51
|
Stanic M, Mekhail K. Integration of DNA damage responses with dynamic spatial genome organization. Trends Genet 2021; 38:290-304. [PMID: 34598804 DOI: 10.1016/j.tig.2021.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
The maintenance of genome stability and cellular homeostasis depends on the temporal and spatial coordination of successive events constituting the classical DNA damage response (DDR). Recent findings suggest close integration and coordination of DDR signaling with specific cellular processes. The mechanisms underlying such coordination remain unclear. We review emerging crosstalk between DNA repair factors, chromatin remodeling, replication, transcription, spatial genome organization, cytoskeletal forces, and liquid-liquid phase separation (LLPS) in mediating DNA repair. We present an overarching DNA repair framework within which these dynamic processes intersect in nuclear space over time. Collectively, this interplay ensures the efficient assembly of DNA repair proteins onto shifting genome structures to preserve genome stability and cell survival.
Collapse
Affiliation(s)
- Mia Stanic
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Canada Research Chairs Program, Temerty Faculty of Medicine, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
52
|
Caron P, Pobega E, Polo SE. DNA Double-Strand Break Repair: All Roads Lead to HeterochROMAtin Marks. Front Genet 2021; 12:730696. [PMID: 34539757 PMCID: PMC8440905 DOI: 10.3389/fgene.2021.730696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/06/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), chromatin modifications orchestrate DNA repair pathways thus safeguarding genome integrity. Recent studies have uncovered a key role for heterochromatin marks and associated factors in shaping DSB repair within the nucleus. In this review, we present our current knowledge of the interplay between heterochromatin marks and DSB repair. We discuss the impact of heterochromatin features, either pre-existing in heterochromatin domains or de novo established in euchromatin, on DSB repair pathway choice. We emphasize how heterochromatin decompaction and mobility further support DSB repair, focusing on recent mechanistic insights into these processes. Finally, we speculate about potential molecular players involved in the maintenance or the erasure of heterochromatin marks following DSB repair, and their implications for restoring epigenome function and integrity.
Collapse
Affiliation(s)
- Pierre Caron
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Enrico Pobega
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| |
Collapse
|
53
|
Savocco J, Piazza A. Recombination-mediated genome rearrangements. Curr Opin Genet Dev 2021; 71:63-71. [PMID: 34325160 DOI: 10.1016/j.gde.2021.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/20/2021] [Accepted: 06/29/2021] [Indexed: 12/14/2022]
Abstract
Homologous recombination (HR) is a universal DNA double-strand break (DSB) repair pathway that uses an intact DNA molecule as a template. Signature HR reactions are homology search and DNA strand invasion catalyzed by the prototypical RecA-ssDNA filament (Rad51 and Dmc1 in eukaryotes), which produces heteroduplex DNA-containing joint molecules (JMs). These reactions uniquely infringe on the DNA strands association established at replication, on the basis of substantial sequence similarity. For that reason, and despite the high fidelity of its templated nature, DSB repair by HR authorizes the alteration of genome structure, guided by repetitive DNA elements. The resulting structural variations (SVs) can involve vast genomic regions, potentially affecting multiple coding sequences and regulatory elements at once, with possible pathological consequences. Here, we discuss recent advances in our understanding of genetic and molecular vulnerabilities of HR leading to SVs, and of the various fidelity-enforcing factors acting across scales on the balancing act of this complex pathway. An emphasis is put on extra-chomosomal DNAs, both product of, and substrate for HR-mediated chromosomal rearrangements.
Collapse
Affiliation(s)
- Jérôme Savocco
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Aurèle Piazza
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.
| |
Collapse
|
54
|
Wang Q, Wang Y, Du L, Xu C, Liu Y, Liu Q, Fan S. Quantitative proteomic analysis of the effects of melatonin treatment for mice suffered from small intestinal damage induced by γ-ray radiation. Int J Radiat Biol 2021; 97:1206-1216. [PMID: 34264173 DOI: 10.1080/09553002.2021.1956006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE Intestinal damage induced by radiation exposure is a major clinic concern of radiotherapy for patients with abdominal or pelvic tumor. Melatonin (N-acetyl-5-methoxytryptamine) is likely be an ideal radioprotector to protect individuals from radiation exposure. The study aimed to define the role of melatonin in small intestinal damage caused by abdominal irradiation (ABI). MATERIALS AND METHODS 30-day survival rate and pathological histology of the intestines from melatonin-treated mice after 13 Gy ABI exposure was first detected. Next, quantitative proteomics analysis of the small intestines tissue was examined and GO term and KEGG pathways analysis were performed. RESULTS Melatonin treatment before ABI exposure significantly increased 30-day survival rate to 83% and ameliorated damage to the intestinal epithelial cells. Melatonin significantly altered the proteins profile of the small intestines following irradiation. For the irradiated mice treated with melatonin in comparison with the irradiated mice, the enriched GO terms were mainly involved in defense response to other organism (BP, GO: 0098542), response to other organism (BP, GO: 0051707), anion transmembrane transporter activity (MF, GO: 0008509), and secondary active transmembrane transporter activity (MF, GO: 0015291). In the process of antioxidant activity (MF, GO: 0016209), melatonin treatment prior to radiation exhibited high protein levels of Sod3 and Gpx3. The markedly KEGG pathways for melatonin treatment prior to radiation mainly included protein digestion and absorption (ko 04974) and mineral absorption (ko 04978). p53 signaling pathway and DNA repair pathways were enriched in melatonin treated mice. The amount of radiation-induced DNA damage and the cell apoptosis of the small intestines was decreased in the melatonin-treated mice. CONCLUSIONS Melatonin may protect small intestines from radiation damage through increasing DNA repair and decreasing cell apoptosis of the small intestines. Our data provided perspective for the study of melatonin in mitigating ABI-caused intestinal damage.
