1
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Teng Z, Yang L, Zhang Q, Chen Y, Wang X, Zheng Y, Tian A, Tian D, Lin Z, Deng WM, Liu H. Topoisomerase I is an evolutionarily conserved key regulator for satellite DNA transcription. Nat Commun 2024; 15:5151. [PMID: 38886382 PMCID: PMC11183047 DOI: 10.1038/s41467-024-49567-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
RNA Polymerase (RNAP) II transcription on non-coding repetitive satellite DNAs plays an important role in chromosome segregation, but a little is known about the regulation of satellite transcription. We here show that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite DNAs on human centromeres. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation. Interestingly, in response to DNA double-stranded breaks (DSBs), α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner, and these DSB-induced α-satellite RNAs form into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, our findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.
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Affiliation(s)
- Zhen Teng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Lu Yang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Qian Zhang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Yujue Chen
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Xianfeng Wang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Yiran Zheng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Aiguo Tian
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Di Tian
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Wu-Min Deng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hong Liu
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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2
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Geraud M, Cristini A, Salimbeni S, Bery N, Jouffret V, Russo M, Ajello AC, Fernandez Martinez L, Marinello J, Cordelier P, Trouche D, Favre G, Nicolas E, Capranico G, Sordet O. TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks. Cell Rep 2024; 43:114214. [PMID: 38761375 DOI: 10.1016/j.celrep.2024.114214] [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: 03/02/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024] Open
Abstract
TDP1 removes transcription-blocking topoisomerase I cleavage complexes (TOP1ccs), and its inactivating H493R mutation causes the neurodegenerative syndrome SCAN1. However, the molecular mechanism underlying the SCAN1 phenotype is unclear. Here, we generate human SCAN1 cell models using CRISPR-Cas9 and show that they accumulate TOP1ccs along with changes in gene expression and genomic distribution of R-loops. SCAN1 cells also accumulate transcriptional DNA double-strand breaks (DSBs) specifically in the G1 cell population due to increased DSB formation and lack of repair, both resulting from abortive removal of transcription-blocking TOP1ccs. Deficient TDP1 activity causes increased DSB production, and the presence of mutated TDP1 protein hampers DSB repair by a TDP2-dependent backup pathway. This study provides powerful models to study TDP1 functions under physiological and pathological conditions and unravels that a gain of function of the mutated TDP1 protein, which prevents DSB repair, rather than a loss of TDP1 activity itself, could contribute to SCAN1 pathogenesis.
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Affiliation(s)
- Mathéa Geraud
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Agnese Cristini
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Simona Salimbeni
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France; Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Nicolas Bery
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Virginie Jouffret
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France; BigA Core Facility, Centre de Biologie Intégrative (CBI), Université de Toulouse, 31062 Toulouse, France
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Andrea Carla Ajello
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Lara Fernandez Martinez
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Pierre Cordelier
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Didier Trouche
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Estelle Nicolas
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy.
| | - Olivier Sordet
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France.
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3
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Duardo RC, Marinello J, Russo M, Morelli S, Pepe S, Guerra F, Gómez-González B, Aguilera A, Capranico G. Human DNA topoisomerase I poisoning causes R loop-mediated genome instability attenuated by transcription factor IIS. SCIENCE ADVANCES 2024; 10:eadm8196. [PMID: 38787953 PMCID: PMC11122683 DOI: 10.1126/sciadv.adm8196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/18/2024] [Indexed: 05/26/2024]
Abstract
DNA topoisomerase I can contribute to cancer genome instability. During catalytic activity, topoisomerase I forms a transient intermediate, topoisomerase I-DNA cleavage complex (Top1cc) to allow strand rotation and duplex relaxation, which can lead to elevated levels of DNA-RNA hybrids and micronuclei. To comprehend the underlying mechanisms, we have integrated genomic data of Top1cc-triggered hybrids and DNA double-strand breaks (DSBs) shortly after Top1cc induction, revealing that Top1ccs increase hybrid levels with different mechanisms. DSBs are at highly transcribed genes in early replicating initiation zones and overlap with hybrids downstream of accumulated RNA polymerase II (RNAPII) at gene 5'-ends. A transcription factor IIS mutant impairing transcription elongation further increased RNAPII accumulation likely due to backtracking. Moreover, Top1ccs can trigger micronuclei when occurring during late G1 or early/mid S, but not during late S. As micronuclei and transcription-replication conflicts are attenuated by transcription factor IIS, our results support a role of RNAPII arrest in Top1cc-induced transcription-replication conflicts leading to DSBs and micronuclei.
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Affiliation(s)
- Renée C. Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Sara Morelli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Universidad de Sevilla–CSIC, Calle Américo Vespucio 24, 41092 Seville, Spain
- Departamento de Genetica, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Universidad de Sevilla–CSIC, Calle Américo Vespucio 24, 41092 Seville, Spain
- Departamento de Genetica, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
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4
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Teng Z, Yang L, Zhang Q, Chen Y, Wang X, Zheng Y, Tian A, Tian D, Lin Z, Deng WM, Liu H. Topoisomerase I is an Evolutionarily Conserved Key Regulator for Satellite DNA Transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592391. [PMID: 38746280 PMCID: PMC11092777 DOI: 10.1101/2024.05.03.592391] [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
Repetitive satellite DNAs, divergent in nucleic-acid sequence and size across eukaryotes, provide a physical site for centromere assembly to orchestrate chromosome segregation during the cell cycle. These non-coding DNAs are transcribed by RNA polymerase (RNAP) II and the transcription has been shown to play a role in chromosome segregation, but a little is known about the regulation of centromeric transcription, especially in higher organisms with tandemly-repeated-DNA-sequence centromeres. Using RNA interference knockdown, chemical inhibition and AID/IAA degradation, we show that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite on centromeres in human cells. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation on centromeres. Interestingly, in response to DNA double-stranded breaks (DSBs) induced by chemotherapy drugs or CRSPR/Cas9, α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner. These DSB-induced α-satellite RNAs were predominantly derived from the α-satellite high-order repeats of human centromeres and forms into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, our findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.
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Affiliation(s)
- Zhen Teng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Lu Yang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Qian Zhang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Yujue Chen
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Xianfeng Wang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Yiran Zheng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Aiguo Tian
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Di Tian
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Wu-Min Deng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hong Liu
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
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5
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Liang HT, Yan JY, Yao HJ, Zhang XN, Xing ZM, Liu L, Chen YQ, Li GR, Huang J, He YD, Zheng KW. G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity. Nucleic Acids Res 2024; 52:2142-2156. [PMID: 38340342 PMCID: PMC10954455 DOI: 10.1093/nar/gkae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/03/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Human DNA topoisomerase 1 (Top1) is a crucial enzyme responsible for alleviating torsional stress on DNA during transcription and replication, thereby maintaining genome stability. Previous researches had found that non-working Top1 interacted extensively with chromosomal DNA in human cells. However, the reason for its retention on chromosomal DNA remained unclear. In this study, we discovered a close association between Top1 and chromosomal DNA, specifically linked to the presence of G-quadruplex (G4) structures. G4 structures, formed during transcription, trap Top1 and hinder its ability to relax neighboring DNAs. Disruption of the Top1-G4 interaction using G4 ligand relieved the inhibitory effect of G4 on Top1 activity, resulting in a further reduction of R-loop levels in cells. Additionally, the activation of Top1 through the use of a G4 ligand enhanced the toxicity of Top1 inhibitors towards cancer cells. Our study uncovers a negative regulation mechanism of human Top1 and highlights a novel pathway for activating Top1.
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Affiliation(s)
- Hui-ting Liang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Jiang-yu Yan
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Hao-jun Yao
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Xue-nan Zhang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Zhi-ming Xing
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yao-qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Guo-rui Li
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Huang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Yi-de He
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Ke-wei Zheng
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
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6
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Hidmi O, Oster S, Monin J, Aqeilan RI. TOP1 and R-loops facilitate transcriptional DSBs at hypertranscribed cancer driver genes. iScience 2024; 27:109082. [PMID: 38375218 PMCID: PMC10875566 DOI: 10.1016/j.isci.2024.109082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/26/2023] [Accepted: 01/28/2024] [Indexed: 02/21/2024] Open
Abstract
DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employ several techniques to map DSBs, R-loops, and topoisomerase 1 cleavage complex (TOP1cc) to comprehensively investigate the interplay between transcription, DSBs, topoisomerase 1 (TOP1), and R-loops. Our findings reveal the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops. Remarkably, transcription-associated DSBs at these loci are significantly reduced upon depletion of R-loops and TOP1, uncovering the pivotal roles of TOP1 and R-loops in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development, highlighting the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations.
