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Lee JJ, Kim H, Park H, Lee U, Kim C, Lee M, Shin Y, Jung JJ, Lee HB, Han W, Lee H. Disruption of G-quadruplex dynamicity by BRCA2 abrogation instigates phase separation and break-induced replication at telomeres. Nucleic Acids Res 2024; 52:5756-5773. [PMID: 38587189 PMCID: PMC11162766 DOI: 10.1093/nar/gkae251] [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: 09/04/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 04/09/2024] Open
Abstract
Dynamic interaction between BRCA2 and telomeric G-quadruplexes (G4) is crucial for maintaining telomere replication homeostasis. Cells lacking BRCA2 display telomeric damage with a subset of these cells bypassing senescence to initiate break-induced replication (BIR) for telomere synthesis. Here we show that the abnormal stabilization of telomeric G4 following BRCA2 depletion leads to telomeric repeat-containing RNA (TERRA)-R-loop accumulation, triggering liquid-liquid phase separation (LLPS) and the assembly of Alternative Lengthening of Telomeres (ALT)-associated promyelocytic leukemia (PML) bodies (APBs). Disruption of R-loops abolishes LLPS and impairs telomere synthesis. Artificial engineering of telomeric LLPS restores telomere synthesis, underscoring the critical role of LLPS in ALT. TERRA-R-loops also recruit Polycomb Repressive Complex 2 (PRC2), leading to tri-methylation of Lys27 on histone H3 (H3K27me3) at telomeres. Half of paraffin-embedded tissue sections from human breast cancers exhibit APBs and telomere length heterogeneity, suggesting that BRCA2 mutations can predispose individuals to ALT-type tumorigenesis. Overall, BRCA2 abrogation disrupts the dynamicity of telomeric G4, producing TERRA-R-loops, finally leading to the assembly of telomeric liquid condensates crucial for ALT. We propose that modulating the dynamicity of telomeric G4 and targeting TERRA-R-loops in telomeric LLPS maintenance may represent effective therapeutic strategies for treating ALT-like cancers with APBs, including those with BRCA2 disruptions.
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Affiliation(s)
- Jennifer J Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea
| | - Hyungmin Kim
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea
| | - Haemin Park
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea
| | - UkJin Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Korea
| | - Min Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Korea
| | - Ji-Jung Jung
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University, Seoul 03080, Korea
| | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University, Seoul 03080, Korea
| | - Hyunsook Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea
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Zhao R, Xu M, Wondisford AR, Lackner RM, Salsman J, Dellaire G, Chenoweth DM, O’Sullivan RJ, Zhao X, Zhang H. SUMO Promotes DNA Repair Protein Collaboration to Support Alterative Telomere Lengthening in the Absence of PML. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582813. [PMID: 38463993 PMCID: PMC10925274 DOI: 10.1101/2024.02.29.582813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Alternative lengthening of telomeres (ALT) pathway maintains telomeres in a significant fraction of cancers associated with poor clinical outcomes. A better understanding of ALT mechanisms can provide a basis for developing new treatment strategies for ALT cancers. SUMO modification of telomere proteins plays a critical role in the formation of ALT telomere-associated PML bodies (APBs), where telomeres are clustered and DNA repair proteins are enriched to promote homology-directed telomere DNA synthesis in ALT. However, whether and how SUMO contributes to ALT beyond APB formation remains elusive. Here, we report that SUMO promotes collaboration among DNA repair proteins to achieve APB-independent telomere maintenance. By using ALT cancer cells with PML protein knocked out and thus devoid of APBs, we show that sumoylation is required for manifesting ALT features, including telomere clustering and telomeric DNA synthesis, independent of PML and APBs. Further, small molecule-induced telomere targeting of SUMO produces signatures of phase separation and ALT features in PML null cells in a manner depending on both sumoylation and SUMO interaction with SUMO interaction motifs (SIMs). Mechanistically, SUMO-induced effects are linked to the enrichment of DNA repair proteins, including Rad52, Rad51AP1, and BLM, to the SUMO-containing telomere foci. Finally, we find that Rad52 can undergo phase separation, enrich SUMO on telomeres, and promote telomere DNA synthesis in collaboration with the BLM helicase in a SUMO-dependent manner. Collectively, our findings suggest that, in addition to forming APBs, SUMO also promotes collaboration among DNA repair proteins to support telomere maintenance in ALT cells. Given the promising effects of sumoylation inhibitors in cancer treatment, our findings suggest their potential use in perturbing telomere maintenance in ALT cancer cells.
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Affiliation(s)
- Rongwei Zhao
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Meng Xu
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Anne R. Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rachel M. Lackner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19014 , USA
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - David M. Chenoweth
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19014 , USA
| | - Roderick J. O’Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Huaiying Zhang
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Cai Y, Guo H, Zhou J, Zhu G, Qu H, Liu L, Shi T, Ge S, Qu Y. An alternative extension of telomeres related prognostic model to predict survival in lower grade glioma. J Cancer Res Clin Oncol 2023; 149:13575-13589. [PMID: 37515613 DOI: 10.1007/s00432-023-05155-6] [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: 05/25/2023] [Accepted: 07/09/2023] [Indexed: 07/31/2023]
Abstract
OBJECTIVE The alternative extension of the telomeres (ALT) mechanism is activated in lower grade glioma (LGG), but the role of the ALT mechanism has not been well discussed. The primary purpose was to demonstrate the significance of the ALT mechanism in prognosis estimation for LGG patients. METHOD Gene expression and clinical data of LGG patients were collected from the Chinese Glioma Genome Atlas (CGGA) and the Cancer Genome Atlas (TCGA) cohort, respectively. ALT-related genes obtained from the TelNet database and potential prognostic genes related to ALT were selected by LASSO regression to calculate an ALT-related risk score. Multivariate Cox regression analysis was performed to construct a prognosis signature, and a nomogram was used to represent this signature. Possible pathways of the ALT-related risk score are explored by enrichment analysis. RESULT The ALT-related risk score was calculated based on the LASSO regression coefficients of 22 genes and then divided into high-risk and low-risk groups according to the median. The ALT-related risk score is an independent predictor of LGG (HR and 95% CI in CGGA cohort: 5.70 (3.79, 8.58); in TCGA cohort: 1.96 (1.09, 3.54)). ROC analysis indicated that the model contained ALT-related risk score was superior to conventional clinical features (AUC: 0.818 vs 0.729) in CGGA cohorts. The results in the TCGA cohort also shown a powerful ability of ALT-related risk score (AUC: 0.766 vs 0.691). The predicted probability and actual probability of the nomogram are consistent. Enrichment analysis demonstrated that the ALT mechanism was involved in the cell cycle, DNA repair, immune processes, and others. CONCLUSION ALT-related risk score based on the 22-gene is an important factor in predicting the prognosis of LGG patients.
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Affiliation(s)
- Yaning Cai
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China
| | - Hao Guo
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China
| | - JinPeng Zhou
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China
| | - Gang Zhu
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China
| | - Hongwen Qu
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China
| | - Lingyu Liu
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China
| | - Tao Shi
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China
| | - Shunnan Ge
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China.
| | - Yan Qu
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an 710038, China.
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Loe TK, Lazzerini Denchi E, Tricola GM, Azeroglu B. ALTercations at telomeres: stress, recombination and extrachromosomal affairs. Biochem Soc Trans 2023; 51:1935-1946. [PMID: 37767563 DOI: 10.1042/bst20230265] [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: 08/11/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Approximately 15% of human cancers depend on the alternative lengthening of telomeres (ALT) pathway to maintain telomeres and proliferate. Telomeres that are elongated using ALT display unique features raising the exciting prospect of tailored cancer therapies. ALT-mediated telomere elongation shares several features with recombination-based DNA repair. Strikingly, cells that use the ALT pathway display abnormal levels of replication stress at telomeres and accumulate abundant extrachromosomal telomeric DNA. In this review, we examine recent findings that shed light on the ALT mechanisms and the strategies currently available to suppress this telomere elongation mechanism.
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Affiliation(s)
- Taylor K Loe
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, U.S.A
| | - Eros Lazzerini Denchi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Gianna M Tricola
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Benura Azeroglu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
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Kleijwegt C, Bressac F, Seurre C, Bouchereau W, Cohen C, Texier P, Simonet T, Schaeffer L, Lomonte P, Corpet A. Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus. eLife 2023; 12:e80156. [PMID: 37227756 PMCID: PMC10212570 DOI: 10.7554/elife.80156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
Promyelocytic leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. By using specific approaches, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. Hence, we describe a role of PML NBs as nuclear depot centers to regulate HIRA distribution in the nucleus, dependent both on SP100 and DAXX/H3.3 levels. Upon IFN-I stimulation, PML is required for interferon-stimulated genes (ISGs) transcription and PML NBs become juxtaposed to ISGs loci at late time points of IFN-I treatment. HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of ISGs, well beyond the peak of transcription. Though, HIRA accumulation in PML NBs is dispensable for H3.3 deposition on ISGs. We thus uncover a dual function for PML/PML NBs, as buffering centers modulating the nuclear distribution of HIRA, and as chromosomal hubs regulating ISGs transcription and thus HIRA-mediated H3.3 deposition at ISGs upon inflammatory response.
