1
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Thosar SA, Barnes RP, Detwiler A, Bhargava R, Wondisford A, O'Sullivan RJ, Opresko PL. Oxidative guanine base damage plays a dual role in regulating productive ALT-associated homology-directed repair. Cell Rep 2024; 43:113656. [PMID: 38194346 PMCID: PMC10851105 DOI: 10.1016/j.celrep.2023.113656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/06/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Cancer cells maintain telomeres by upregulating telomerase or alternative lengthening of telomeres (ALT) via homology-directed repair at telomeric DNA breaks. 8-Oxoguanine (8oxoG) is a highly prevalent endogenous DNA lesion in telomeric sequences, altering telomere structure and telomerase activity, but its impact on ALT is unclear. Here, we demonstrate that targeted 8oxoG formation at telomeres stimulates ALT activity and homologous recombination specifically in ALT cancer cells. Mechanistically, an acute 8oxoG induction increases replication stress, as evidenced by increased telomere fragility and ATR kinase activation at ALT telomeres. Furthermore, ALT cells are more sensitive to chronic telomeric 8oxoG damage than telomerase-positive cancer cells, consistent with increased 8oxoG-induced replication stress. However, telomeric 8oxoG production in G2 phase, when ALT telomere elongation occurs, impairs telomeric DNA synthesis. Our study demonstrates that a common oxidative base lesion has a dual role in regulating ALT depending on when the damage arises in the cell cycle.
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Affiliation(s)
- Sanjana A Thosar
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ryan P Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ariana Detwiler
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ragini Bhargava
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Wondisford
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Roderick J O'Sullivan
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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2
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De Rosa M, Opresko PL. Translating the telomeres. Trends Genet 2023:S0168-9525(23)00123-3. [PMID: 37179160 DOI: 10.1016/j.tig.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Telomeres are transcribed into long noncoding telomeric repeat-containing RNA (TERRA). Or so we thought. Recently, Al-Turki and Griffith provided evidence that TERRA can code for valine-arginine (VR) or glycine-leucine (GL) dipeptide repeat proteins by undergoing repeat-associated non-ATG (RAN) translation. This finding uncovers a new mechanism by which telomeres can impact cellular function.
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Affiliation(s)
- Mariarosaria De Rosa
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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3
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Liu M, Pan H, Kaur P, Wang LJ, Jin M, Detwiler AC, Opresko PL, Tao YJ, Wang H, Riehn R. Assembly Path Dependence of Telomeric DNA Compaction by TRF1, TIN2, and SA1. Biophys J 2023; 122:1822-1832. [PMID: 37081787 DOI: 10.1016/j.bpj.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/10/2023] [Accepted: 04/12/2023] [Indexed: 04/22/2023] Open
Abstract
Telomeres, complexes of DNA and proteins, protect ends of linear chromosomes. In humans, the two shelterin proteins TRF1 and TIN2, along with cohesin subunit SA1, were proposed to mediate telomere cohesion. While the ability of the TRF1-TIN2 and TRF1-SA1 systems to compact telomeric DNA by DNA-DNA bridging has been reported, the function of the full ternary TRF1-TIN2-SA1 system has not been explored in detail. Here, we quantify the compaction of nanochannel-stretched DNA by the ternary system, as well as its constituents, and obtain estimates of the relative impact of its constituents and their interactions. We find that TRF1, TIN2, and SA1 work synergistically to cause a compaction of the DNA substrate, and that maximal compaction occurs if all three proteins are present. By altering the sequence with which DNA substrates are exposed to proteins, we establish that compaction by TRF1 and TIN2 can proceed through binding of TRF1 to DNA, followed by compaction as TIN2 recognizes the previously bound TRF1. We further establish that SA1 alone can also lead to a compaction, and that compaction in a combined system of all three proteins can be understood as an additive effect of TRF1-TIN2 and SA1-based compaction. Atomic force microscopy (AFM) of intermolecular aggregation confirms that a conbination of TRF1, TIN2, and SA1 together drive strong intermolecular aggregation as it would be required during chromosome cohesion.