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Affiliation(s)
- Osama Hidmi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sara Oster
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan Monin
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rami I. Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Cyprus Cancer Research Institute (CCRI), Nicosia, Cyprus
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7
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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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8
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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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9
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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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10
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Benham CJ. DNA superhelicity. Nucleic Acids Res 2024; 52:22-48. [PMID: 37994702 PMCID: PMC10783518 DOI: 10.1093/nar/gkad1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs. Fixing L has a range of structural, energetic and functional consequences. Here we consider how L having different integer values (that is, different superhelicities) affects ccDNA molecules. The approaches used are primarily theoretical, and are developed from a historical perspective. In brief, processes that either relax or increase superhelicity, or repartition what is there, may either release or require free energy. The energies involved can be substantial, sufficient to influence many events, directly or indirectly. Here two examples are developed. The changes of unconstrained superhelicity that occur during nucleosome attachment and release are examined. And a simple theoretical model of superhelically driven DNA structural transitions is described that calculates equilibrium distributions for populations of identical topoisomers. This model is used to examine how these distributions change with superhelicity and other factors, and applied to analyze several situations of biological interest.
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Affiliation(s)
- Craig J Benham
- UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
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11
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Vega M, Barrios R, Fraile R, de Castro Cogle K, Castillo D, Anglada R, Casals F, Ayté J, Lowy-Gallego E, Hidalgo E. Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery. Nucleic Acids Res 2023; 51:12161-12173. [PMID: 37956308 PMCID: PMC10711424 DOI: 10.1093/nar/gkad1066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Chromatin remodeling is essential to allow full development of alternative gene expression programs in response to environmental changes. In fission yeast, oxidative stress triggers massive transcriptional changes including the activation of hundreds of genes, with the participation of histone modifying complexes and chromatin remodelers. DNA transcription is associated to alterations in DNA topology, and DNA topoisomerases facilitate elongation along gene bodies. Here, we test whether the DNA topoisomerase Top1 participates in the RNA polymerase II-dependent activation of the cellular response to oxidative stress. Cells lacking Top1 are resistant to H2O2 stress. The transcriptome of Δtop1 strain was not greatly affected in the absence of stress, but activation of the anti-stress gene expression program was more sustained than in wild-type cells. Top1 associated to stress open reading frames. While the nucleosomes of stress genes are partially and transiently evicted during stress, the chromatin configuration remains open for longer times in cells lacking Top1, facilitating RNA polymerase II progression. We propose that, by removing DNA tension arising from transcription, Top1 facilitates nucleosome reassembly and works in synergy with the chromatin remodeler Hrp1 as opposing forces to transcription and to Snf22 / Hrp3 opening remodelers.
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Affiliation(s)
- Montserrat Vega
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rubén Barrios
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rodrigo Fraile
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | | | - Roger Anglada
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ferran Casals
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ernesto Lowy-Gallego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
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12
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D'Alessio Y, D'Alfonso A, Camilloni G. Chromatin conformations of HSP12 during transcriptional activation in the Saccharomyces cerevisiae stationary phase. Adv Biol Regul 2023; 90:100986. [PMID: 37741159 DOI: 10.1016/j.jbior.2023.100986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/17/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
During evolution, living cells have developed sophisticated molecular and physiological processes to cope with a variety of stressors. These mechanisms, which collectively constitute the Environmental Stress Response, involve the activation/repression of hundreds of genes that are regulated to respond rapidly and effectively to protect the cell. The main stressors include sudden increases in environmental temperature and osmolarity, exposure to heavy metals, nutrient limitation, ROS accumulation, and protein-damaging events. The growth stages of the yeast S. cerevisiae proceed from the exponential to the diauxic phase, finally reaching the stationary phase. It is in this latter phase that the main stressor events are more active. In the present work, we aim to understand whether the responses evoked by the sudden onset of a stressor, like what happens to cells going through the stationary phase, would be different or similar to those induced by a gradual increase in the same stimulus. To this aim, we studied the expression of the HSP12 gene of the HSP family of proteins, typically induced by stress conditions, with a focus on the role of chromatin in this regulation. Analyses of nucleosome occupancy and three-dimensional chromatin conformation suggest the activation of a different response pathway upon a sudden vs a gradual onset of a stress stimulus. Here we show that it is the three-dimensional chromatin structure of HSP12, rather than nucleosome remodeling, that becomes altered in HSP12 transcription during the stationary phase.
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Affiliation(s)
- Yuri D'Alessio
- Dipartimento di Biologia e Biotecnologie, University of Rome, Sapienza Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Anna D'Alfonso
- Dipartimento di Biologia e Biotecnologie, University of Rome, Sapienza Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Giorgio Camilloni
- Dipartimento di Biologia e Biotecnologie, University of Rome, Sapienza Piazzale A. Moro 5, 00185, Rome, Italy.
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13
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Vihervaara A, Versluis P, Himanen SV, Lis JT. PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution. Nat Commun 2023; 14:7039. [PMID: 37923726 PMCID: PMC10624850 DOI: 10.1038/s41467-023-42715-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. Here, we develop Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq), which double-selects nascent RNAs and transcription complexes, and track phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. We uncover precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide (+1 nt), through early (+18 to +30 nt) and late (+31 to +60 nt) promoter-proximal pause, and into productive elongation. Pol II CTD is predominantly unphosphorylated from initiation until the early pause-region, whereas serine-2- and serine-5-phosphorylations are preferentially deposited in the later pause-region. Upon pause-release, serine-7-phosphorylation rapidly increases and dominates over the region where Pol II assembles elongation factors and accelerates to its full elongational speed. Interestingly, tracking CTD modifications upon heat-induced transcriptional reprogramming demonstrates that Pol II with phosphorylated CTD remains paused on thousands of heat-repressed genes. These results uncover dynamic Pol II regulation at rate-limiting steps of transcription and provide a nucleotide-resolution technique for tracking composition of engaged transcription complexes.
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Affiliation(s)
- Anniina Vihervaara
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden.
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
| | - Philip Versluis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Samu V Himanen
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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14
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El-Khamisy SF. Oxidative DNA damage and repair at non-coding regulatory regions. Trends Cell Biol 2023; 33:939-949. [PMID: 37029073 DOI: 10.1016/j.tcb.2023.03.004] [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: 01/05/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 04/09/2023]
Abstract
DNA breaks at protein-coding sequences are well-established threats to tissue homeostasis and maintenance. They arise from the exposure to intracellular and environmental genotoxins, causing damage in one or two strands of the DNA. DNA breaks have been also reported in non-coding regulatory regions such as enhancers and promoters. They arise from essential cellular processes required for gene transcription, cell identity and function. One such process that has attracted recent attention is the oxidative demethylation of DNA and histones, which generates abasic sites and DNA single-strand breaks. Here, we discuss how oxidative DNA breaks at non-coding regulatory regions are generated and the recently reported role of NuMA (nuclear mitotic apparatus) protein in promoting transcription and repair at these regions.
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Affiliation(s)
- Sherif F El-Khamisy
- School of Biosciences, The Healthy Lifespan and Neuroscience Institutes, Firth Court, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK.
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15
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Lau MS, Hu Z, Zhao X, Tan YS, Liu J, Huang H, Yeo CJ, Leong HF, Grinchuk OV, Chan JK, Yan J, Tee WW. Transcriptional repression by a secondary DNA binding surface of DNA topoisomerase I safeguards against hypertranscription. Nat Commun 2023; 14:6464. [PMID: 37833256 PMCID: PMC10576097 DOI: 10.1038/s41467-023-42078-9] [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: 07/23/2022] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Regulation of global transcription output is important for normal development and disease, but little is known about the mechanisms involved. DNA topoisomerase I (TOP1) is an enzyme well-known for its role in relieving DNA supercoils for enabling transcription. Here, we report a non-enzymatic function of TOP1 that downregulates RNA synthesis. This function is dependent on specific DNA-interacting residues located on a conserved protein surface. A loss-of-function knock-in mutation on this surface, R548Q, is sufficient to cause hypertranscription and alter differentiation outcomes in mouse embryonic stem cells (mESCs). Hypertranscription in mESCs is accompanied by reduced TOP1 chromatin binding and change in genomic supercoiling. Notably, the mutation does not impact TOP1 enzymatic activity; rather, it diminishes TOP1-DNA binding and formation of compact protein-DNA structures. Thus, TOP1 exhibits opposing influences on transcription through distinct activities which are likely to be coordinated. This highlights TOP1 as a safeguard of appropriate total transcription levels in cells.