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Affiliation(s)
- Constance Kleijwegt
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Florent Bressac
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Coline Seurre
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Wilhelm Bouchereau
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Camille Cohen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Pascale Texier
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Thomas Simonet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Laurent Schaeffer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Patrick Lomonte
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Armelle Corpet
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
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6
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Gao J, Pickett HA. Targeting telomeres: advances in telomere maintenance mechanism-specific cancer therapies. Nat Rev Cancer 2022; 22:515-532. [PMID: 35790854 DOI: 10.1038/s41568-022-00490-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/31/2022]
Abstract
Cancer cells establish replicative immortality by activating a telomere-maintenance mechanism (TMM), be it telomerase or the alternative lengthening of telomeres (ALT) pathway. Targeting telomere maintenance represents an intriguing opportunity to treat the vast majority of all cancer types. Whilst telomerase inhibitors have historically been heralded as promising anticancer agents, the reality has been more challenging, and there are currently no therapeutic options for cancer types that use ALT despite their aggressive nature and poor prognosis. In this Review, we discuss the mechanistic differences between telomere maintenance by telomerase and ALT, the current methods used to detect each mechanism, the utility of these tests for clinical diagnosis, and recent developments in the therapeutic strategies being employed to target both telomerase and ALT. We present notable developments in repurposing established therapeutic agents and new avenues that are emerging to target cancer types according to which TMM they employ. These opportunities extend beyond inhibition of telomere maintenance, by finding and exploiting inherent weaknesses in the telomeres themselves to trigger rapid cellular effects that lead to cell death.
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Affiliation(s)
- Jixuan Gao
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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7
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Soranno A, Incicco JJ, De Bona P, Tomko EJ, Galburt EA, Holehouse AS, Galletto R. Shelterin Components Modulate Nucleic Acids Condensation and Phase Separation in the Context of Telomeric DNA. J Mol Biol 2022; 434:167685. [PMID: 35724929 PMCID: PMC9378516 DOI: 10.1016/j.jmb.2022.167685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/26/2022] [Accepted: 06/10/2022] [Indexed: 01/13/2023]
Abstract
Telomeres are nucleoprotein complexes that protect the ends of chromosomes and are essential for chromosome stability in Eukaryotes. In cells, individual telomeres form distinct globules of finite size that appear to be smaller than expected for bare DNA. Moreover, telomeres can cluster together, form telomere-induced-foci or co-localize with promyelocytic leukemia (PML) nuclear bodies. The physical basis for collapse of individual telomeres and coalescence of multiple ones remains unclear, as does the relationship between these two phenomena. By combining single-molecule force spectroscopy measurements, optical microscopy, turbidity assays, and simulations, we show that the telomere scaffolding protein TRF2 can condense individual DNA chains and drives coalescence of multiple DNA molecules, leading to phase separation and the formation of liquid-like droplets. Addition of the TRF2 binding protein hRap1 modulates phase boundaries and tunes the specificity of solution demixing while simultaneously altering the degree of DNA compaction. Our results suggest that the condensation of single telomeres and formation of biomolecular condensates containing multiple telomeres are two different outcomes driven by the same set of molecular interactions. Moreover, binding partners, such as other telomere components, can alter those interactions to promote single-chain DNA compaction over multiple-chain phase separation.
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Affiliation(s)
- Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States; Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, United States.
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Paolo De Bona
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Eric J Tomko
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States; Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States.
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8
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Bhargava R, Lynskey ML, O’Sullivan RJ. New twists to the ALTernative endings at telomeres. DNA Repair (Amst) 2022; 115:103342. [DOI: 10.1016/j.dnarep.2022.103342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
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Hou K, Yu Y, Li D, Zhang Y, Zhang K, Tong J, Yang K, Jia S. Alternative Lengthening of Telomeres and Mediated Telomere Synthesis. Cancers (Basel) 2022; 14:cancers14092194. [PMID: 35565323 PMCID: PMC9105334 DOI: 10.3390/cancers14092194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Alternative lengthing of telomere (ALT) is an important mechanism for maintaining telomere length and cell proliferation in telomerase-negative tumor cells. However, the molecular mechanism of ALT is still poorly understood. ALT occurs in a wide range of tumor types and usually associated with a worse clinical consequence. Here, we review the recent findings of ALT mechanisms, which promise ALT could be a valuable drug target for clinical telomerase-negative tumor treatment. Abstract Telomeres are DNA–protein complexes that protect eukaryotic chromosome ends from being erroneously repaired by the DNA damage repair system, and the length of telomeres indicates the replicative potential of the cell. Telomeres shorten during each division of the cell, resulting in telomeric damage and replicative senescence. Tumor cells tend to ensure cell proliferation potential and genomic stability by activating telomere maintenance mechanisms (TMMs) for telomere lengthening. The alternative lengthening of telomeres (ALT) pathway is the most frequently activated TMM in tumors of mesenchymal and neuroepithelial origin, and ALT also frequently occurs during experimental cellular immortalization of mesenchymal cells. ALT is a process that relies on homologous recombination (HR) to elongate telomeres. However, some processes in the ALT mechanism remain poorly understood. Here, we review the most recent understanding of ALT mechanisms and processes, which may help us to better understand how the ALT pathway is activated in cancer cells and determine the potential therapeutic targets in ALT pathway-stabilized tumors.
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Affiliation(s)
- Kailong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China;
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
| | - Yuyang Yu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Duda Li
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Yanduo Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Ke Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Jinkai Tong
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Kunxian Yang
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
- Correspondence: (K.Y.); (S.J.)
| | - Shuting Jia
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- Correspondence: (K.Y.); (S.J.)
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Hornofova T, Pokorna B, Hubackova SS, Uvizl A, Kosla J, Bartek J, Hodny Z, Vasicova P. Phospho-SIM and exon8b of PML protein regulate formation of doxorubicin-induced rDNA-PML compartment. DNA Repair (Amst) 2022; 114:103319. [DOI: 10.1016/j.dnarep.2022.103319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/25/2022] [Accepted: 03/10/2022] [Indexed: 12/18/2022]
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11
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Fonin AV, Silonov SA, Fefilova AS, Stepanenko OV, Gavrilova AA, Petukhov AV, Romanovich AE, Modina AL, Zueva TS, Nedelyaev EM, Pleskach NM, Kuranova ML, Kuznetsova IM, Uversky VN, Turoverov KK. New Evidence of the Importance of Weak Interactions in the Formation of PML-Bodies. Int J Mol Sci 2022; 23:ijms23031613. [PMID: 35163537 PMCID: PMC8835755 DOI: 10.3390/ijms23031613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 12/31/2022] Open
Abstract
In this work, we performed a comparative study of the formation of PML bodies by full-length PML isoforms and their C-terminal domains in the presence and absence of endogenous PML. Based on the analysis of the distribution of intrinsic disorder predisposition in the amino acid sequences of PML isoforms, regions starting from the amino acid residue 395 (i.e., sequences encoded by exons 4–6) were assigned as the C-terminal domains of these proteins. We demonstrate that each of the full-sized nuclear isoforms of PML is capable of forming nuclear liquid-droplet compartments in the absence of other PML isoforms. These droplets possess dynamic characteristics of the exchange with the nucleoplasm close to those observed in the wild-type cells. Only the C-terminal domains of the PML-II and PML-V isoforms are able to be included in the composition of the endogenous PML bodies, while being partially distributed in the nucleoplasm. The bodies formed by the C-terminal domain of the PML-II isoform are dynamic liquid droplet compartments, regardless of the presence or absence of endogenous PML. The C-terminal domain of PML-V forms dynamic liquid droplet compartments in the knockout cells (PML−/−), but when the C-terminus of the PML-V isoform is inserted into the existing endogenous PML bodies, the molecules of this protein cease to exchange with the nucleoplasm. It was demonstrated that the K490R substitution, which disrupts the PML sumoylation, promotes diffuse distribution of the C-terminal domains of PML-II and PML-V isoforms in endogenous PML knockout HeLa cells, but not in the wild-type cells. These data indicate the ability of the C-terminal domains of the PML-II and PML-V isoforms to form dynamic liquid droplet-like compartments, regardless of the ordered N-terminal RBCC motifs of the PML. This indicates a significant role of the non-specific interactions between the mostly disordered C-terminal domains of PML isoforms for the initiation of liquid–liquid phase separation (LLPS) leading to the formation of PML bodies.
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Affiliation(s)
- Alexander V. Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
- Correspondence: (A.V.F.); (K.K.T.); Tel.: +7-812-2971957 (K.K.T.); Fax: +7-812-2970341 (K.K.T.)
| | - Sergey A. Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Anna S. Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Anastasia A. Gavrilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Alexey V. Petukhov
- Almazov National Medical Research Centre, Institute of Hematology, 197341 St. Petersburg, Russia;
| | - Anna E. Romanovich
- Resource Center of Molecular and Cell Technologies, St-Petersburg State University Research Park, Universitetskaya Emb. 7–9, 199034 St. Petersburg, Russia;
| | - Anna L. Modina
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Tatiana S. Zueva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Evgeniy M. Nedelyaev
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Nadejda M. Pleskach
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Mirya L. Kuranova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (A.S.F.); (O.V.S.); (A.A.G.); (A.L.M.); (T.S.Z.); (E.M.N.); (N.M.P.); (M.L.K.); (I.M.K.)
- Correspondence: (A.V.F.); (K.K.T.); Tel.: +7-812-2971957 (K.K.T.); Fax: +7-812-2970341 (K.K.T.)