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Affiliation(s)
- Ming Liu
- Department of Physics, NC State University, Raleigh, NC 27695
| | - Hai Pan
- Department of Physics, NC State University, Raleigh, NC 27695
| | - Parminder Kaur
- Department of Physics, NC State University, Raleigh, NC 27695
| | - Lucia J Wang
- Department of Physics, NC State University, Raleigh, NC 27695
| | - Miao Jin
- Department of BioSciences, Rice University, Houston, TX 77251
| | - Ariana C Detwiler
- Department of Environmental and Occupational Health, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15219
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15219
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, TX 77251
| | - Hong Wang
- Department of Physics, NC State University, Raleigh, NC 27695
| | - Robert Riehn
- Department of Physics, NC State University, Raleigh, NC 27695.
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4
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De Rosa M, Barnes RP, Nyalapatla PR, Wipf P, Opresko PL. OGG1 and MUTYH repair activities promote telomeric 8-oxoguanine induced cellular senescence. bioRxiv 2023:2023.04.10.536247. [PMID: 37090589 PMCID: PMC10120708 DOI: 10.1101/2023.04.10.536247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Telomeres are prone to formation of the common oxidative lesion 8-oxoguanine (8oxoG), and the acute production of 8oxoG damage at telomeres is sufficient to drive rapid cellular senescence. OGG1 and MUTYH glycosylases initiate base excision repair (BER) at 8oxoG sites to remove the lesion or prevent mutation. Here, we show OGG1 loss or inhibition, or MUTYH loss, partially rescues telomeric 8oxoG-induced senescence, and loss of both glycosylases results in a near complete rescue. Loss of these glycosylases also suppresses 8oxoG-induced telomere fragility and dysfunction, indicating that single-stranded break (SSB) intermediates arising downstream of glycosylase activity impair telomere replication. The failure to initiate BER in glycosylase-deficient cells suppresses PARylation at SSB intermediates and confers resistance to the synergistic effects of PARP inhibitors on damage-induced senescence. Our studies reveal that inefficient completion of 8oxoG BER at telomeres triggers cellular senescence via SSB intermediates which impair telomere replication and stability.
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Affiliation(s)
- Mariarosaria De Rosa
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ryan P. Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | | | - Peter Wipf
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Deparment of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patricia L. Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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5
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Liu M, Pan H, Kaur P, Wang LJ, Detwiler ACC, Tao YJ, Opresko PL, Wang H, Riehn R. Assembly of a three-protein complex on DNA probed by nanofluidic stretching. Biophys J 2023; 122:74a-75a. [PMID: 36784989 DOI: 10.1016/j.bpj.2022.11.609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Ming Liu
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Hai Pan
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Lucia J Wang
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | | | - Yizhi J Tao
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | | | - Hong Wang
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, NC, USA
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6
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Sanford SL, Opresko PL. UV light-induced dual promoter mutations dismantle the telomeric guardrails in melanoma. DNA Repair (Amst) 2023; 122:103446. [PMID: 36603239 PMCID: PMC9892262 DOI: 10.1016/j.dnarep.2022.103446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Understanding how benign nevi can progress to invasive and metastatic Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, USAelanoma is critical for developing interventions and therapeutics for this most deadly form of skin cancer. UV-induced mutations in the telomerase TERT gene promoter occur in the majority of melanomas but fail to prevent telomere shortening despite telomerase upregulation. This suggests additional "hits" are required to enable telomere maintenance. A new study in Science identified somatic variants in the promoter of the gene that encodes telomere shelterin protein TPP1 in human melanomas. These variants show mutational signatures of UV-induced DNA damage and upregulate TPP1 expression, which synergizes with telomerase to lengthen telomeres. This study provides evidence that TPP1 promoter variants are a critical second hit to prevent telomere shortening and promote immortalization of melanoma cells.
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Affiliation(s)
- Samantha L Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, USA; UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, USA; UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, USA.
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7
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Barnes RP, Thosar SA, Opresko PL. Telomere Fragility and MiDAS: Managing the Gaps at the End of the Road. Genes (Basel) 2023; 14:genes14020348. [PMID: 36833275 PMCID: PMC9956152 DOI: 10.3390/genes14020348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Telomeres present inherent difficulties to the DNA replication machinery due to their repetitive sequence content, formation of non-B DNA secondary structures, and the presence of the nucleo-protein t-loop. Especially in cancer cells, telomeres are hot spots for replication stress, which can result in a visible phenotype in metaphase cells termed "telomere fragility". A mechanism cells employ to mitigate replication stress, including at telomeres, is DNA synthesis in mitosis (MiDAS). While these phenomena are both observed in mitotic cells, the relationship between them is poorly understood; however, a common link is DNA replication stress. In this review, we will summarize what is known to regulate telomere fragility and telomere MiDAS, paying special attention to the proteins which play a role in these telomere phenotypes.