Collapse
Affiliation(s)
- Qin Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| | - Yan Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| | - Liqing Du
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| | - Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| | - Yang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| | - Qiang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| |
Collapse
|
55
|
Wang S, Xu F, Li Y, Wang J, Zhang K, Liu Y, Wu M, Zheng J. KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers. Bioinformatics 2021; 37:i418-i425. [PMID: 34252965 PMCID: PMC8336442 DOI: 10.1093/bioinformatics/btab271] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Motivation Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer drug targets. Wet-lab screening of SL pairs is afflicted with high cost, batch-effect, and off-target problems. Current computational methods for SL prediction include gene knock-out simulation, knowledge-based data mining and machine learning methods. Most of the existing methods tend to assume that SL pairs are independent of each other, without taking into account the shared biological mechanisms underlying the SL pairs. Although several methods have incorporated genomic and proteomic data to aid SL prediction, these methods involve manual feature engineering that heavily relies on domain knowledge. Results Here, we propose a novel graph neural network (GNN)-based model, named KG4SL, by incorporating knowledge graph (KG) message-passing into SL prediction. The KG was constructed using 11 kinds of entities including genes, compounds, diseases, biological processes and 24 kinds of relationships that could be pertinent to SL. The integration of KG can help harness the independence issue and circumvent manual feature engineering by conducting message-passing on the KG. Our model outperformed all the state-of-the-art baselines in area under the curve, area under precision-recall curve and F1. Extensive experiments, including the comparison of our model with an unsupervised TransE model, a vanilla graph convolutional network model, and their combination, demonstrated the significant impact of incorporating KG into GNN for SL prediction. Availability and implementation : KG4SL is freely available at https://github.com/JieZheng-ShanghaiTech/KG4SL. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Shike Wang
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fan Xu
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yunyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jie Wang
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ke Zhang
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Yong Liu
- Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly, Nanyang Technological University, Singapore 639798, Singapore
| | - Min Wu
- Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR), Singapore 138632, Singapore
| | - Jie Zheng
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Shanghai Engineering Research Center of Intelligent Vision and Imaging, Shanghai, 201210, China
| |
Collapse
|
56
|
Wang L, Liu F, Du L, Qin G. Single-Cell Transcriptome Analysis in Melanoma Using Network Embedding. Front Genet 2021; 12:700036. [PMID: 34290746 PMCID: PMC8287331 DOI: 10.3389/fgene.2021.700036] [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: 04/25/2021] [Accepted: 06/10/2021] [Indexed: 11/28/2022] Open
Abstract
Single-cell sequencing technology provides insights into the pathology of complex diseases like cancer. Here, we proposed a novel computational framework to explore the molecular mechanisms of cancer called melanoma. We first constructed a disease-specific cell–cell interaction network after data preprocessing and dimensionality reduction. Second, the features of cells in the cell–cell interaction network were learned by node2vec which is a graph embedding technology proposed previously. Then, consensus clusters were identified by considering different clustering algorithms. Finally, cell markers and cancer-related genes were further analyzed by integrating gene regulation pairs. We exploited our model on two independent datasets, which showed interesting results that the differences between clusters obtained by consensus clustering based on network embedding (CCNE) were observed obviously through visualization. For the KEGG pathway analysis of clusters, we found that all clusters are extremely related to MicroRNAs in cancer and HTLV-I infection, and the hub genes in cluster specific regulatory networks, i.e., ETS1, TP53, E2F1, and GATA3 are highly associated with melanoma. Furthermore, our method can also be extended to other scRNA-seq data.