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12
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Xu Y, Qiao H. A Hypothesis: Linking Phase Separation to Meiotic Sex Chromosome Inactivation and Sex-Body Formation. Front Cell Dev Biol 2021; 9:674203. [PMID: 34485277 PMCID: PMC8415632 DOI: 10.3389/fcell.2021.674203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/22/2021] [Indexed: 01/12/2023] Open
Abstract
During meiotic prophase I, X and Y chromosomes in mammalian spermatocytes only stably pair at a small homologous region called the pseudoautosomal region (PAR). However, the rest of the sex chromosomes remain largely unsynapsed. The extensive asynapsis triggers transcriptional silencing - meiotic sex chromosome inactivation (MSCI). Along with MSCI, a special nuclear territory, sex body or XY body, forms. In the early steps of MSCI, DNA damage response (DDR) factors, such as BRCA1, ATR, and γH2AX, function as sensors and effectors of the silencing signals. Downstream canonical repressive histone modifications, including methylation, acetylation, ubiquitylation, and SUMOylation, are responsible for the transcriptional repression of the sex chromosomes. Nevertheless, mechanisms of the sex-body formation remain unclear. Liquid-liquid phase separation (LLPS) may drive the formation of several chromatin subcompartments, such as pericentric heterochromatin, nucleoli, inactive X chromosomes. Although several proteins involved in phase separation are found in the sex bodies, when and whether these proteins exert functions in the sex-body formation and MSCI is still unknown. Here, we reviewed recent publications on the mechanisms of MSCI and LLPS, pointed out the potential link between LLPS and the formation of sex bodies, and discussed its implications for future research.
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Affiliation(s)
| | - Huanyu Qiao
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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13
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Lamm N, Rogers S, Cesare AJ. Chromatin mobility and relocation in DNA repair. Trends Cell Biol 2021; 31:843-855. [PMID: 34183232 DOI: 10.1016/j.tcb.2021.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 01/17/2023]
Abstract
The nucleus is a dynamic environment containing chromatin, membraneless organelles, and specialized molecular structures at the nuclear membrane. Within the spectrum of DNA repair activities are observations of increased mobility of damaged chromatin and the displacement of DNA lesions to specific nuclear environments. Here, we focus on the role that nuclear-specific filamentous actin plays in mobilizing damaged chromatin in response to DNA double-strand breaks and replication stress. We also examine nuclear pore complexes and promyelocytic leukemia-nuclear bodies as specialized platforms for homology-directed repair. The literature suggests an emerging model where specific types of DNA lesions are subjected to nuclear-derived forces that mobilize damaged chromatin and promote interaction with repair hubs to facilitate specialized repair reactions.
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Affiliation(s)
- Noa Lamm
- Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, 2145, Australia
| | - Samuel Rogers
- Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, 2145, Australia
| | - Anthony J Cesare
- Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, 2145, Australia.
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14
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Fonin AV, Silonov SA, Shpironok OG, Antifeeva IA, Petukhov AV, Romanovich AE, Kuznetsova IM, Uversky VN, Turoverov KK. The Role of Non-Specific Interactions in Canonical and ALT-Associated PML-Bodies Formation and Dynamics. Int J Mol Sci 2021; 22:ijms22115821. [PMID: 34072343 PMCID: PMC8198325 DOI: 10.3390/ijms22115821] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/30/2021] [Accepted: 05/22/2021] [Indexed: 12/19/2022] Open
Abstract
In this work, we put forward a hypothesis about the decisive role of multivalent nonspecific interactions in the early stages of PML body formation. Our analysis of the PML isoform sequences showed that some of the PML isoforms, primarily PML-II, are prone to phase separation due to their polyampholytic properties and the disordered structure of their C-terminal domains. The similarity of the charge properties of the C-terminal domains of PML-II and PML-VI isoforms made it possible for the first time to detect migration of PML-VI from PML bodies to the periphery of the cell nucleus, similar to the migration of PML-II isoforms. We found a population of “small” (area less than 1 µm2) spherical PML bodies with high dynamics of PML isoforms exchange with nucleoplasm and a low fraction of immobilized proteins, which indicates their liquid state properties. Such structures can act as “seeds” of functionally active PML bodies, providing the necessary concentration of PML isoforms for the formation of intermolecular disulfide bonds between PML monomers. FRAP analysis of larger bodies of toroidal topology showed the existence of an insoluble scaffold in their structure. The hypothesis about the role of nonspecific multiple weak interactions in the formation of PML bodies is further supported by the change in the composition of the scaffold proteins of PML bodies, but not their solidification, under conditions of induction of dimerization of PML isoforms under oxidative stress. Using the colocalization of ALT-associated PML bodies (APBs) with TRF1, we identified APBs and showed the difference in the dynamic properties of APBs and canonical PML bodies.
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Affiliation(s)
- Alexander V. Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (O.G.S.); (I.A.A.); (I.M.K.)
- Correspondence: (A.V.F.); (V.N.U.); (K.K.T.); Tel.: +7-812-2971957 (K.K.T.); Fax: +7-812-2970341(K.K.T.)
| | - Sergey A. Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (O.G.S.); (I.A.A.); (I.M.K.)
| | - Olesya G. Shpironok
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (O.G.S.); (I.A.A.); (I.M.K.)
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Iuliia A. Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (O.G.S.); (I.A.A.); (I.M.K.)
| | - Alexey V. Petukhov
- Institute of Hematology, Almazov National Medical Research Centre, 197341 St. Petersburg, Russia;
| | - Anna E. Romanovich
- St-Petersburg State University Science Park, Resource Center of Molecular and Cell Technologies, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (O.G.S.); (I.A.A.); (I.M.K.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: (A.V.F.); (V.N.U.); (K.K.T.); Tel.: +7-812-2971957 (K.K.T.); Fax: +7-812-2970341(K.K.T.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia; (S.A.S.); (O.G.S.); (I.A.A.); (I.M.K.)
- Peter the Great St.-Petersburg Polytechnic University, Polytechnicheskaya 29, 195251 St. Petersburg, Russia
- Correspondence: (A.V.F.); (V.N.U.); (K.K.T.); Tel.: +7-812-2971957 (K.K.T.); Fax: +7-812-2970341(K.K.T.)
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15
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Zhao R, Chenoweth DM, Zhang H. Chemical Dimerization-Induced Protein Condensates on Telomeres. J Vis Exp 2021. [PMID: 33900288 DOI: 10.3791/62173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Chromatin-associated condensates are implicated in many nuclear processes, but the underlying mechanisms remain elusive. This protocol describes a chemically-induced protein dimerization system to create condensates on telomeres. The chemical dimerizer consists of two linked ligands that can each bind to a protein: Halo ligand to Halo-enzyme and trimethoprim (TMP) to E. coli dihydrofolate reductase (eDHFR), respectively. Fusion of Halo enzyme to a telomere protein anchors dimerizers to telomeres through covalent Halo ligand-enzyme binding. Binding of TMP to eDHFR recruits eDHFR-fused phase separating proteins to telomeres and induces condensate formation. Because TMP-eDHFR interaction is non-covalent, condensation can be reversed by using excess free TMP to compete with the dimerizer for eDHFR binding. An example of inducing promyelocytic leukemia (PML) nuclear body formation on telomeres and determining condensate growth, dissolution, localization and composition is shown. This method can be easily adapted to induce condensates at other genomic locations by fusing Halo to a protein that directly binds to the local chromatin or to dCas9 that is targeted to the genomic locus with a guide RNA. By offering the temporal resolution required for single cell live imaging while maintaining phase separation in a population of cells for biochemical assays, this method is suitable for probing both the formation and function of chromatin-associated condensates.
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Affiliation(s)
- Rongwei Zhao
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University
| | - David M Chenoweth
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania
| | - Huaiying Zhang
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University;
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16
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Zhang JM, Genois MM, Ouyang J, Lan L, Zou L. Alternative lengthening of telomeres is a self-perpetuating process in ALT-associated PML bodies. Mol Cell 2021; 81:1027-1042.e4. [PMID: 33453166 PMCID: PMC8245000 DOI: 10.1016/j.molcel.2020.12.030] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/03/2020] [Accepted: 12/15/2020] [Indexed: 01/16/2023]
Abstract
Alternative lengthening of telomeres (ALT) is mediated by break-induced replication (BIR), but how BIR is regulated at telomeres is poorly understood. Here, we show that telomeric BIR is a self-perpetuating process. By tethering PML-IV to telomeres, we induced telomere clustering in ALT-associated PML bodies (APBs) and a POLD3-dependent ATR response at telomeres, showing that BIR generates replication stress. Ablation of BLM helicase activity in APBs abolishes telomere synthesis but causes multiple chromosome bridges between telomeres, revealing a function of BLM in processing inter-telomere BIR intermediates. Interestingly, the accumulation of BLM in APBs requires its own helicase activity and POLD3, suggesting that BIR triggers a feedforward loop to further recruit BLM. Enhancing BIR induces PIAS4-mediated TRF2 SUMOylation, and PIAS4 loss deprives APBs of repair proteins and compromises ALT telomere synthesis. Thus, a BLM-driven and PIAS4-mediated feedforward loop operates in APBs to perpetuate BIR, providing a critical mechanism to extend ALT telomeres.
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Affiliation(s)
- Jia-Min Zhang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Marie-Michelle Genois
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, 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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17
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Abstract
Cancers and developmental disorders are associated with alterations in the 3D genome architecture in space and time (the fourth dimension). Mammalian 3D genome organization is complex and dynamic and plays an essential role in regulating gene expression and cellular function. To study the causal relationship between genome function and its spatio-temporal organization in the nucleus, new technologies for engineering and manipulating the 3D organization of the genome have been developed. In particular, CRISPR-Cas technologies allow programmable manipulation at specific genomic loci, enabling unparalleled opportunities in this emerging field of 3D genome engineering. We review advances in mammalian 3D genome engineering with a focus on recent manipulative technologies using CRISPR-Cas and related technologies.