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Affiliation(s)
- Ryan P. Barnes
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
- Correspondence: (R.P.B.); (P.L.O.)
| | - Sanjana A. Thosar
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Patricia L. Opresko
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Correspondence: (R.P.B.); (P.L.O.)
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8
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Yu T, Slone J, Liu W, Barnes R, Opresko PL, Wark L, Mai S, Horvath S, Huang T. Premature aging is associated with higher levels of 8-oxoguanine and increased DNA damage in the Polg mutator mouse. Aging Cell 2022; 21:e13669. [PMID: 35993394 PMCID: PMC9470903 DOI: 10.1111/acel.13669] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/07/2022] [Accepted: 06/24/2022] [Indexed: 01/24/2023] Open
Abstract
Mitochondrial dysfunction plays an important role in the aging process. However, the mechanism by which this dysfunction causes aging is not fully understood. The accumulation of mutations in the mitochondrial genome (or "mtDNA") has been proposed as a contributor. One compelling piece of evidence in support of this hypothesis comes from the PolgD257A/D257A mutator mouse (Polgmut/mut ). These mice express an error-prone mitochondrial DNA polymerase that results in the accumulation of mtDNA mutations, accelerated aging, and premature death. In this paper, we have used the Polgmut/mut model to investigate whether the age-related biological effects observed in these mice are triggered by oxidative damage to the DNA that compromises the integrity of the genome. Our results show that mutator mouse has significantly higher levels of 8-oxoguanine (8-oxoGua) that are correlated with increased nuclear DNA (nDNA) strand breakage and oxidative nDNA damage, shorter average telomere length, and reduced mtDNA integrity. Based on these results, we propose a model whereby the increased level of reactive oxygen species (ROS) associated with the accumulation of mtDNA mutations in Polgmut/mut mice results in higher levels of 8-oxoGua, which in turn lead to compromised DNA integrity and accelerated aging via increased DNA fragmentation and telomere shortening. These results suggest that mitochondrial play a central role in aging and may guide future research to develop potential therapeutics for mitigating aging process.
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Affiliation(s)
- Tenghui Yu
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Human Aging Research Institute, School of Life ScienceNanchang UniversityNanchangChina,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Jesse Slone
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Wensheng Liu
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA
| | - Ryan Barnes
- Department of Environmental and Occupational HealthUniversity of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer CenterPittsburghPennsylvaniaUSA
| | - Patricia L. Opresko
- Department of Environmental and Occupational HealthUniversity of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer CenterPittsburghPennsylvaniaUSA
| | - Landon Wark
- CancerCare Manitoba Research Institute, The Genomic Center for Cancer Research & DiagnosisUniversity of ManitobaWinnipegManitobaCanada
| | - Sabine Mai
- CancerCare Manitoba Research Institute, The Genomic Center for Cancer Research & DiagnosisUniversity of ManitobaWinnipegManitobaCanada
| | - Steve Horvath
- Human Genetics, David Geffen School of MedicineUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Taosheng Huang
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
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9
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Schmauck-Medina T, Molière A, Lautrup S, Zhang J, Chlopicki S, Madsen HB, Cao S, Soendenbroe C, Mansell E, Vestergaard MB, Li Z, Shiloh Y, Opresko PL, Egly JM, Kirkwood T, Verdin E, Bohr VA, Cox LS, Stevnsner T, Rasmussen LJ, Fang EF. New hallmarks of ageing: a 2022 Copenhagen ageing meeting summary. Aging (Albany NY) 2022; 14:6829-6839. [PMID: 36040386 PMCID: PMC9467401 DOI: 10.18632/aging.204248] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/14/2022] [Indexed: 01/02/2023]
Abstract
Genomic instability, telomere attrition, epigenetic alterations, mitochondrial dysfunction, loss of proteostasis, deregulated nutrient-sensing, cellular senescence, stem cell exhaustion, and altered intercellular communication were the original nine hallmarks of ageing proposed by López-Otín and colleagues in 2013. The proposal of these hallmarks of ageing has been instrumental in guiding and pushing forward research on the biology of ageing. In the nearly past 10 years, our in-depth exploration on ageing research has enabled us to formulate new hallmarks of ageing which are compromised autophagy, microbiome disturbance, altered mechanical properties, splicing dysregulation, and inflammation, among other emerging ones. Amalgamation of the 'old' and 'new' hallmarks of ageing may provide a more comprehensive explanation of ageing and age-related diseases, shedding light on interventional and therapeutic studies to achieve healthy, happy, and productive lives in the elderly.