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Affiliation(s)
- Mei Sheng Lau
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Zhenhua Hu
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaodan Zhao
- Department of Physics, National University of Singapore, Singapore, 117551, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
| | - Jinyue Liu
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Hua Huang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Electrophysiology Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Clarisse Jingyi Yeo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwei Fen Leong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Oleg V Grinchuk
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Justin Kaixuan Chan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, 117551, Singapore.
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117557, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
| | - Wee-Wei Tee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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16
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Cameron DP, Grosser J, Ladigan S, Kuzin V, Iliopoulou E, Wiegard A, Benredjem H, Jackson K, Liffers ST, Lueong S, Cheung PF, Vangala D, Pohl M, Viebahn R, Teschendorf C, Wolters H, Usta S, Geng K, Kutter C, Arsenian-Henriksson M, Siveke JT, Tannapfel A, Schmiegel W, Hahn SA, Baranello L. Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription. SCIENCE ADVANCES 2023; 9:eadg5109. [PMID: 37831776 PMCID: PMC10575591 DOI: 10.1126/sciadv.adg5109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Pancreatic carcinoma lacks effective therapeutic strategies resulting in poor prognosis. Transcriptional dysregulation due to alterations in KRAS and MYC affects initiation, development, and survival of this tumor type. Using patient-derived xenografts of KRAS- and MYC-driven pancreatic carcinoma, we show that coinhibition of topoisomerase 1 (TOP1) and bromodomain-containing protein 4 (BRD4) synergistically induces tumor regression by targeting promoter pause release. Comparing the nascent transcriptome with the recruitment of elongation and termination factors, we found that coinhibition of TOP1 and BRD4 disrupts recruitment of transcription termination factors. Thus, RNA polymerases transcribe downstream of genes for hundreds of kilobases leading to readthrough transcription. This occurs during replication, perturbing replisome progression and inducing DNA damage. The synergistic effect of TOP1 + BRD4 inhibition is specific to cancer cells leaving normal cells unaffected, highlighting the tumor's vulnerability to transcriptional defects. This preclinical study provides a mechanistic understanding of the benefit of combining TOP1 and BRD4 inhibitors to treat pancreatic carcinomas addicted to oncogenic drivers of transcription and replication.
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Affiliation(s)
- Donald P. Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Grosser
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Swetlana Ladigan
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Evanthia Iliopoulou
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anika Wiegard
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hajar Benredjem
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kathryn Jackson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sven T. Liffers
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Smiths Lueong
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Phyllis F. Cheung
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Deepak Vangala
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Michael Pohl
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Richard Viebahn
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Surgery, Bochum, Germany
| | | | - Heiner Wolters
- Department of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Selami Usta
- Department of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Keyi Geng
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Jens T. Siveke
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Wolff Schmiegel
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Stephan A. Hahn
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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17
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Papadopoulos D, Uhl L, Ha SA, Eilers M. Beyond gene expression: how MYC relieves transcription stress. Trends Cancer 2023; 9:805-816. [PMID: 37422352 DOI: 10.1016/j.trecan.2023.06.008] [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: 04/23/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
MYC oncoproteins are key drivers of tumorigenesis. As transcription factors, MYC proteins regulate transcription by all three nuclear polymerases and gene expression. Accumulating evidence shows that MYC proteins are also crucial for enhancing the stress resilience of transcription. MYC proteins relieve torsional stress caused by active transcription, prevent collisions between the transcription and replication machineries, resolve R-loops, and repair DNA damage by participating in a range of protein complexes and forming multimeric structures at sites of genomic instability. We review the key complexes and multimerization properties of MYC proteins that allow them to mitigate transcription-associated DNA damage, and propose that the oncogenic functions of MYC extend beyond the modulation of gene expression.
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Affiliation(s)
- Dimitrios Papadopoulos
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University Hospital Würzburg, Würzburg, Germany
| | - Leonie Uhl
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefanie Anh Ha
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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18
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Kotekar A, Singh AK, Devaiah BN. BRD4 and MYC: power couple in transcription and disease. FEBS J 2023; 290:4820-4842. [PMID: 35866356 PMCID: PMC9867786 DOI: 10.1111/febs.16580] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 01/26/2023]
Abstract
The MYC proto-oncogene and BRD4, a BET family protein, are two cardinal proteins that have a broad influence in cell biology and disease. Both proteins are expressed ubiquitously in mammalian cells and play central roles in controlling growth, development, stress responses and metabolic function. As chromatin and transcriptional regulators, they play a critical role in regulating the expression of a burgeoning array of genes, maintaining chromatin architecture and genome stability. Consequently, impairment of their function or regulation leads to many diseases, with cancer being the most predominant. Interestingly, accumulating evidence indicates that regulation of the expression and functions of MYC are tightly intertwined with BRD4 at both transcriptional and post-transcriptional levels. Here, we review the mechanisms by which MYC and BRD4 are regulated, their functions in governing various molecular mechanisms and the consequences of their dysregulation that lead to disease. We present a perspective of how the regulatory mechanisms for the two proteins could be entwined at multiple points in a BRD4-MYC nexus that leads to the modulation of their functions and disease upon dysregulation.
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Affiliation(s)
- Aparna Kotekar
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Amit Kumar Singh
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
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19
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Herbert A. Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation. J Biol Chem 2023; 299:105140. [PMID: 37544644 PMCID: PMC10474125 DOI: 10.1016/j.jbc.2023.105140] [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: 05/11/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023] Open
Abstract
The role of alternate DNA conformations such as Z-DNA in the regulation of transcription is currently underappreciated. These structures are encoded by sequences called flipons, many of which are enriched in promoter and enhancer regions. Through a change in their conformation, flipons provide a tunable mechanism to mechanically reset promoters for the next round of transcription. They act as actuators that capture and release energy to ensure that the turnover of the proteins at promoters is optimized to cell state. Likewise, the single-stranded DNA formed as flipons cycle facilitates the docking of RNAs that are able to microcode promoter conformations and canalize the pervasive transcription commonly observed in metazoan genomes. The strand-specific nature of the interaction between RNA and DNA likely accounts for the known asymmetry of epigenetic marks present on the histone tetramers that pair to form nucleosomes. The role of these supercoil-dependent processes in promoter choice and transcriptional interference is reviewed. The evolutionary implications are examined: the resilience and canalization of flipon-dependent gene regulation is contrasted with the rapid adaptation enabled by the spread of flipon repeats throughout the genome. Overall, the current findings underscore the important role of flipons in modulating the readout of genetic information and how little we know about their biology.
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Affiliation(s)
- Alan Herbert
- Discovery Division, InsideOutBio, Charlestown, Massachusetts, USA.
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20
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Winter LM, Reinhardt D, Schatter A, Tissen V, Wiora H, Gerlach D, Tontsch-Grunt U, Colbatzky F, Stierstorfer B, Yun SW. Molecular basis of GDF15 induction and suppression by drugs in cardiomyocytes and cancer cells toward precision medicine. Sci Rep 2023; 13:12061. [PMID: 37495707 PMCID: PMC10372009 DOI: 10.1038/s41598-023-38450-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023] Open
Abstract
GDF15 has recently emerged as a key driver of the development of various disease conditions including cancer cachexia. Not only the tumor itself but also adverse effects of chemotherapy have been reported to contribute to increased GDF15. Although regulation of GDF15 transcription by BET domain has recently been reported, the molecular mechanisms of GDF15 gene regulation by drugs are still unknown, leaving uncertainty about the safe and effective therapeutic strategies targeting GDF15. We screened various cardiotoxic drugs and BET inhibitors for their effects on GDF15 regulation in human cardiomyocytes and cancer cell lines and analyzed in-house and public gene signature databases. We found that DNA damaging drugs induce GDF15 in cardiomyocytes more strongly than drugs with other modes of action. In cancer cells, GDF15 induction varied depending on drug- and cell type-specific gene signatures including mutations in PI3KCA, TP53, BRAF and MUC16. GDF15 suppression by BET inhibition is particularly effective in cancer cells with low activity of the PI3K/Akt axis and high extracellular concentrations of pantothenate. Our findings provide insights that the risk for GDF15 overexpression and concomitant cachexia can be reduced by a personalized selection of anticancer drugs and patients for precision medicine.