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18
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Corpet A, Kleijwegt C, Roubille S, Juillard F, Jacquet K, Texier P, Lomonte P. PML nuclear bodies and chromatin dynamics: catch me if you can! Nucleic Acids Res 2020; 48:11890-11912. [PMID: 33068409 PMCID: PMC7708061 DOI: 10.1093/nar/gkaa828] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic cells compartmentalize their internal milieu in order to achieve specific reactions in time and space. This organization in distinct compartments is essential to allow subcellular processing of regulatory signals and generate specific cellular responses. In the nucleus, genetic information is packaged in the form of chromatin, an organized and repeated nucleoprotein structure that is a source of epigenetic information. In addition, cells organize the distribution of macromolecules via various membrane-less nuclear organelles, which have gathered considerable attention in the last few years. The macromolecular multiprotein complexes known as Promyelocytic Leukemia Nuclear Bodies (PML NBs) are an archetype for nuclear membrane-less organelles. Chromatin interactions with nuclear bodies are important to regulate genome function. In this review, we will focus on the dynamic interplay between PML NBs and chromatin. We report how the structure and formation of PML NBs, which may involve phase separation mechanisms, might impact their functions in the regulation of chromatin dynamics. In particular, we will discuss how PML NBs participate in the chromatinization of viral genomes, as well as in the control of specific cellular chromatin assembly pathways which govern physiological mechanisms such as senescence or telomere maintenance.
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Affiliation(s)
- Armelle Corpet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Constance Kleijwegt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Simon Roubille
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Franceline Juillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Karine Jacquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Pascale Texier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
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19
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TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes. Genes (Basel) 2020; 11:genes11070834. [PMID: 32708340 PMCID: PMC7397314 DOI: 10.3390/genes11070834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Telomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85–90% reactivate telomerase, while 10–15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors switch from a telomerase-dependent mechanism to ALT; in fact, the co-existence between both mechanisms has been observed in some cancers. Although different elements in the ALT pathway are uncovered, some molecular mechanisms are still poorly understood. Therefore, with the aim to identify potential molecular markers for the study of ALT, we combined in silico approaches in a 411 telomere maintenance gene set. As a consequence, we conducted a genomic analysis of these genes in 31 Pan-Cancer Atlas studies from The Cancer Genome Atlas and found 325,936 genomic alterations; from which, we identified 20 genes highly mutated in the cancer studies. Finally, we made a protein-protein interaction network and enrichment analysis to observe the main pathways of these genes and discuss their role in ALT-related processes, like homologous recombination and homology directed repair. Overall, due to the lack of understanding of the molecular mechanisms of ALT cancers, we proposed a group of genes, which after ex vivo validations, could represent new potential therapeutic markers in the study of ALT.
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20
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Zhang H, Zhao R, Tones J, Liu M, Dilley RL, Chenoweth DM, Greenberg RA, Lampson MA. Nuclear body phase separation drives telomere clustering in ALT cancer cells. Mol Biol Cell 2020; 31:2048-2056. [PMID: 32579423 PMCID: PMC7543070 DOI: 10.1091/mbc.e19-10-0589] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Telomerase-free cancer cells employ a recombination-based alternative lengthening of telomeres (ALT) pathway that depends on ALT-associated promyelocytic leukemia nuclear bodies (APBs), whose function is unclear. We find that APBs behave as liquid condensates in response to telomere DNA damage, suggesting two potential functions: condensation to enrich DNA repair factors and coalescence to cluster telomeres. To test these models, we developed a chemically induced dimerization approach to induce de novo APB condensation in live cells without DNA damage. We show that telomere-binding protein sumoylation nucleates APB condensation via interactions between small ubiquitin-like modifier (SUMO) and SUMO interaction motif (SIM), and that APB coalescence drives telomere clustering. The induced APBs lack DNA repair factors, indicating that APB functions in promoting telomere clustering can be uncoupled from enriching DNA repair factors. Indeed, telomere clustering relies only on liquid properties of the condensate, as an alternative condensation chemistry also induces clustering independent of sumoylation. Our findings introduce a chemical dimerization approach to manipulate phase separation and demonstrate how the material properties and chemical composition of APBs independently contribute to ALT, suggesting a general framework for how chromatin condensates promote cellular functions.
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Affiliation(s)
- Huaiying Zhang
- Departments of Biology, University of Pennsylvania, Philadelphia, PA 19104.,Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Rongwei Zhao
- Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Jason Tones
- Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Michel Liu
- Departments of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert L Dilley
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
| | - David M Chenoweth
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine
| | - Roger A Greenberg
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael A Lampson
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
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21
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Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y. Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion. Mol Cell 2020; 78:493-505.e8. [PMID: 32353257 DOI: 10.1016/j.molcel.2020.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/06/2019] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
Abstract
The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with ∼300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypo-methylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D nuclear space and provides insights into the functional properties of nuclear structures for genome function.
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Affiliation(s)
- Misuzu Kurihara
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan
| | - Kagayaki Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Center for Novel Science Initiatives (CNSI), National Institutes of Natural Sciences (NINS), Okazaki, 444-8787, Japan
| | - Chiaki Sanbo
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, Hayama, 240-0193, Japan
| | - Yasuyuki Ohkawa
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Takeshi Fuchigami
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Yusuke Miyanari
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, Hayama, 240-0193, Japan.
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22
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Hsu RYC, Lin YC, Redon C, Sun Q, Singh DK, Wang Y, Aggarwal V, Mitra J, Matur A, Moriarity B, Ha T, Aladjem MI, Prasanth KV, Prasanth SG. ORCA/LRWD1 Regulates Homologous Recombination at ALT-Telomeres by Modulating Heterochromatin Organization. iScience 2020; 23:101038. [PMID: 32344376 PMCID: PMC7186530 DOI: 10.1016/j.isci.2020.101038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 12/23/2022] Open
Abstract
Telomeres are maintained by telomerase or in a subset of cancer cells by a homologous recombination (HR)-based mechanism, Alternative Lengthening of Telomeres (ALT). The mechanisms regulating telomere-homeostasis in ALT cells remain unclear. We report that a replication initiator protein, Origin Recognition Complex-Associated (ORCA/LRWD1), by localizing at the ALT-telomeres, modulates HR activity. ORCA's localization to the ALT-telomeres is facilitated by its interaction to SUMOylated shelterin components. The loss of ORCA in ALT-positive cells elevates the levels of two mediators of HR, RPA and RAD51, and consistent with this, we observe increased ALT-associated promyelocytic leukemia body formation and telomere sister chromatid exchange. ORCA binds to RPA and modulates the association of RPA to telomeres. Finally, the loss of ORCA causes global chromatin decondensation, including at the telomeres. Our results demonstrate that ORCA acts as an inhibitor of HR by modulating RPA binding to ssDNA and inducing chromatin compaction.
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Affiliation(s)
- Rosaline Y C Hsu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Christophe Redon
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda MD 20892, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Yating Wang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Vasudha Aggarwal
- Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jaba Mitra
- Materials Engineering Department, UIUC, Urbana, IL 61801, USA
| | - Abhijith Matur
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | | | - Taekjip Ha
- Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda MD 20892, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA; Cancer Center at Illinois, UIUC, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA; Cancer Center at Illinois, UIUC, Urbana, IL 61801, USA.
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23
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Loe TK, Li JSZ, Zhang Y, Azeroglu B, Boddy MN, Denchi EL. Telomere length heterogeneity in ALT cells is maintained by PML-dependent localization of the BTR complex to telomeres. Genes Dev 2020; 34:650-662. [PMID: 32217664 PMCID: PMC7197349 DOI: 10.1101/gad.333963.119] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022]
Abstract
In this study, Loe et al. sought to understand ALT-associated PML bodies (APBs) and their function in the alternative lengthening of telomeres (ALT) pathway, a telomerase-independent mechanism of telomere extension that some cancer cells that use. Using CRISPR/Cas9 to delete PML and APB components from ALT-positive cells, they found that PML is required for the ALT mechanism, and that this necessity stems from APBs’ role in localizing the BLM–TOP3A–RMI (BTR) complex to ALT telomere ends, suggesting that BTR localization to telomeres is sufficient to sustain ALT activity. Telomeres consist of TTAGGG repeats bound by protein complexes that serve to protect the natural end of linear chromosomes. Most cells maintain telomere repeat lengths by using the enzyme telomerase, although there are some cancer cells that use a telomerase-independent mechanism of telomere extension, termed alternative lengthening of telomeres (ALT). Cells that use ALT are characterized, in part, by the presence of specialized PML nuclear bodies called ALT-associated PML bodies (APBs). APBs localize to and cluster telomeric ends together with telomeric and DNA damage factors, which led to the proposal that these bodies act as a platform on which ALT can occur. However, the necessity of APBs and their function in the ALT pathway has remained unclear. Here, we used CRISPR/Cas9 to delete PML and APB components from ALT-positive cells to cleanly define the function of APBs in ALT. We found that PML is required for the ALT mechanism, and that this necessity stems from APBs’ role in localizing the BLM–TOP3A–RMI (BTR) complex to ALT telomere ends. Strikingly, recruitment of the BTR complex to telomeres in a PML-independent manner bypasses the need for PML in the ALT pathway, suggesting that BTR localization to telomeres is sufficient to sustain ALT activity.
