. Targeting Non-homologous and Alternative End Joining Repair to Enhance Cancer Radiosensitivity. Semin Radiat Oncol 2021; 32:29-41. [PMID: 34861993 DOI: 10.1016/j.semradonc.2021.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Many cancer therapies, including radiotherapy, induce DSBs as the major driving mechanism for inducing cancer cell death. Thus, modulating DSB repair has immense potential for radiosensitization, although such interventions must be carefully designed to be tumor selective to ensure that normal tissue toxicities are not also increased. Here, we review mechanisms of error-prone DSB repair through a highly efficient process called end joining. There are two major pathways of end-joining repair: non-homologous end joining (NHEJ) and alternative end joining (a-EJ), both of which can be selectively upregulated in cancer and thus represent attractive therapeutic targets for radiosensitization. These EJ pathways each have therapeutically targetable pioneer factors - DNA-dependent protein kinase catalytic subunit (DNA-PKcs) for NHEJ and DNA Polymerase Theta (Pol θ) for a-EJ. We summarize the current status of therapeutic targeting of NHEJ and a-EJ to enhance the effects of radiotherapy - focusing on challenges that must be overcome and opportunities that require further exploration. By leveraging preclinical insights into mechanisms of altered DSB repair programs in cancer, selective radiosensitization through NHEJ and/or a-EJ targeting remains a highly attractive avenue for ongoing and future clinical investigation.
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Affiliation(s)
| | - Chelsea M Smith
- Lineberger Comprehensive Cancer Center; Pathobiology and Translational Science Graduate Program
| | | | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center; Pathobiology and Translational Science Graduate Program; Department of Radiation Oncology; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC.
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Crewe M, Madabhushi R. Topoisomerase-Mediated DNA Damage in Neurological Disorders. Front Aging Neurosci 2021; 13:751742. [PMID: 34899270 PMCID: PMC8656403 DOI: 10.3389/fnagi.2021.751742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/23/2021] [Indexed: 12/12/2022] Open
Abstract
The nervous system is vulnerable to genomic instability and mutations in DNA damage response factors lead to numerous developmental and progressive neurological disorders. Despite this, the sources and mechanisms of DNA damage that are most relevant to the development of neuronal dysfunction are poorly understood. The identification of primarily neurological abnormalities in patients with mutations in TDP1 and TDP2 suggest that topoisomerase-mediated DNA damage could be an important underlying source of neuronal dysfunction. Here we review the potential sources of topoisomerase-induced DNA damage in neurons, describe the cellular mechanisms that have evolved to repair such damage, and discuss the importance of these repair mechanisms for preventing neurological disorders.
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