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Affiliation(s)
- Lisa-Maria Winter
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65, 88397, Biberach an Der Riß, Germany
| | - Diana Reinhardt
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65, 88397, Biberach an Der Riß, Germany
| | - Ariane Schatter
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65, 88397, Biberach an Der Riß, Germany
| | - Vivien Tissen
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65, 88397, Biberach an Der Riß, Germany
| | - Heike Wiora
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65, 88397, Biberach an Der Riß, Germany
| | - Daniel Gerlach
- Boehringer Ingelheim RCV, GmbH & Co KG, 1120, Vienna, Austria
| | | | - Florian Colbatzky
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65, 88397, Biberach an Der Riß, Germany
| | - Birgit Stierstorfer
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65, 88397, Biberach an Der Riß, Germany
| | - Seong-Wook Yun
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65, 88397, Biberach an Der Riß, Germany.
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21
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Lista MJ, Jousset AC, Cheng M, Saint-André V, Perrot E, Rodrigues M, Di Primo C, Gadelle D, Toccafondi E, Segeral E, Berlioz-Torrent C, Emiliani S, Mergny JL, Lavigne M. DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence. Retrovirology 2023; 20:10. [PMID: 37254203 DOI: 10.1186/s12977-023-00625-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/20/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Once integrated in the genome of infected cells, HIV-1 provirus is transcribed by the cellular transcription machinery. This process is regulated by both viral and cellular factors, which are necessary for an efficient viral replication as well as for the setting up of viral latency, leading to a repressed transcription of the integrated provirus. RESULTS In this study, we examined the role of two parameters in HIV-1 LTR promoter activity. We identified DNA topoisomerase1 (TOP1) to be a potent repressor of this promoter and linked this repression to its catalytic domain. Additionally, we confirmed the folding of a Guanine quadruplex (G4) structure in the HIV-1 promoter and its repressive effect. We demonstrated a direct interaction between TOP1 and this G4 structure, providing evidence of a functional relationship between the two repressive elements. Mutations abolishing G4 folding affected TOP1/G4 interaction and hindered G4-dependent inhibition of TOP1 catalytic activity in vitro. As a result, HIV-1 promoter activity was reactivated in a native chromatin environment. Lastly, we noticed an enrichment of predicted G4 sequences in the promoter of TOP1-repressed cellular genes. CONCLUSIONS Our results demonstrate the formation of a TOP1/G4 complex on the HIV-1 LTR promoter and its repressive effect on the promoter activity. They reveal the existence of a new mechanism of TOP1/G4-dependent transcriptional repression conserved between viral and human genes. This mechanism contrasts with the known property of TOP1 as global transcriptional activator and offers new perspectives for anti-cancer and anti-viral strategies.
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Affiliation(s)
- María José Lista
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Anne-Caroline Jousset
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
- Université de Strasbourg, CNRS UPR 9002, Architecture et réactivité de l'ARN, 67000, Strasbourg, France
| | - Mingpan Cheng
- CNRS UMR 5320, INSERM U1212, ARNA, Univ. Bordeaux, IECB, 33000, Bordeaux, France
- School of Engineering, China Pharmaceutical University, Nanjing, 211198, China
| | - Violaine Saint-André
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université Paris Cité, 75015, Paris, France
| | - Elouan Perrot
- Institut Pasteur, Departement of Virology, Université Paris Cité, 75015, Paris, France
| | - Melissa Rodrigues
- Institut Pasteur, Departement of Virology, Université Paris Cité, 75015, Paris, France
| | - Carmelo Di Primo
- CNRS UMR 5320, INSERM U1212, ARNA, Univ. Bordeaux, IECB, 33000, Bordeaux, France
| | - Danielle Gadelle
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif Sur Yvette, Cedex, France
| | - Elenia Toccafondi
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
- Université de Strasbourg, CNRS UPR 9002, Architecture et réactivité de l'ARN, 67000, Strasbourg, France
| | - Emmanuel Segeral
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
| | | | - Stéphane Emiliani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
| | - Jean-Louis Mergny
- CNRS UMR 5320, INSERM U1212, ARNA, Univ. Bordeaux, IECB, 33000, Bordeaux, France
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Marc Lavigne
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France.
- Institut Pasteur, Departement of Virology, Université Paris Cité, 75015, Paris, France.
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22
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Straub S, Sampaio NG. Activation of cytosolic RNA sensors by endogenous ligands: roles in disease pathogenesis. Front Immunol 2023; 14:1092790. [PMID: 37292201 PMCID: PMC10244536 DOI: 10.3389/fimmu.2023.1092790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
Early detection of infection is a central and critical component of our innate immune system. Mammalian cells have developed specialized receptors that detect RNA with unusual structures or of foreign origin - a hallmark of many virus infections. Activation of these receptors induces inflammatory responses and an antiviral state. However, it is increasingly appreciated that these RNA sensors can also be activated in the absence of infection, and that this 'self-activation' can be pathogenic and promote disease. Here, we review recent discoveries in sterile activation of the cytosolic innate immune receptors that bind RNA. We focus on new aspects of endogenous ligand recognition uncovered in these studies, and their roles in disease pathogenesis.
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Affiliation(s)
- Sarah Straub
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Natalia G. Sampaio
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
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23
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Patel HP, Coppola S, Pomp W, Aiello U, Brouwer I, Libri D, Lenstra TL. DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes. Mol Cell 2023; 83:1573-1587.e8. [PMID: 37207624 DOI: 10.1016/j.molcel.2023.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 02/14/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
DNA supercoiling has emerged as a major contributor to gene regulation in bacteria, but how DNA supercoiling impacts transcription dynamics in eukaryotes is unclear. Here, using single-molecule dual-color nascent transcription imaging in budding yeast, we show that transcriptional bursting of divergent and tandem GAL genes is coupled. Temporal coupling of neighboring genes requires rapid release of DNA supercoils by topoisomerases. When DNA supercoils accumulate, transcription of one gene inhibits transcription at its adjacent genes. Transcription inhibition of the GAL genes results from destabilized binding of the transcription factor Gal4. Moreover, wild-type yeast minimizes supercoiling-mediated inhibition by maintaining sufficient levels of topoisomerases. Overall, we discover fundamental differences in transcriptional control by DNA supercoiling between bacteria and yeast and show that rapid supercoiling release in eukaryotes ensures proper gene expression of neighboring genes.
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Affiliation(s)
- Heta P Patel
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Stefano Coppola
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Wim Pomp
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Ineke Brouwer
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands.
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24
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Kumar S, Gahramanov V, Patel S, Yaglom J, Kaczmarczyk L, Alexandrov IA, Gerlitz G, Salmon-Divon M, Sherman MY. Evolution of Resistance to Irinotecan in Cancer Cells Involves Generation of Topoisomerase-Guided Mutations in Non-Coding Genome That Reduce the Chances of DNA Breaks. Int J Mol Sci 2023; 24:ijms24108717. [PMID: 37240063 DOI: 10.3390/ijms24108717] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/01/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Resistance to chemotherapy is a leading cause of treatment failure. Drug resistance mechanisms involve mutations in specific proteins or changes in their expression levels. It is commonly understood that resistance mutations happen randomly prior to treatment and are selected during the treatment. However, the selection of drug-resistant mutants in culture could be achieved by multiple drug exposures of cloned genetically identical cells and thus cannot result from the selection of pre-existent mutations. Accordingly, adaptation must involve the generation of mutations de novo upon drug treatment. Here we explored the origin of resistance mutations to a widely used Top1 inhibitor, irinotecan, which triggers DNA breaks, causing cytotoxicity. The resistance mechanism involved the gradual accumulation of recurrent mutations in non-coding regions of DNA at Top1-cleavage sites. Surprisingly, cancer cells had a higher number of such sites than the reference genome, which may define their increased sensitivity to irinotecan. Homologous recombination repairs of DNA double-strand breaks at these sites following initial drug exposures gradually reverted cleavage-sensitive "cancer" sequences back to cleavage-resistant "normal" sequences. These mutations reduced the generation of DNA breaks upon subsequent exposures, thus gradually increasing drug resistance. Together, large target sizes for mutations and their Top1-guided generation lead to their gradual and rapid accumulation, synergistically accelerating the development of resistance.