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Affiliation(s)
- Taylor K Loe
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Julia Su Zhou Li
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuxiang Zhang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Benura Azeroglu
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael Nicholas Boddy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Eros Lazzerini Denchi
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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24
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Zhang JM, Yadav T, Ouyang J, Lan L, Zou L. Alternative Lengthening of Telomeres through Two Distinct Break-Induced Replication Pathways. Cell Rep 2020; 26:955-968.e3. [PMID: 30673617 PMCID: PMC6366628 DOI: 10.1016/j.celrep.2018.12.102] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/09/2018] [Accepted: 12/26/2018] [Indexed: 12/11/2022] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomerase-independent but recombination-dependent pathway that maintains telomeres. Here, we describe an assay to visualize ALT-mediated telomeric DNA synthesis in ALT-associated PML bodies (APBs) without DNA-damaging agents or replication inhibitors. Using this assay, we find that ALT occurs through two distinct mechanisms. One of the ALT mechanisms requires RAD52, a protein implicated in break-induced DNA replication (BIR). We demonstrate that RAD52 directly promotes telomeric D-loop formation in vitro and is required for maintaining telomeres in ALT-positive cells. Unexpectedly, however, RAD52 is dispensable for C-circle formation, a hallmark of ALT. In RAD52-knockout ALT cells, C-circle formation and RAD52-independent ALT DNA synthesis gradually increase as telomeres are shortened, and these activities are dependent on BLM and BIR proteins POLD3 and POLD4. These results suggest that ALT occurs through a RAD52-dependent and a RAD52-independent BIR pathway, revealing the bifurcated framework and dynamic nature of this process.
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Affiliation(s)
- Jia-Min Zhang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, 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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25
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Alternative Lengthening of Telomeres: Building Bridges To Connect Chromosome Ends. Trends Cancer 2020; 6:247-260. [PMID: 32101727 DOI: 10.1016/j.trecan.2019.12.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a mechanism of telomere maintenance that is observed in many of the most recalcitrant cancer subtypes. Telomeres in ALT cancer cells exhibit a distinctive nucleoprotein architecture shaped by the mismanagement of chromatin that fosters cycles of DNA damage and replicative stress that activate homology-directed repair (HDR). Mutations in specific chromatin-remodeling factors appear to be key determinants of the emergence and survival of ALT cancer cells. However, these may represent vulnerabilities for the targeted elimination of ALT cancer cells that infiltrate tissues and organs to become devastating tumors. In this review we examine recent findings that provide new insights into the factors and mechanisms that mediate telomere length maintenance and survival of ALT cancer cells.
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26
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Ackermann S, Fischer M. Telomere Maintenance in Pediatric Cancer. Int J Mol Sci 2019; 20:E5836. [PMID: 31757062 PMCID: PMC6928840 DOI: 10.3390/ijms20235836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Telomere length has been proposed as a biomarker of biological age and a risk factor for age-related diseases and cancer. Substantial progress has been made in recent decades in understanding the complex molecular relationships in this research field. However, the majority of telomere studies have been conducted in adults. The data on telomere dynamics in pediatric cancers is limited, and interpretation can be challenging, especially in cases where results are contrasting to those in adult entities. This review describes recent advances in the molecular characterization of structure and function of telomeres, regulation of telomerase activity in cancer pathogenesis in general, and highlights the key advances that have expanded our views on telomere biology in pediatric cancer, with special emphasis on the central role of telomere maintenance in neuroblastoma. Furthermore, open questions in the field of telomere maintenance research are discussed in the context of recently published literature.
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Affiliation(s)
- Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, Faculty of Medicine and University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, Faculty of Medicine and University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
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27
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Min J, Wright WE, Shay JW. Clustered telomeres in phase-separated nuclear condensates engage mitotic DNA synthesis through BLM and RAD52. Genes Dev 2019; 33:814-827. [PMID: 31171703 PMCID: PMC6601508 DOI: 10.1101/gad.324905.119] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/24/2019] [Indexed: 11/25/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism that occurs in a subset of cancers. One of the hallmarks of ALT cancer is the excessively clustered telomeres in promyelocytic leukemia (PML) bodies, represented as large bright telomere foci. Here, we present a model system that generates telomere clustering in nuclear polySUMO (small ubiquitin-like modification)/polySIM (SUMO-interacting motif) condensates, analogous to PML bodies, and thus artificially engineered ALT-associated PML body (APB)-like condensates in vivo. We observed that the ALT-like phenotypes (i.e., a small fraction of heterogeneous telomere lengths and formation of C circles) are rapidly induced by introducing the APB-like condensates together with BLM through its helicase domain, accompanied by ssDNA generation and RPA accumulation at telomeres. Moreover, these events lead to mitotic DNA synthesis (MiDAS) at telomeres mediated by RAD52 through its highly conserved N-terminal domain. We propose that the clustering of large amounts of telomeres in human cancers promotes ALT that is mediated by MiDAS, analogous to Saccharomyces cerevisiae type II ALT survivors.
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Affiliation(s)
- Jaewon Min
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Woodring E Wright
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
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28
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Han M, Napier CE, Frölich S, Teber E, Wong T, Noble JR, Choi EHY, Everett RD, Cesare AJ, Reddel RR. Synthetic lethality of cytolytic HSV-1 in cancer cells with ATRX and PML deficiency. J Cell Sci 2019; 132:jcs.222349. [PMID: 30745338 PMCID: PMC6432714 DOI: 10.1242/jcs.222349] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 02/04/2019] [Indexed: 12/17/2022] Open
Abstract
Cancers that utilize the alternative lengthening of telomeres (ALT) mechanism for telomere maintenance are often difficult to treat and have a poor prognosis. They are also commonly deficient for expression of ATRX protein, a repressor of ALT activity, and a component of promyelocytic leukemia nuclear bodies (PML NBs) that are required for intrinsic immunity to various viruses. Here, we asked whether ATRX deficiency creates a vulnerability in ALT cancer cells that could be exploited for therapeutic purposes. We showed in a range of cell types that a mutant herpes simplex virus type 1 (HSV-1) lacking ICP0, a protein that degrades PML NB components including ATRX, was ten- to one thousand-fold more effective in infecting ATRX-deficient cells than wild-type ATRX-expressing cells. Infection of co-cultured primary and ATRX-deficient cancer cells revealed that mutant HSV-1 selectively killed ATRX-deficient cells. Sensitivity to mutant HSV-1 infection also correlated inversely with PML protein levels, and we showed that ATRX upregulates PML expression at both the transcriptional and post-transcriptional levels. These data provide a basis for predicting, based on ATRX or PML levels, which tumors will respond to a selective oncolytic herpesvirus. Summary: ATRX deficiency in cancer cells induces downregulation of PML, rendering the cells highly sensitive to lysis with ICP0-null mutant herpes simplex virus-1, with potential therapeutic applications.
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Affiliation(s)
- Mingqi Han
- Cancer Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Sonja Frölich
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Erdahl Teber
- Bioinformatics Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Ted Wong
- Bioinformatics Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Jane R Noble
- Cancer Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Eugene H Y Choi
- Cancer Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Roger D Everett
- MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow G61 1QH, Scotland, UK
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
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29
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Brc1 Promotes the Focal Accumulation and SUMO Ligase Activity of Smc5-Smc6 during Replication Stress. Mol Cell Biol 2019; 39:MCB.00271-18. [PMID: 30348841 DOI: 10.1128/mcb.00271-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/12/2018] [Indexed: 11/20/2022] Open
Abstract
As genetic instability drives disease or loss of cell fitness, cellular safeguards have evolved to protect the genome, especially during sensitive cell cycle phases, such as DNA replication. Fission yeast Brc1 has emerged as a key factor in promoting cell survival when replication forks are stalled or collapsed. Brc1 is a multi-BRCT protein that is structurally related to the budding yeast Rtt107 and human PTIP DNA damage response factors, but functional similarities appear limited. Brc1 is a dosage suppressor of a mutation in the essential Smc5-Smc6 genome stability complex and is thought to act in a bypass pathway. In this study, we reveal an unexpectedly intimate connection between Brc1 and Smc5-Smc6 function. Brc1 is required for the accumulation of the Smc5-Smc6 genome stability complex in foci during replication stress and for activation of the intrinsic SUMO ligase activity of the complex by collapsed replication forks. Moreover, we show that the chromatin association and SUMO ligase activity of Smc5-Smc6 require the Nse5-Nse6 heterodimer, explaining how this nonessential cofactor critically supports the DNA repair roles of Smc5-Smc6. We also found that Brc1 interacts with Nse5-Nse6, as well as gamma-H2A, so it can tether Smc5-Smc6 at replicative DNA lesions to promote survival.
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30
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Braun DM, Chung I, Kepper N, Deeg KI, Rippe K. TelNet - a database for human and yeast genes involved in telomere maintenance. BMC Genet 2018; 19:32. [PMID: 29776332 PMCID: PMC5960154 DOI: 10.1186/s12863-018-0617-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/30/2018] [Indexed: 02/05/2023] Open
Abstract
Background The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway. The different telomere maintenance (TM) mechanisms appear to involve hundreds of proteins but their telomere repeat length related activities are only partly understood. Currently, a database that integrates information on TM relevant genes is missing. Description To provide a resource for studies that dissect TM features, we here introduce the TelNet database at http://www.cancertelsys.org/telnet/. It offers a comprehensive compilation of more than 2000 human and 1100 yeast genes linked to telomere maintenance. These genes were annotated in terms of TM mechanism, associated specific functions and orthologous genes, a TM significance score and information from peer-reviewed literature. This TM information can be retrieved via different search and view modes and evaluated for a set of genes as demonstrated for an exemplary application. Conclusion TelNet supports the annotation of genes identified from bioinformatics analysis pipelines to reveal possible connections with TM networks. We anticipate that TelNet will be a helpful resource for researchers that study telomeres. Electronic supplementary material The online version of this article (10.1186/s12863-018-0617-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Delia M Braun
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany
| | - Inn Chung
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany
| | - Nick Kepper
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany
| | - Katharina I Deeg
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany.