Collapse
Affiliation(s)
- Liming Wang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Fangfang Liu
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Longting Du
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Guimin Qin
- School of Computer Science and Technology, Xidian University, Xi'an, China
| |
Collapse
|
57
|
Kang MA, Lee JS. A Newly Assigned Role of CTCF in Cellular Response to Broken DNAs. Biomolecules 2021; 11:363. [PMID: 33673494 PMCID: PMC7997455 DOI: 10.3390/biom11030363] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 02/07/2023] Open
Abstract
Best known as a transcriptional factor, CCCTC-binding factor (CTCF) is a highly conserved multifunctional DNA-binding protein with 11 zinc fingers. It functions in diverse genomic processes, including transcriptional activation/repression, insulation, genome imprinting and three-dimensional genome organization. A big surprise has recently emerged with the identification of CTCF engaging in the repair of DNA double-strand breaks (DSBs) and in the maintenance of genome fidelity. This discovery now adds a new dimension to the multifaceted attributes of this protein. CTCF facilitates the most accurate DSB repair via homologous recombination (HR) that occurs through an elaborate pathway, which entails a chain of timely assembly/disassembly of various HR-repair complexes and chromatin modifications and coordinates multistep HR processes to faithfully restore the original DNA sequences of broken DNA sites. Understanding the functional crosstalks between CTCF and other HR factors will illuminate the molecular basis of various human diseases that range from developmental disorders to cancer and arise from impaired repair. Such knowledge will also help understand the molecular mechanisms underlying the diverse functions of CTCF in genome biology. In this review, we discuss the recent advances regarding this newly assigned versatile role of CTCF and the mechanism whereby CTCF functions in DSB repair.
Collapse
Affiliation(s)
| | - Jong-Soo Lee
- Department of Life Sciences, Ajou University, Suwon 16499, Korea;
| |
Collapse
|
58
|
Arnould C, Rocher V, Finoux AL, Clouaire T, Li K, Zhou F, Caron P, Mangeot PE, Ricci EP, Mourad R, Haber JE, Noordermeer D, Legube G. Loop extrusion as a mechanism for formation of DNA damage repair foci. Nature 2021; 590:660-665. [PMID: 33597753 PMCID: PMC7116834 DOI: 10.1038/s41586-021-03193-z] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 01/06/2021] [Indexed: 12/26/2022]
Abstract
The repair of DNA double-strand breaks (DSBs) is essential for safeguarding genome integrity. When a DSB forms, the PI3K-related ATM kinase rapidly triggers the establishment of megabase-sized, chromatin domains decorated with phosphorylated histone H2AX (γH2AX), which act as seeds for the formation of DNA-damage response foci1. It is unclear how these foci are rapidly assembled to establish a 'repair-prone' environment within the nucleus. Topologically associating domains are a key feature of 3D genome organization that compartmentalize transcription and replication, but little is known about their contribution to DNA repair processes2,3. Here we show that topologically associating domains are functional units of the DNA damage response, and are instrumental for the correct establishment of γH2AX-53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model in which H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the importance of chromosome conformation in the maintenance of genome integrity and demonstrates the establishment of a chromatin modification by loop extrusion.
Collapse
Affiliation(s)
- Coline Arnould
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Vincent Rocher
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Anne-Laure Finoux
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Thomas Clouaire
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Kevin Li
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Felix Zhou
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Pierre Caron
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Philippe E Mangeot
- CIRI - International Center for Infectiology Research, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, INSERM U1293, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Raphaël Mourad
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - James E Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Gaëlle Legube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France.
| |
Collapse
|
59
|
Jiang Y, Li W, Lindsey-Boltz LA, Yang Y, Li Y, Sancar A. Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome. J Biol Chem 2021; 296:100581. [PMID: 33771559 PMCID: PMC8081918 DOI: 10.1016/j.jbc.2021.100581] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
The formation of UV-induced DNA damage and its repair are influenced by many factors that modulate lesion formation and the accessibility of repair machinery. However, it remains unknown which genomic sites are prioritized for immediate repair after UV damage induction, and whether these prioritized sites overlap with hotspots of UV damage. We identified the super hotspots subject to the earliest repair for (6-4) pyrimidine-pyrimidone photoproduct by using the eXcision Repair-sequencing (XR-seq) method. We further identified super coldspots for (6-4) pyrimidine-pyrimidone photoproduct repair and super hotspots for cyclobutane pyrimidine dimer repair by analyzing available XR-seq time-course data. By integrating datasets of XR-seq, Damage-seq, adductSeq, and cyclobutane pyrimidine dimer-seq, we show that neither repair super hotspots nor repair super coldspots overlap hotspots of UV damage. Furthermore, we demonstrate that repair super hotspots are significantly enriched in frequently interacting regions and superenhancers. Finally, we report our discovery of an enrichment of cytosine in repair super hotspots and super coldspots. These findings suggest that local DNA features together with large-scale chromatin features contribute to the orders of magnitude variability in the rates of UV damage repair.
Collapse
Affiliation(s)
- Yuchao Jiang
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.
| | - Wentao Li
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yuchen Yang
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yun Li
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Computer Science, College of Arts and Sciences, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Aziz Sancar
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA.
| |
Collapse
|