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Affiliation(s)
- Santosh Kumar
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Valid Gahramanov
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Shivani Patel
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Julia Yaglom
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Lukasz Kaczmarczyk
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Ivan A Alexandrov
- Department of Anatomy and Anthropology & Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | | | - Michael Y Sherman
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
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25
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Kumar S, Sherman MY. Resistance to TOP-1 Inhibitors: Good Old Drugs Still Can Surprise Us. Int J Mol Sci 2023; 24:ijms24087233. [PMID: 37108395 PMCID: PMC10138578 DOI: 10.3390/ijms24087233] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Irinotecan (SN-38) is a potent and broad-spectrum anticancer drug that targets DNA topoisomerase I (Top1). It exerts its cytotoxic effects by binding to the Top1-DNA complex and preventing the re-ligation of the DNA strand, leading to the formation of lethal DNA breaks. Following the initial response to irinotecan, secondary resistance is acquired relatively rapidly, compromising its efficacy. There are several mechanisms contributing to the resistance, which affect the irinotecan metabolism or the target protein. In addition, we have demonstrated a major resistance mechanism associated with the elimination of hundreds of thousands of Top1 binding sites on DNA that can arise from the repair of prior Top1-dependent DNA cleavages. Here, we outline the major mechanisms of irinotecan resistance and highlight recent advancements in the field. We discuss the impact of resistance mechanisms on clinical outcomes and the potential strategies to overcome resistance to irinotecan. The elucidation of the underlying mechanisms of irinotecan resistance can provide valuable insights for the development of effective therapeutic strategies.
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Affiliation(s)
- Santosh Kumar
- Department of Molecular Biology, Ariel University, Ariel 40700, Israel
| | - Michael Y Sherman
- Department of Molecular Biology, Ariel University, Ariel 40700, Israel
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26
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Stoeger T. The Road Less Traveled: Uncovering the Convergence Toward Specific Pleiotropic Phenotypes in Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534472. [PMID: 37034589 PMCID: PMC10081180 DOI: 10.1101/2023.03.28.534472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Aging is a complex process influenced by a wide range of environmental and molecular factors. Despite this complexity, individuals tend to age in highly similar ways, leading to the question of what drives this convergence. Recent research, including my own discoveries, suggests that the length of transcript molecules plays a crucial role in age-dependent changes to the transcriptome. Drawing inspiration from the road trip analogy of cellular transcription, I propose that a non-linear scaling law drives convergence towards specific pleiotropic phenotypes in biological aging. This scaling law is based on the notion that molecular changes observed during aging may reflect unspecific damage to cellular physiology. By validating this hypothesis, I can improve our understanding of biological aging and identify new candidate compounds for anti-aging interventions, as well as re-identify one known intervention. This work has actionable implications for improving human health and extending lifespans.
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Affiliation(s)
- Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
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27
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de Vasconcelos Junior AA, Tirado-Vélez JM, Martín-Galiano AJ, Megias D, Ferrándiz MJ, Hernández P, Amblar M, de la Campa AG. StaR Is a Positive Regulator of Topoisomerase I Activity Involved in Supercoiling Maintenance in Streptococcus pneumoniae. Int J Mol Sci 2023; 24:ijms24065973. [PMID: 36983048 PMCID: PMC10053502 DOI: 10.3390/ijms24065973] [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: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
The DNA topoisomerases gyrase and topoisomerase I as well as the nucleoid-associated protein HU maintain supercoiling levels in Streptococcus pneumoniae, a main human pathogen. Here, we characterized, for the first time, a topoisomerase I regulator protein (StaR). In the presence of sub-inhibitory novobiocin concentrations, which inhibit gyrase activity, higher doubling times were observed in a strain lacking staR, and in two strains in which StaR was over-expressed either under the control of the ZnSO4-inducible PZn promoter (strain ΔstaRPZnstaR) or of the maltose-inducible PMal promoter (strain ΔstaRpLS1ROMstaR). These results suggest that StaR has a direct role in novobiocin susceptibility and that the StaR level needs to be maintained within a narrow range. Treatment of ΔstaRPZnstaR with inhibitory novobiocin concentrations resulted in a change of the negative DNA supercoiling density (σ) in vivo, which was higher in the absence of StaR (σ = -0.049) than when StaR was overproduced (σ = -0.045). We have located this protein in the nucleoid by using super-resolution confocal microscopy. Through in vitro activity assays, we demonstrated that StaR stimulates TopoI relaxation activity, while it has no effect on gyrase activity. Interaction between TopoI and StaR was detected both in vitro and in vivo by co-immunoprecipitation. No alteration of the transcriptome was associated with StaR amount variation. The results suggest that StaR is a new streptococcal nucleoid-associated protein that activates topoisomerase I activity by direct protein-protein interaction.
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Affiliation(s)
| | - Jose M Tirado-Vélez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Antonio J Martín-Galiano
- Unidades Centrales Científico-Técnicas, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Diego Megias
- Unidad de Microscopía Confocal, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - María-José Ferrándiz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Pablo Hernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Mónica Amblar
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Adela G de la Campa
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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28
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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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29
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Herbert A, Pavlov F, Konovalov D, Poptsova M. Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations. Int J Mol Sci 2023; 24:ijms24054884. [PMID: 36902315 PMCID: PMC10003719 DOI: 10.3390/ijms24054884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
The classical view of gene regulation draws from prokaryotic models, where responses to environmental changes involve operons regulated by sequence-specific protein interactions with DNA, although it is now known that operons are also modulated by small RNAs. In eukaryotes, pathways based on microRNAs (miR) regulate the readout of genomic information from transcripts, while alternative nucleic acid structures encoded by flipons influence the readout of genetic programs from DNA. Here, we provide evidence that miR- and flipon-based mechanisms are deeply connected. We analyze the connection between flipon conformation and the 211 highly conserved human miR that are shared with other placental and other bilateral species. The direct interaction between conserved miR (c-miR) and flipons is supported by sequence alignments and the engagement of argonaute proteins by experimentally validated flipons as well as their enrichment in promoters of coding transcripts important in multicellular development, cell surface glycosylation and glutamatergic synapse specification with significant enrichments at false discovery rates as low as 10-116. We also identify a second subset of c-miR that targets flipons essential for retrotransposon replication, exploiting that vulnerability to limit their spread. We propose that miR can act in a combinatorial manner to regulate the readout of genetic information by specifying when and where flipons form non-B DNA (NoB) conformations, providing the interactions of the conserved hsa-miR-324-3p with RELA and the conserved hsa-miR-744 with ARHGAP5 genes as examples.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
- Correspondence:
| | - Fedor Pavlov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Dmitrii Konovalov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
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30
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Singh AK, Chen Q, Nguyen C, Meerzaman D, Singer DS. Cohesin regulates alternative splicing. SCIENCE ADVANCES 2023; 9:eade3876. [PMID: 36857449 PMCID: PMC9977177 DOI: 10.1126/sciadv.ade3876] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Cohesin, a trimeric complex that establishes sister chromatid cohesion, has additional roles in chromatin organization and transcription. We report that among those roles is the regulation of alternative splicing through direct interactions and in situ colocalization with splicing factors. Degradation of cohesin results in marked changes in splicing, independent of its effects on transcription. Introduction of a single cohesin point mutation in embryonic stem cells alters splicing patterns, demonstrating causality. In primary human acute myeloid leukemia, mutations in cohesin are highly correlated with distinct patterns of alternative splicing. Cohesin also directly interacts with BRD4, another splicing regulator, to generate a pattern of splicing that is distinct from either factor alone, documenting their functional interaction. These findings identify a role for cohesin in regulating alternative splicing in both normal and leukemic cells and provide insights into the role of cohesin mutations in human disease.
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Affiliation(s)
- Amit K. Singh
- Experimental Immunology Branch, Center for Cancer Research, Bethesda, MD, USA
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Qingrong Chen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Cu Nguyen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Dinah S. Singer
- Experimental Immunology Branch, Center for Cancer Research, Bethesda, MD, USA
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
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31
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Saha S, Pommier Y. R-loops, type I topoisomerases and cancer. NAR Cancer 2023; 5:zcad013. [PMID: 37600974 PMCID: PMC9984992 DOI: 10.1093/narcan/zcad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
R-loops are abundant and dynamic structures ubiquitously present in human cells both in the nuclear and mitochondrial genomes. They form in cis in the wake of transcription complexes and in trans apart from transcription complexes. In this review, we focus on the relationship between R-loops and topoisomerases, and cancer genomics and therapies. We summarize the topological parameters associated with the formation and resolution of R-loops, which absorb and release high levels of genomic negative supercoiling (Sc-). We review the deleterious consequences of excessive R-loops and rationalize how human type IA (TOP3B) and type IB (TOP1) topoisomerases regulate and resolve R-loops in coordination with helicase and RNase H enzymes. We also review the drugs (topoisomerase inhibitors, splicing inhibitors, G4 stabilizing ligands) and cancer predisposing genes (BRCA1/2, transcription, and splicing genes) known to induce R-loops, and whether stabilizing R-loops and thereby inducing genomic damage can be viewed as a strategy for cancer treatment.