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31
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Lallemand-Breitenbach V, de Thé H. PML nuclear bodies: from architecture to function. Curr Opin Cell Biol 2018; 52:154-161. [PMID: 29723661 DOI: 10.1016/j.ceb.2018.03.011] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/06/2018] [Accepted: 03/30/2018] [Indexed: 12/11/2022]
Abstract
PML nuclear bodies are nucleated by the PML protein, which polymerizes into spherical shells where it concentrates many unrelated partner proteins. Emerging data has connected PML bodies to post-translational control, notably conjugation by SUMOs. High concentrations of SUMO-bound proteins were proposed to condense into liquid-like droplets and such phase transition may occur within NBs. Many stress pathways modulate NB formation and recent findings have directly implicated PML in oxidative stress response in vivo. PML may also undergo SUMO-dependent ubiquitination/degradation. We highlight recent advances linking PML to partner degradation and other adaptative post-translational modifications in the context of chromatin remodeling, telomere biology, senescence or viral infections.
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Affiliation(s)
- Valérie Lallemand-Breitenbach
- INSERM U944-CNRS UMR 7212, Equipe labellisée par la Ligue Nationale contre le Cancer, France; Université Paris Diderot, Sorbonne Paris Cité, Hôpital St. Louis, 1 Avenue Claude Vellefaux, 75475 Paris cedex 10, France; Collège de France, PSL Research University, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05, France.
| | - Hugues de Thé
- INSERM U944-CNRS UMR 7212, Equipe labellisée par la Ligue Nationale contre le Cancer, France; Université Paris Diderot, Sorbonne Paris Cité, Hôpital St. Louis, 1 Avenue Claude Vellefaux, 75475 Paris cedex 10, France; Collège de France, PSL Research University, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05, France; Service de Biochimie, Hôpital St. Louis, AP-HP, Paris, France
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32
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He J, Mansouri A, Das S. Alpha Thalassemia/Mental Retardation Syndrome X-Linked, the Alternative Lengthening of Telomere Phenotype, and Gliomagenesis: Current Understandings and Future Potential. Front Oncol 2018; 7:322. [PMID: 29359122 PMCID: PMC5766634 DOI: 10.3389/fonc.2017.00322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/12/2017] [Indexed: 11/13/2022] Open
Abstract
Gliomas are the most common primary malignant brain tumor in humans. Lower grade gliomas are usually less aggressive but many cases eventually progress to a more aggressive secondary glioblastoma (GBM, WHO Grade IV), which has a universally fatal prognosis despite maximal surgical resection and concurrent chemo-radiation. With the identification of molecular markers, however, there is promise for improving diagnostic and therapeutic strategies. One of the key molecular alterations in gliomas is the alpha thalassemia/mental retardation syndrome X-linked (ATRX) gene, which is frequently mutated. One-third of pediatric GBM cases are also found to have the ATRX mutation and the genetic signatures are different from adult cases. The exact role of ATRX mutations in gliomagenesis, however, is unclear. In this review, we describe the normal cellular function of the ATRX gene product followed by consequences of its dysfunction. Furthermore, its possible association with the alternative lengthening of telomeres (ALT) phenotype is outlined. Lastly, therapeutic options potentiated through a better understanding of ATRX and the ALT phenotype are explored.
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Affiliation(s)
- Jenny He
- McGill University, Montreal, QC, Canada
| | - Alireza Mansouri
- National Institutes of Health (NIH), Bethesda, MD, United States
| | - Sunit Das
- St. Michael's Hospital, Toronto, ON, Canada.,Hospital for Sick Children, Toronto, ON, Canada
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Hoffmeister H, Fuchs A, Erdel F, Pinz S, Gröbner-Ferreira R, Bruckmann A, Deutzmann R, Schwartz U, Maldonado R, Huber C, Dendorfer AS, Rippe K, Längst G. CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Nucleic Acids Res 2017; 45:10534-10554. [PMID: 28977666 PMCID: PMC5737555 DOI: 10.1093/nar/gkx711] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/08/2017] [Indexed: 12/22/2022] Open
Abstract
CHD3 and CHD4 (Chromodomain Helicase DNA binding protein), two highly similar representatives of the Mi-2 subfamily of SF2 helicases, are coexpressed in many cell lines and tissues and have been reported to act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). Besides CHD proteins, NuRD contains several repressors like HDAC1/2, MTA2/3 and MBD2/3, arguing for a role as a transcriptional repressor. However, the subunit composition varies among cell- and tissue types and physiological conditions. In particular, it is unclear if CHD3 and CHD4 coexist in the same NuRD complex or whether they form distinct NuRD complexes with specific functions. We mapped the CHD composition of NuRD complexes in mammalian cells and discovered that they are isoform-specific, containing either the monomeric CHD3 or CHD4 ATPase. Both types of complexes exhibit similar intranuclear mobility, interact with HP1 and rapidly accumulate at UV-induced DNA repair sites. But, CHD3 and CHD4 exhibit distinct nuclear localization patterns in unperturbed cells, revealing a subset of specific target genes. Furthermore, CHD3 and CHD4 differ in their nucleosome remodeling and positioning behaviour in vitro. The proteins form distinct CHD3- and CHD4-NuRD complexes that do not only repress, but can just as well activate gene transcription of overlapping and specific target genes.
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Affiliation(s)
- Helen Hoffmeister
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Andreas Fuchs
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Fabian Erdel
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sophia Pinz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Regina Gröbner-Ferreira
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Rainer Deutzmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Uwe Schwartz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Rodrigo Maldonado
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Claudia Huber
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Anne-Sarah Dendorfer
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Karsten Rippe
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Gernot Längst
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
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34
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Wang Z, Deng Z, Tutton S, Lieberman PM. The Telomeric Response to Viral Infection. Viruses 2017; 9:v9080218. [PMID: 28792463 PMCID: PMC5580475 DOI: 10.3390/v9080218] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/06/2017] [Accepted: 08/06/2017] [Indexed: 12/16/2022] Open
Abstract
The ends of linear genomes, whether viral or cellular, can elicit potent DNA damage and innate immune signals. DNA viruses entering the nucleus share many features with telomeres in their ability to either suppress or co-opt these pathways. Here, we review some of the common mechanisms that viruses and telomeres use to manage the DNA damage and innate immune response pathways. We highlight recent studies on the role of the telomere repeat-containing RNA (TERRA) in response to viral infection. We discuss how TERRA can be activated through a p53-response element embedded in a retrotransposon-like repeat found in human subtelomeres. We consider how TERRA can function as a danger signal when secreted in extracellular vesicles to induce inflammatory cytokines in neighboring cells. These findings suggest that TERRA may be part of the innate immune response to viral infection, and support the hypothesis that telomeres and viruses utilize common mechanisms to maintain genome integrity and regulate innate immunity.
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Affiliation(s)
- Zhuo Wang
- The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Zhong Deng
- The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Steve Tutton
- The Wistar Institute, Philadelphia, PA 19104, USA.
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35
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Pankert T, Jegou T, Caudron-Herger M, Rippe K. Tethering RNA to chromatin for fluorescence microscopy based analysis of nuclear organization. Methods 2017; 123:89-101. [DOI: 10.1016/j.ymeth.2017.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/23/2017] [Accepted: 01/30/2017] [Indexed: 12/22/2022] Open
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Banani SF, Lee HO, Hyman AA, Rosen MK. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 2017; 18:285-298. [PMID: 28225081 PMCID: PMC7434221 DOI: 10.1038/nrm.2017.7] [Citation(s) in RCA: 3157] [Impact Index Per Article: 451.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated.
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Affiliation(s)
- Salman F. Banani
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hyun O. Lee
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Michael K. Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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37
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Rademacher A, Erdel F, Trojanowski J, Schumacher S, Rippe K. Real-time observation of light-controlled transcription in living cells. J Cell Sci 2017. [DOI: 10.1242/jcs.205534] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Gene expression is tightly regulated in space and time. To dissect this process with high temporal resolution, we introduce an optogenetic tool termed BLInCR (Blue Light-Induced Chromatin Recruitment) that combines rapid and reversible light-dependent recruitment of effector proteins with a real-time readout for transcription. We used BLInCR to control the activity of a reporter gene cluster in the human osteosarcoma cell line U2OS by reversibly recruiting the viral transactivator VP16. RNA production was detectable ∼2 minutes after VP16 recruitment and readily decreased when VP16 dissociated from the cluster in the absence of light. Quantitative assessment of the activation process revealed biphasic activation kinetics with a pronounced early phase in cells treated with the histone deacetylase inhibitor SAHA. Comparison with kinetic models for transcription activation suggests that the gene cluster undergoes a maturation process when activated. We anticipate that BLInCR will facilitate the study of transcription dynamics in living cells.
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Affiliation(s)
- Anne Rademacher
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Fabian Erdel
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jorge Trojanowski
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Schumacher
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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38
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Gunkel M, Chung I, Wörz S, Deeg KI, Simon R, Sauter G, Jones DTW, Korshunov A, Rohr K, Erfle H, Rippe K. Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow. Methods 2016; 114:60-73. [PMID: 27725304 DOI: 10.1016/j.ymeth.2016.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 01/08/2023] Open
Abstract
The microscopic analysis of telomere features provides a wealth of information on the mechanism by which tumor cells maintain their unlimited proliferative potential. Accordingly, the analysis of telomeres in tissue sections of patient tumor samples can be exploited to obtain diagnostic information and to define tumor subgroups. In many instances, however, analysis of the image data is conducted by manual inspection of 2D images at relatively low resolution for only a small part of the sample. As the telomere feature signal distribution is frequently heterogeneous, this approach is prone to a biased selection of the information present in the image and lacks subcellular details. Here we address these issues by using an automated high-resolution imaging and analysis workflow that quantifies individual telomere features on tissue sections for a large number of cells. The approach is particularly suited to assess telomere heterogeneity and low abundant cellular subpopulations with distinct telomere characteristics in a reproducible manner. It comprises the integration of multi-color fluorescence in situ hybridization, immunofluorescence and DNA staining with targeted automated 3D fluorescence microscopy and image analysis. We apply our method to telomeres in glioblastoma and prostate cancer samples, and describe how the imaging data can be used to derive statistically reliable information on telomere length distribution or colocalization with PML nuclear bodies. We anticipate that relating this approach to clinical outcome data will prove to be valuable for pretherapeutic patient stratification.
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Affiliation(s)
- Manuel Gunkel
- VIROQUANT CellNetworks RNAi Screening Facility and Research Group High-Content Analysis of the Cell (HiCell), Bioquant Center, University of Heidelberg, Germany
| | - Inn Chung
- Research Group Genome Organization & Function, German Cancer Research Center (DKFZ) and Bioquant Center, Germany.
| | - Stefan Wörz
- Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, Bioquant Center and IPMB, University of Heidelberg and German Cancer Research Center (DKFZ), Germany
| | - Katharina I Deeg
- Research Group Genome Organization & Function, German Cancer Research Center (DKFZ) and Bioquant Center, Germany
| | - Ronald Simon
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Guido Sauter
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Germany
| | - Karl Rohr
- Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, Bioquant Center and IPMB, University of Heidelberg and German Cancer Research Center (DKFZ), Germany.
| | - Holger Erfle
- VIROQUANT CellNetworks RNAi Screening Facility and Research Group High-Content Analysis of the Cell (HiCell), Bioquant Center, University of Heidelberg, Germany.
| | - Karsten Rippe
- Research Group Genome Organization & Function, German Cancer Research Center (DKFZ) and Bioquant Center, Germany.
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39
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Banani SF, Rice AM, Peeples WB, Lin Y, Jain S, Parker R, Rosen MK. Compositional Control of Phase-Separated Cellular Bodies. Cell 2016; 166:651-663. [PMID: 27374333 DOI: 10.1016/j.cell.2016.06.010] [Citation(s) in RCA: 771] [Impact Index Per Article: 96.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 03/13/2016] [Accepted: 06/01/2016] [Indexed: 12/12/2022]
Abstract
Cellular bodies such as P bodies and PML nuclear bodies (PML NBs) appear to be phase-separated liquids organized by multivalent interactions among proteins and RNA molecules. Although many components of various cellular bodies are known, general principles that define body composition are lacking. We modeled cellular bodies using several engineered multivalent proteins and RNA. In vitro and in cells, these scaffold molecules form phase-separated liquids that concentrate low valency client proteins. Clients partition differently depending on the ratio of scaffolds, with a sharp switch across the phase diagram diagonal. Composition can switch rapidly through changes in scaffold concentration or valency. Natural PML NBs and P bodies show analogous partitioning behavior, suggesting how their compositions could be controlled by levels of PML SUMOylation or cellular mRNA concentration, respectively. The data suggest a conceptual framework for considering the composition and control thereof of cellular bodies assembled through heterotypic multivalent interactions.
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Affiliation(s)
- Salman F Banani
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Allyson M Rice
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - William B Peeples
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuan Lin
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Saumya Jain
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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40
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Wilson FR, Ho A, Walker JR, Zhu XD. Cdk-dependent phosphorylation regulates TRF1 recruitment to PML bodies and promotes C-circle production in ALT cells. J Cell Sci 2016; 129:2559-72. [PMID: 27185864 DOI: 10.1242/jcs.186098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
TRF1, a duplex telomeric DNA binding protein, is implicated in homologous-recombination-based alternative lengthening of telomeres, known as ALT. However, how TRF1 promotes ALT activity has yet to be fully characterized. Here we report that Cdk-dependent TRF1 phosphorylation on T371 acts as a switch to create a pool of TRF1, referred to as (pT371)TRF1, which is recruited to ALT-associated PML bodies (APBs) in S and G2 phases independently of its binding to telomeric DNA. We find that phosphorylation of T371 is essential for APB formation and C-circle production, both of which are hallmarks of ALT. We show that the interaction of (pT371)TRF1 with APBs is dependent upon ATM and homologous-recombination-promoting factors Mre11 and BRCA1. In addition, (pT371)TRF1 interaction with APBs is sensitive to transcription inhibition, which also reduces DNA damage at telomeres. Furthermore, overexpression of RNaseH1 impairs (pT371)TRF1 recruitment to APBs in the presence of campothecin, an inhibitor that prevents topoisomerase I from resolving RNA-DNA hybrids. These results suggest that transcription-associated DNA damage, perhaps arising from processing RNA-DNA hybrids at telomeres, triggers (pT371)TRF1 recruitment to APBs to facilitate ALT activity.
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Affiliation(s)
- Florence R Wilson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Angus Ho
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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41
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Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015; 34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.
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Affiliation(s)
- Maïwen Caudron-Herger
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Teresa Pankert
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Jeanette Seiler
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Attila Németh
- Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
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42
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Mallm JP, Rippe K. Aurora Kinase B Regulates Telomerase Activity via a Centromeric RNA in Stem Cells. Cell Rep 2015; 11:1667-78. [PMID: 26051938 DOI: 10.1016/j.celrep.2015.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/28/2015] [Accepted: 05/11/2015] [Indexed: 11/29/2022] Open
Abstract
Non-coding RNAs can modulate histone modifications that, at the same time, affect transcript expression levels. Here, we dissect such a network in mouse embryonic stem cells (ESCs). It regulates the activity of the reverse transcriptase telomerase, which synthesizes telomeric repeats at the chromosome ends. We find that histone H3 serine 10 phosphorylation set by Aurora kinase B (AURKB) in ESCs during the S phase of the cell cycle at centromeric and (sub)telomeric loci promotes the expression of non-coding minor satellite RNA (cenRNA). Inhibition of AURKB induces silencing of cenRNA transcription and establishment of a repressive chromatin state with histone H3 lysine 9 trimethylation and heterochromatin protein 1 accumulation. This process results in a continuous shortening of telomeres. We further show that AURKB interacts with both telomerase and cenRNA and activates telomerase in trans. Thus, in mouse ESCs, telomere maintenance is regulated via expression of cenRNA in a cell-cycle-dependent manner.
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Affiliation(s)
- Jan-Philipp Mallm
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Bioquant Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
| | - Karsten Rippe
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Bioquant Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
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43
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Osterwald S, Deeg KI, Chung I, Parisotto D, Wörz S, Rohr K, Erfle H, Rippe K. PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening. J Cell Sci 2015; 128:1887-1900. [DOI: 10.1242/jcs.148296] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
ABSTRACT
The alternative lengthening of telomeres (ALT) mechanism allows cancer cells to escape senescence and apoptosis in the absence of active telomerase. A characteristic feature of this pathway is the assembly of ALT-associated promyelocytic leukemia (PML) nuclear bodies (APBs) at telomeres. Here, we dissected the role of APBs in a human ALT cell line by performing an RNA interference screen using an automated 3D fluorescence microscopy platform and advanced 3D image analysis. We identified 29 proteins that affected APB formation, which included proteins involved in telomere and chromatin organization, protein sumoylation and DNA repair. By integrating and extending these findings, we found that APB formation induced clustering of telomere repeats, telomere compaction and concomitant depletion of the shelterin protein TRF2 (also known as TERF2). These APB-dependent changes correlated with the induction of a DNA damage response at telomeres in APBs as evident by a strong enrichment of the phosphorylated form of the ataxia telangiectasia mutated (ATM) kinase. Accordingly, we propose that APBs promote telomere maintenance by inducing a DNA damage response in ALT-positive tumor cells through changing the telomeric chromatin state to trigger ATM phosphorylation.