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Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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32
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Vihervaara A, Versluis P, Lis JT. PRO-IP-seq Tracks Molecular Modifications of Engaged Pol II Complexes at Nucleotide Resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.04.527107. [PMID: 36778434 PMCID: PMC9915724 DOI: 10.1101/2023.02.04.527107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. Here, we developed Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq) and tracked phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. We uncovered precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide, through early and late promoter-proximal pause, and into productive elongation. Pol II CTD was predominantly unphosphorylated in the early pause-region, whereas serine-2- and serine-5-phosphorylations occurred preferentially in the later pause-region. Serine-7-phosphorylation dominated after the pause-release in a region where Pol II accelerates to its full elongational speed. Interestingly, tracking transcription upon heat-induced reprogramming demonstrated that Pol II with phosphorylated CTD remains paused on heat-repressed genes.
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Affiliation(s)
- Anniina Vihervaara
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Lead contact
| | - Philip Versluis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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Tan Y, Yao L, Gamliel A, Nair SJ, Taylor H, Ohgi K, Aggarwal AK, Rosenfeld MG. Signal-induced enhancer activation requires Ku70 to read topoisomerase1-DNA covalent complexes. Nat Struct Mol Biol 2023; 30:148-158. [PMID: 36747093 PMCID: PMC9935399 DOI: 10.1038/s41594-022-00883-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 10/27/2022] [Indexed: 02/08/2023]
Abstract
Enhancer activation serves as the main mechanism regulating signal-dependent transcriptional programs, ensuring cellular plasticity, yet central questions persist regarding their mechanism of activation. Here, by successfully mapping topoisomerase I-DNA covalent complexes genome-wide, we find that most, if not all, acutely activated enhancers, including those induced by 17β-estradiol, dihydrotestosterone, tumor necrosis factor alpha and neuronal depolarization, are hotspots for topoisomerase I-DNA covalent complexes, functioning as epigenomic signatures read by the classic DNA damage sensor protein, Ku70. Ku70 in turn nucleates a heterochromatin protein 1 gamma (HP1γ)-mediator subunit Med26 complex to facilitate acute, but not chronic, transcriptional activation programs. Together, our data uncover a broad, unappreciated transcriptional code, required for most, if not all, acute signal-dependent enhancer activation events in both mitotic and postmitotic cells.
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Affiliation(s)
- Yuliang Tan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Lu Yao
- Familial and Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Amir Gamliel
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sreejith J Nair
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Oncology Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
| | - Havilah Taylor
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kenny Ohgi
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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Eischer N, Arnold M, Mayer A. Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1734. [PMID: 35491403 DOI: 10.1002/wrna.1734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 01/31/2023]
Abstract
Transcription by RNA polymerase II (Pol II) gives rise to all nuclear protein-coding and a large set of non-coding RNAs, and is strictly regulated and coordinated with RNA processing. Bromodomain and extraterminal (BET) family proteins including BRD2, BRD3, and BRD4 have been implicated in the regulation of Pol II transcription in mammalian cells. However, only recent technological advances have allowed the analysis of direct functions of individual BET proteins with high precision in cells. These studies shed new light on the molecular mechanisms of transcription control by BET proteins challenging previous longstanding views. The most studied BET protein, BRD4, emerges as a master regulator of transcription elongation with roles also in coupling nascent transcription with RNA processing. In contrast, BRD2 is globally required for the formation of transcriptional boundaries to restrict enhancer activity to nearby genes. Although these recent findings suggest non-redundant functions of BRD4 and BRD2 in Pol II transcription, more research is needed for further clarification. Little is known about the roles of BRD3. Here, we illuminate experimental work that has initially linked BET proteins to Pol II transcription in mammalian cells, outline main methodological breakthroughs that have strongly advanced the understanding of BET protein functions, and discuss emerging roles of individual BET proteins in transcription and transcription-coupled RNA processing. Finally, we propose an updated model for the function of BRD4 in transcription and co-transcriptional RNA maturation. This article is categorized under: RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Nicole Eischer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mirjam Arnold
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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Meroni A, Grosser J, Agashe S, Ramakrishnan N, Jackson J, Verma P, Baranello L, Vindigni A. NEDDylated Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors. SCIENCE ADVANCES 2022; 8:eabq0648. [PMID: 36490343 PMCID: PMC9733930 DOI: 10.1126/sciadv.abq0648] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/26/2022] [Indexed: 05/30/2023]
Abstract
DNA topoisomerase 1 (TOP11) inhibitors are mainstays of anticancer therapy. These drugs trap TOP1 on DNA, stabilizing the TOP1-cleavage complex (TOP1-cc). The accumulation of TOP1-ccs perturbs DNA replication fork progression, leading to DNA breaks and cell death. By analyzing the genomic occupancy and activity of TOP1, we show that cells adapt to treatment with multiple doses of TOP1 inhibitor by promoting the degradation of TOP1-ccs, allowing cells to better tolerate subsequent doses of TOP1 inhibitor. The E3-RING Cullin 3 ligase in complex with the BTBD1 and BTBD2 adaptor proteins promotes TOP1-cc ubiquitination and subsequent proteasomal degradation. NEDDylation of Cullin 3 activates this pathway, and inhibition of protein NEDDylation or depletion of Cullin 3 sensitizes cancer cells to TOP1 inhibitors. Collectively, our data uncover a previously unidentified NEDD8-Cullin 3 pathway involved in the adaptive response to TOP1 inhibitors, which can be targeted to improve the efficacy of TOP1 drugs in cancer therapy.
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Affiliation(s)
- Alice Meroni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jan Grosser
- Karolinska Institutet, CMB, 171 65 Solna, Sweden
| | - Sumedha Agashe
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Natasha Ramakrishnan
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Priyanka Verma
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | | | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
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36
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Herbert A. Nucleosomes and flipons exchange energy to alter chromatin conformation, the readout of genomic information, and cell fate. Bioessays 2022; 44:e2200166. [DOI: 10.1002/bies.202200166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
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Murat P, Perez C, Crisp A, van Eijk P, Reed SH, Guilbaud G, Sale JE. DNA replication initiation shapes the mutational landscape and expression of the human genome. SCIENCE ADVANCES 2022; 8:eadd3686. [PMID: 36351018 PMCID: PMC9645720 DOI: 10.1126/sciadv.add3686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The interplay between active biological processes and DNA repair is central to mutagenesis. Here, we show that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with two distinct mechanisms, reflecting the two-step process of origin activation, triggering the formation of DNA breaks at the center of origins and local error-prone DNA synthesis in their immediate vicinity. We demonstrate that these replication initiation-dependent mutational processes exert an influence on phenotypic diversity in humans that is disproportionate to the origins' genomic size: By increasing mutational loads at gene promoters and splice junctions, the presence of an origin significantly influences both gene expression and mRNA isoform usage. Last, we show that mutagenesis at origins not only drives the evolution of origin sequences but also contributes to sculpting regulatory domains of the human genome.
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Affiliation(s)
- Pierre Murat
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alastair Crisp
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Patrick van Eijk
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Simon H. Reed
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Guillaume Guilbaud
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julian E. Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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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: 39] [Impact Index Per Article: 19.5] [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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39
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Johnstone CP, Galloway KE. Supercoiling-mediated feedback rapidly couples and tunes transcription. Cell Rep 2022; 41:111492. [PMID: 36261020 PMCID: PMC9624111 DOI: 10.1016/j.celrep.2022.111492] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/04/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA polymerases and reshaping the biochemical landscape of gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes the regulation of proximal genes, forming a complex feedback loop. However, a theoretical framework is needed to integrate biophysical regulation with biochemical transcriptional regulation. To investigate the role of supercoiling-mediated feedback within multi-gene systems, we model transcriptional regulation under the influence of supercoiling-mediated polymerase dynamics, allowing us to identify patterns of expression that result from physical inter-gene coupling. We find that gene syntax—the relative ordering and orientation of genes—defines the expression profiles, variance, burst dynamics, and inter-gene correlation of two-gene systems. Furthermore, supercoiling can enhance or weaken biochemical regulation. Our results suggest that supercoiling couples behavior between neighboring genes, providing a regulatory mechanism that tunes transcriptional variance in engineered gene networks and explains the behavior of co-localized native circuits. Supercoiling-mediated feedback couples the transcription of proximal genes. Here, Johnstone and Galloway provide a framework for integrating biochemical gene regulation with the biophysical effects of DNA supercoiling. This unified model provides design principles for improving the performance of gene networks, developing novel regulatory functions, and accessing previously inaccessible regulatory dynamics.