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Affiliation(s)
- Sarah Osterwald
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, 69120 Heidelberg, Germany
| | - Katharina I. Deeg
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, 69120 Heidelberg, Germany
| | - Inn Chung
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, 69120 Heidelberg, Germany
| | - Daniel Parisotto
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, 69120 Heidelberg, Germany
| | - Stefan Wörz
- Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg & DKFZ, BioQuant, IPMB, 69120 Heidelberg, Germany
| | - Karl Rohr
- Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg & DKFZ, BioQuant, IPMB, 69120 Heidelberg, Germany
| | - Holger Erfle
- ViroQuant-CellNetworks RNAi Screening Facility, University of Heidelberg & BioQuant, 69120 Heidelberg, Germany
| | - Karsten Rippe
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, 69120 Heidelberg, Germany
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44
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Cho NW, Dilley RL, Lampson MA, Greenberg RA. Interchromosomal homology searches drive directional ALT telomere movement and synapsis. Cell 2015; 159:108-121. [PMID: 25259924 DOI: 10.1016/j.cell.2014.08.030] [Citation(s) in RCA: 261] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 06/16/2014] [Accepted: 08/25/2014] [Indexed: 12/17/2022]
Abstract
Telomere length maintenance is a requisite feature of cellular immortalization and a hallmark of human cancer. While most human cancers express telomerase activity, ∼10%-15% employ a recombination-dependent telomere maintenance pathway known as alternative lengthening of telomeres (ALT) that is characterized by multitelomere clusters and associated promyelocytic leukemia protein bodies. Here, we show that a DNA double-strand break (DSB) response at ALT telomeres triggers long-range movement and clustering between chromosome termini, resulting in homology-directed telomere synthesis. Damaged telomeres initiate increased random surveillance of nuclear space before displaying rapid directional movement and association with recipient telomeres over micron-range distances. This phenomenon required Rad51 and the Hop2-Mnd1 heterodimer, which are essential for homologous chromosome synapsis during meiosis. These findings implicate a specialized homology searching mechanism in ALT-dependent telomere maintenance and provide a molecular basis underlying the preference for recombination between nonsister telomeres during ALT.
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Affiliation(s)
- Nam Woo Cho
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA
| | - Robert L Dilley
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA; Department of Pathology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA; Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA.
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45
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Böhm S, Bernstein KA. The role of post-translational modifications in fine-tuning BLM helicase function during DNA repair. DNA Repair (Amst) 2014; 22:123-32. [PMID: 25150915 DOI: 10.1016/j.dnarep.2014.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 07/14/2014] [Indexed: 12/12/2022]
Abstract
RecQ-like helicases are a highly conserved family of proteins which are critical for preserving genome integrity. Genome instability is considered a hallmark of cancer and mutations within three of the five human RECQ genes cause hereditary syndromes that are associated with cancer predisposition. The human RecQ-like helicase BLM has a central role in DNA damage signaling, repair, replication, and telomere maintenance. BLM and its budding yeast orthologue Sgs1 unwind double-stranded DNA intermediates. Intriguingly, BLM functions in both a pro- and anti-recombinogenic manner upon replicative damage, acting on similar substrates. Thus, BLM activity must be intricately controlled to prevent illegitimate recombination events that could have detrimental effects on genome integrity. In recent years it has become evident that post-translational modifications (PTMs) of BLM allow a fine-tuning of its function. To date, BLM phosphorylation, ubiquitination, and SUMOylation have been identified, in turn regulating its subcellular localization, protein-protein interactions, and protein stability. In this review, we will discuss the cellular context of when and how these different modifications of BLM occur. We will reflect on the current model of how PTMs control BLM function during DNA damage repair and compare this to what is known about post-translational regulation of the budding yeast orthologue Sgs1. Finally, we will provide an outlook toward future research, in particular to dissect the cross-talk between the individual PTMs on BLM.
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Affiliation(s)
- Stefanie Böhm
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States
| | - Kara Anne Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States.
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Müller-Ott K, Erdel F, Matveeva A, Mallm JP, Rademacher A, Hahn M, Bauer C, Zhang Q, Kaltofen S, Schotta G, Höfer T, Rippe K. Specificity, propagation, and memory of pericentric heterochromatin. Mol Syst Biol 2014; 10:746. [PMID: 25134515 PMCID: PMC4299515 DOI: 10.15252/msb.20145377] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The cell establishes heritable patterns of active and silenced chromatin via interacting factors
that set, remove, and read epigenetic marks. To understand how the underlying networks operate, we
have dissected transcriptional silencing in pericentric heterochromatin (PCH) of mouse fibroblasts.
We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in
living cells and found that stably bound complexes of the histone methyltransferase SUV39H1/2
demarcate the PCH state. From the experimental data, we developed a predictive mathematical model
that explains how chromatin-bound SUV39H1/2 complexes act as nucleation sites and propagate a
spatially confined PCH domain with elevated histone H3 lysine 9 trimethylation levels via chromatin
dynamics. This “nucleation and looping” mechanism is particularly robust toward
transient perturbations and stably maintains the PCH state. These features make it an attractive
model for establishing functional epigenetic domains throughout the genome based on the localized
immobilization of chromatin-modifying enzymes.
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Affiliation(s)
- Katharina Müller-Ott
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Fabian Erdel
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Anna Matveeva
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Anne Rademacher
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Matthias Hahn
- Munich Center for Integrated Protein Science and Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Caroline Bauer
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Qin Zhang
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Sabine Kaltofen
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Gunnar Schotta
- Munich Center for Integrated Protein Science and Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Thomas Höfer
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Karsten Rippe
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
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Berkholz J, Michalick L, Munz B. The E3 SUMO ligase Nse2 regulates sumoylation and nuclear-to-cytoplasmic translocation of skNAC-Smyd1 in myogenesis. J Cell Sci 2014; 127:3794-804. [PMID: 25002400 DOI: 10.1242/jcs.150334] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Skeletal and heart muscle-specific variant of the α subunit of nascent polypeptide associated complex (skNAC; encoded by NACA) is exclusively found in striated muscle cells. Its function, however, is largely unknown. Previous reports have demonstrated that skNAC binds to m-Bop/Smyd1, a multi-functional protein that regulates myogenesis both through the control of transcription and the modulation of sarcomerogenesis, and that both proteins undergo nuclear-to-cytoplasmic translocation at the later stages of myogenic differentiation. Here, we show that skNAC binds to the E3 SUMO ligase mammalian Mms21/Nse2 and that knockdown of Nse2 expression inhibits specific aspects of myogenic differentiation, accompanied by a partial blockade of the nuclear-to-cytoplasmic translocation of the skNAC-Smyd1 complex, retention of the complex in promyelocytic leukemia (PML)-like nuclear bodies and disturbed sarcomerogenesis. In addition, we show that the skNAC interaction partner Smyd1 contains a putative sumoylation motif and is sumoylated in muscle cells, with depletion of Mms21/Nse2 leading to reduced concentrations of sumoylated Smyd1. Taken together, our data suggest that the function, specifically the balance between the nuclear and cytosolic roles, of the skNAC-Smyd1 complex might be regulated by sumoylation.
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Affiliation(s)
- Janine Berkholz
- Charité - University Medicine Berlin, Institute of Physiology, Charitéplatz 1, D-10117 Berlin, Germany
| | - Laura Michalick
- Charité - University Medicine Berlin, Institute of Physiology, Charitéplatz 1, D-10117 Berlin, Germany
| | - Barbara Munz
- University Hospital Tubingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Strasse 6, D-72076 Tubingen, Germany
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48
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Nuclear bodies: new insights into assembly/dynamics and disease relevance. Curr Opin Cell Biol 2014; 28:76-83. [DOI: 10.1016/j.ceb.2014.03.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/15/2023]
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Maicher A, Lockhart A, Luke B. Breaking new ground: digging into TERRA function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:387-94. [PMID: 24698720 DOI: 10.1016/j.bbagrm.2014.03.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 11/30/2022]
Abstract
Despite the fact that telomeres carry chromatin marks typically associated with silent heterochromatin, they are actively transcribed into TElomeric Repeat containing RNA (TERRA). TERRA transcription is conserved from yeast to man, initiates in the subtelomeric region and proceeds through the telomeric tract of presumably each individual telomere. TERRA levels are increased in yeast survivors and in cancer cells employing ALT as a telomere maintenance mechanism (TMM). Thus, TERRA may be a promising biomarker and potential target in anti-cancer therapy. Interestingly, several recent publications implicate TERRA in regulatory processes including telomere end protection and the establishment of the heterochromatic state at telomeres. A picture is emerging whereby TERRA acts as a regulator of telomere length and hence the associated onset of replicative senescence in a cell. In this review we will summarize the latest results regarding TERRA transcription, localization and related function. A special focus will be set on the potential role of TERRA in the regulation of telomere length and replicative senescence. Possible implications of increased TERRA levels in yeast survivors and in ALT cancer cells will be discussed.
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Affiliation(s)
- André Maicher
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Arianna Lockhart
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Brian Luke
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, Heidelberg, Germany.
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Chatterjee D, Bhattacharjee P, Sau TJ, Das JK, Sarma N, Bandyopadhyay AK, Roy SS, Giri AK. Arsenic exposure through drinking water leads to senescence and alteration of telomere length in humans: A case-control study in West Bengal, India. Mol Carcinog 2014; 54:800-9. [PMID: 24665044 DOI: 10.1002/mc.22150] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/14/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Debmita Chatterjee
- Molecular and Human Genetics Division; CSIR-Indian Institute of Chemical Biology; Kolkata India
| | | | - Tanmoy J. Sau
- Sir Nil Ratan Sircar Medical College and Hospital; Kolkata India
| | - Jayanta K. Das
- Department of Dermatology; West Bank Hospital; Howrah, West Bengal India
| | - Nilendu Sarma
- Sir Nil Ratan Sircar Medical College and Hospital; Kolkata India
| | - Apurba K. Bandyopadhyay
- Molecular and Human Genetics Division; CSIR-Indian Institute of Chemical Biology; Kolkata India
| | - Sib Sankar Roy
- Cell Biology and Physiology Division; CSIR-Indian Institute of Chemical Biology; Kolkata India
| | - Ashok K. Giri
- Molecular and Human Genetics Division; CSIR-Indian Institute of Chemical Biology; Kolkata India
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