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Affiliation(s)
| | - Kate E. Galloway
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA,Lead contact,Correspondence:
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40
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Qin S, Yuan Y, Huang X, Tan Z, Hu X, Liu H, Pu Y, Ding YQ, Su Z, He C. Topoisomerase IIA in adult NSCs regulates SVZ neurogenesis by transcriptional activation of Usp37. Nucleic Acids Res 2022; 50:9319-9338. [PMID: 36029179 PMCID: PMC9458435 DOI: 10.1093/nar/gkac731] [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: 12/22/2021] [Revised: 07/31/2022] [Accepted: 08/14/2022] [Indexed: 01/27/2023] Open
Abstract
Topoisomerase IIA (TOP2a) has traditionally been known as an important nuclear enzyme that resolves entanglements and relieves torsional stress of DNA double strands. However, its function in genomic transcriptional regulation remains largely unknown, especially during adult neurogenesis. Here, we show that TOP2a is preferentially expressed in neurogenic niches in the brain of adult mice, such as the subventricular zone (SVZ). Conditional knockout of Top2a in adult neural stem cells (NSCs) of the SVZ significantly inhibits their self-renewal and proliferation, and ultimately reduces neurogenesis. To gain insight into the molecular mechanisms by which TOP2a regulates adult NSCs, we perform RNA-sequencing (RNA-Seq) plus chromatin immunoprecipitation sequencing (ChIP-Seq) and identify ubiquitin-specific protease 37 (Usp37) as a direct TOP2a target gene. Importantly, overexpression of Usp37 is sufficient to rescue the impaired self-renewal ability of adult NSCs caused by Top2a knockdown. Taken together, this proof-of-principle study illustrates a TOP2a/Usp37-mediated novel molecular mechanism in adult neurogenesis, which will significantly expand our understanding of the function of topoisomerase in the adult brain.
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Affiliation(s)
- Shangyao Qin
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yimin Yuan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Xiao Huang
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Zijian Tan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Xin Hu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Hong Liu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yingyan Pu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yu-qiang Ding
- Department of Laboratory Animal Science, and State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhida Su
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Cheng He
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
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41
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van der Noord VE, van de Water B, Le Dévédec SE. Targeting the Heterogeneous Genomic Landscape in Triple-Negative Breast Cancer through Inhibitors of the Transcriptional Machinery. Cancers (Basel) 2022; 14:4353. [PMID: 36139513 PMCID: PMC9496798 DOI: 10.3390/cancers14184353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer defined by lack of the estrogen, progesterone and human epidermal growth factor receptor 2. Although TNBC tumors contain a wide variety of oncogenic mutations and copy number alterations, the direct targeting of these alterations has failed to substantially improve therapeutic efficacy. This efficacy is strongly limited by interpatient and intratumor heterogeneity, and thereby a lack in uniformity of targetable drivers. Most of these genetic abnormalities eventually drive specific transcriptional programs, which may be a general underlying vulnerability. Currently, there are multiple selective inhibitors, which target the transcriptional machinery through transcriptional cyclin-dependent kinases (CDKs) 7, 8, 9, 12 and 13 and bromodomain extra-terminal motif (BET) proteins, including BRD4. In this review, we discuss how inhibitors of the transcriptional machinery can effectively target genetic abnormalities in TNBC, and how these abnormalities can influence sensitivity to these inhibitors. These inhibitors target the genomic landscape in TNBC by specifically suppressing MYC-driven transcription, inducing further DNA damage, improving anti-cancer immunity, and preventing drug resistance against MAPK and PI3K-targeted therapies. Because the transcriptional machinery enables transcription and propagation of multiple cancer drivers, it may be a promising target for (combination) treatment, especially of heterogeneous malignancies, including TNBC.
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Affiliation(s)
| | | | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
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42
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Sun Z, Yin M, Ding Y, Zhu Z, Sun Y, Li K, Yan W. Integrative analysis of synovial sarcoma transcriptome reveals different types of transcriptomic changes. Front Genet 2022; 13:925564. [PMID: 36118864 PMCID: PMC9478865 DOI: 10.3389/fgene.2022.925564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Synovial sarcoma (SS) is a rare and aggressive cancer that can come from distinct soft tissue types including muscle and ligaments. However, the transcriptomic landscape of SS is still poorly understood. This study aimed to systematically dissect the changes in SS transcriptome from different perspectives.Methods: We performed deep total RNA sequencing on ten paired Synovial sarcoma and tumor-adjacent tissues to systematically dissect the transcriptomic profile of SS in terms of gene expression, alternative splicing, gene fusion, and circular RNAs.Results: A total of 2,309 upregulated and 1,977 downregulated genes were identified between SS and tumor-adjacent tissues. Those upregulated genes could lead to the upregulation of the cell cycle, ribosome, and DNA replication pathways, while the downregulated genes may result in the downregulation of a set of metabolic biological processes and signaling pathways. Moreover, 2,511 genes (including 21 splicing factors) were differentially alternative spliced, indicating that the deregulation of alternative splicing could be one important factor that contributes to tumorigenesis. Additionally, we identified the known gene fusions of SS18-SSX1/SSX2 as well as 11 potentially novel gene fusions. Interestingly, 49 circular RNAs were differentially expressed and their parental genes could function in muscle contraction and muscle system processes.Conclusions: Collectively, our comprehensive dissection of the transcriptomic changes of SS from both transcriptional and post-transcriptional levels provides novel insights into the biology and underlying molecular mechanism of SS.
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Affiliation(s)
- Zhengwang Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mengchen Yin
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Ding
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Zixu Zhu
- No.2 High School of East China Normal University, Shanghai,200000, China
| | - Yangbai Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Kun Li
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
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Abstract
TOP1 CAD-seq enables mapping of TOP1 sites of covalent engagement with DNA. The procedure depends upon enrichment of DNA-covalent adducts using chaotropic salts and immunoprecipitation with an antibody specific for TOP1. Here, we describe a step-by-step protocol compatible with Illumina sequencing and bioinformatic pipeline for preliminary data analysis. Compared to other approaches for the genomic study of topoisomerases, TOP1 CAD-seq provides information about active TOP1 engaged on the DNA, taking advantage of low background due to absence of crosslinking. For complete details on the use and execution of this protocol, please refer to Das et al. (2022). TOP1 CAD-seq maps sites of topoisomerase 1 catalytic engagement with the DNA The absence of a cross-linking step reduces the background signal The method is high throughput and takes no longer than a regular ChIP-seq protocol The method can be used as a proxy to assess the level of supercoiling in the genome
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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44
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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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45
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Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli. Nat Commun 2022; 13:4524. [PMID: 35927234 PMCID: PMC9352719 DOI: 10.1038/s41467-022-32106-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/15/2022] [Indexed: 12/30/2022] Open
Abstract
Bacterial topoisomerase I (TopoI) removes excessive negative supercoiling and is thought to relax DNA molecules during transcription, replication and other processes. Using ChIP-Seq, we show that TopoI of Escherichia coli (EcTopoI) is colocalized, genome-wide, with transcribing RNA polymerase (RNAP). Treatment with transcription elongation inhibitor rifampicin leads to EcTopoI relocation to promoter regions, where RNAP also accumulates. When a 14 kDa RNAP-binding EcTopoI C-terminal domain (CTD) is overexpressed, colocalization of EcTopoI and RNAP along the transcription units is reduced. Pull-down experiments directly show that the two enzymes interact in vivo. Using ChIP-Seq and Topo-Seq, we demonstrate that EcTopoI is enriched upstream (within up to 12-15 kb) of highly-active transcription units, indicating that EcTopoI relaxes negative supercoiling generated by transcription. Uncoupling of the RNAP:EcTopoI interaction by either overexpression of EcTopoI competitor (CTD or inactive EcTopoI Y319F mutant) or deletion of EcTopoI domains involved in the interaction is toxic for cells and leads to excessive negative plasmid supercoiling. Moreover, uncoupling of the RNAP:EcTopoI interaction leads to R-loops accumulation genome-wide, indicating that this interaction is required for prevention of R-loops formation. In E. coli, disruption of TopoI and RNAP interaction decreases cells viability and leads to hypernegative DNA supercoiling and R loops accumulation. TopoI and DNA gyrase bind around transcription units and TopoI recognizes cleavage sites by a specific motif and negative supercoiling.
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46
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A tale of topoisomerases and the knotty genetic material in the backdrop of Plasmodium biology. Biosci Rep 2022; 42:231351. [PMID: 35699968 PMCID: PMC9261774 DOI: 10.1042/bsr20212847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/05/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
The untangling or overwinding of genetic material is an inevitable part of DNA
replication, repair, recombination, and transcription. Topoisomerases belong to
a conserved enzyme family that amends DNA topology during various processes of
DNA metabolism. To relax the genetic material, topoisomerases transiently break
the phosphodiester bond on one or both DNA strands and remain associated with
the cleavage site by forming a covalent enzyme–DNA intermediate. This
releases torsional stress and allows the broken DNA to be re-ligated by the
enzyme. The biological function of topoisomerases ranges from the separation of
sister chromatids following DNA replication to the aiding of chromosome
condensation and segregation during mitosis. Topoisomerases are also actively
involved in meiotic recombination. The unicellular apicomplexan parasite,
Plasmodium falciparum, harbors different topoisomerase
subtypes, some of which have substantially different sequences and functions
from their human counterparts. This review highlights the biological function of
each identified Plasmodium topoisomerase along with a
comparative analysis of their orthologs in human or other model organisms. There
is also a focus on recent advancements towards the development of topoisomerase
chemical inhibitors, underscoring the druggability of unique topoisomerase
subunits that are absent in humans. Plasmodium harbors three
distinct genomes in the nucleus, apicoplast, and mitochondria, respectively, and
undergoes non-canonical cell division during the schizont stage of development.
This review emphasizes the specific developmental stages of
Plasmodium on which future topoisomerase research should
focus.
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Su S, Xue Y, Sharov A, Zhang Y, Lee SK, Martindale J, Li W, Ku WL, Zhao K, De S, Shen W, Sen P, Gorospe M, Xu D, Wang W. A dual-activity topoisomerase complex regulates mRNA translation and turnover. Nucleic Acids Res 2022; 50:7013-7033. [PMID: 35748872 PMCID: PMC9262614 DOI: 10.1093/nar/gkac538] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/06/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
Topoisomerase 3β (TOP3B) and TDRD3 form a dual-activity topoisomerase complex that interacts with FMRP and can change the topology of both DNA and RNA. Here, we investigated the post-transcriptional influence of TOP3B and associated proteins on mRNA translation and turnover. First, we discovered that in human HCT116 colon cancer cells, knock-out (KO) of TOP3B had similar effects on mRNA turnover and translation as did TDRD3-KO, while FMRP-KO resulted in rather distinct effects, indicating that TOP3B had stronger coordination with TDRD3 than FMRP in mRNA regulation. Second, we identified TOP3B-bound mRNAs in HCT116 cells; we found that while TOP3B did not directly influence the stability or translation of most TOP3B target mRNAs, it stabilized a subset of target mRNAs but had a more complex effect on translation-enhancing for some mRNAs whereas reducing for others. Interestingly, a point mutation that specifically disrupted TOP3B catalytic activity only partially recapitulated the effects of TOP3B-KO on mRNA stability and translation, suggesting that the impact of TOP3B on target mRNAs is partly linked to its ability to change topology of mRNAs. Collectively, our data suggest that TOP3B-TDRD3 can regulate mRNA translation and turnover by mechanisms that are dependent and independent of topoisomerase activity.
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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
| | - Alexei Sharov
- 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
| | - Seung Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 1000871, China
| | - Wai Lim Ku
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 1000871, China
| | - Weidong Wang
- To whom correspondence should be addressed. Tel: +1 410 454 8418; Fax: +1 410 558 8331.
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48
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Yu C, Lei X, Chen F, Mao S, Lv L, Liu H, Hu X, Wang R, Shen L, Zhang N, Meng Y, Shen Y, Chen J, Li P, Huang S, Lin C, Zhang Z, Yuan K. ARID1A loss derepresses a group of human endogenous retrovirus-H loci to modulate BRD4-dependent transcription. Nat Commun 2022; 13:3501. [PMID: 35715442 PMCID: PMC9205910 DOI: 10.1038/s41467-022-31197-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
Transposable elements (TEs) through evolutionary exaptation have become an integral part of the human genome, offering ample regulatory sequences and shaping chromatin 3D architecture. While the functional impacts of TE-derived sequences on early embryogenesis have been recognized, their roles in malignancy are only starting to emerge. Here we show that many TEs, especially the pluripotency-related human endogenous retrovirus H (HERVH), are abnormally activated in colorectal cancer (CRC) samples. Transcriptional upregulation of HERVH is associated with mutations of several tumor suppressors, particularly ARID1A. Knockout of ARID1A in CRC cells leads to increased transcription at several HERVH loci, which involves compensatory contribution by ARID1B. Suppression of HERVH in CRC cells and patient-derived organoids impairs tumor growth. Mechanistically, HERVH transcripts colocalize with nuclear BRD4 foci, modulating their dynamics and co-regulating many target genes. Altogether, we uncover a critical role for ARID1A in restraining HERVH, whose abnormal activation can promote tumorigenesis by stimulating BRD4-dependent transcription. Here the authors show mutation of the BAF chromatin remodeler subunit ARID1A results in an ARID1B-dependent upregulation of HERVH, an ERV required for the pluripotency regulatory network. These HERVH RNAs can partition into BRD4 foci, affecting BRD4-dependent transcription. Suppression of HERVH in colorectal cancer cells and patient-derived organoids impairs tumor growth.
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Affiliation(s)
- Chunhong Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoyun Lei
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Song Mao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Honglu Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xueying Hu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Runhan Wang
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Licong Shen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Na Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Meng
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yunfan Shen
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jiale Chen
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Pishun Li
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shi Huang
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Changwei Lin
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhuohua Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,The Biobank of Xiangya Hospital, Central South University, Changsha, Hunan, China.
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49
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Differential cofactor dependencies define distinct types of human enhancers. Nature 2022; 606:406-413. [PMID: 35650434 PMCID: PMC7613064 DOI: 10.1038/s41586-022-04779-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 04/20/2022] [Indexed: 12/24/2022]
Abstract
All multicellular organisms rely on differential gene transcription regulated by genomic enhancers, which function through cofactors that are recruited by transcription factors1,2. Emerging evidence suggests that not all cofactors are required at all enhancers3-5, yet whether these observations reflect more general principles or distinct types of enhancers remained unknown. Here we categorized human enhancers by their cofactor dependencies and show that these categories provide a framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes. We quantified enhancer activities along the entire human genome using STARR-seq6 in HCT116 cells, following the rapid degradation of eight cofactors. This analysis identified different types of enhancers with distinct cofactor requirements, sequences and chromatin properties. Some enhancers were insensitive to the depletion of the core Mediator subunit MED14 or the bromodomain protein BRD4 and regulated distinct transcriptional programmes. In particular, canonical Mediator7 seemed dispensable for P53-responsive enhancers, and MED14-depleted cells induced endogenous P53 target genes. Similarly, BRD4 was not required for the transcription of genes that bear CCAAT boxes and a TATA box (including histone genes and LTR12 retrotransposons) or for the induction of heat-shock genes. This categorization of enhancers through cofactor dependencies reveals distinct enhancer types that can bypass broadly utilized cofactors, which illustrates how alternative ways to activate transcription separate gene expression programmes and provide a conceptual framework to understand enhancer function and regulatory specificity.
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50
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Yasuhara T, Xing YH, Bauer NC, Lee L, Dong R, Yadav T, Soberman RJ, Rivera MN, Zou L. Condensates induced by transcription inhibition localize active chromatin to nucleoli. Mol Cell 2022; 82:2738-2753.e6. [PMID: 35662392 PMCID: PMC9357099 DOI: 10.1016/j.molcel.2022.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/25/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
The proper function of the genome relies on spatial organization of DNA, RNA, and proteins, but how transcription contributes to the organization is unclear. Here, we show that condensates induced by transcription inhibition (CITIs) drastically alter genome spatial organization. CITIs are formed by SFPQ, NONO, FUS, and TAF15 in nucleoli upon inhibition of RNA polymerase II (RNAPII). Mechanistically, RNAPII inhibition perturbs ribosomal RNA (rRNA) processing, releases rRNA-processing factors from nucleoli, and enables SFPQ to bind rRNA. While accumulating in CITIs, SFPQ/TAF15 remain associated with active genes and tether active chromatin to nucleoli. In the presence of DNA double-strand breaks (DSBs), the altered chromatin compartmentalization induced by RNAPII inhibition increases gene fusions in CITIs and stimulates the formation of fusion oncogenes. Thus, proper RNAPII transcription and rRNA processing prevent the altered compartmentalization of active chromatin in CITIs, suppressing the generation of gene fusions from DSBs.
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Affiliation(s)
- Takaaki Yasuhara
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, the University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yu-Hang Xing
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Nicholas C Bauer
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lukuo Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Rui Dong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Roy J Soberman
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Miguel N Rivera
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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