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Affiliation(s)
- Tomas Schmauck-Medina
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog 1478, Norway
| | - Adrian Molière
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog 1478, Norway
| | - Sofie Lautrup
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog 1478, Norway
| | - Jianying Zhang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog 1478, Norway
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow 30-348, Poland
| | - Helena Borland Madsen
- Center for Healthy Ageing, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2400, Denmark
| | - Shuqin Cao
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog 1478, Norway
| | - Casper Soendenbroe
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen 2400, Denmark
| | - Els Mansell
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden.,Stem Cell Laboratory, UCL Cancer Institute, University College London, London, UK
| | - Mark Bitsch Vestergaard
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital Rigshospitalet, Glostrup 2600, Denmark
| | - Zhiquan Li
- Center for Healthy Ageing, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2400, Denmark
| | - Yosef Shiloh
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine P.O.B 39040, Tel Aviv, Israel
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA.,UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Jean-Marc Egly
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Equipe labellisée Ligue contre le Cancer, Strasbourg, France.,College of Medicine, Center for Genomics and Precision Medicine, National Taiwan University, Taipei City, Taiwan
| | - Thomas Kirkwood
- Center for Healthy Ageing, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2400, Denmark.,UK National Innovation Centre for Ageing, The Catalyst, 3 Science Square, Newcastle University, Newcastle upon Tyne, NE4 5TG, UK
| | - Eric Verdin
- Buck Institute for Research on Ageing, Novato, CA 94945, USA
| | - Vilhelm A Bohr
- Center for Healthy Ageing, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2400, Denmark.,Section on DNA Repair, National Institute on Ageing, Baltimore, MD 21224, USA
| | - Lynne S Cox
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tinna Stevnsner
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - Lene Juel Rasmussen
- Center for Healthy Ageing, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2400, Denmark
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog 1478, Norway.,The Norwegian Centre on Healthy Ageing (NO-Age), Oslo, Norway
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10
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Barnes RP, de Rosa M, Thosar SA, Detwiler AC, Roginskaya V, Van Houten B, Bruchez MP, Stewart-Ornstein J, Opresko PL. Telomeric 8-oxo-guanine drives rapid premature senescence in the absence of telomere shortening. Nat Struct Mol Biol 2022; 29:639-652. [PMID: 35773409 PMCID: PMC9287163 DOI: 10.1038/s41594-022-00790-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 05/16/2022] [Indexed: 01/10/2023]
Abstract
Oxidative stress is a primary cause of cellular senescence and contributes to the etiology of numerous human diseases. Oxidative damage to telomeric DNA has been proposed to cause premature senescence by accelerating telomere shortening. Here, we tested this model directly using a precision chemoptogenetic tool to produce the common lesion 8-oxo-guanine (8oxoG) exclusively at telomeres in human fibroblasts and epithelial cells. A single induction of telomeric 8oxoG is sufficient to trigger multiple hallmarks of p53-dependent senescence. Telomeric 8oxoG activates ATM and ATR signaling, and enriches for markers of telomere dysfunction in replicating, but not quiescent cells. Acute 8oxoG production fails to shorten telomeres, but rather generates fragile sites and mitotic DNA synthesis at telomeres, indicative of impaired replication. Based on our results, we propose that oxidative stress promotes rapid senescence by producing oxidative base lesions that drive replication-dependent telomere fragility and dysfunction in the absence of shortening and shelterin loss. This study uncovers a new mechanism linking oxidative stress to telomere-driven senescence. A common oxidative lesion at telomeres causes rapid premature cellular aging by inducing telomere fragility, rather than telomere shortening.
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Affiliation(s)
- Ryan P Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA.,UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Mariarosaria de Rosa
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA.,UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Sanjana A Thosar
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA.,UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ariana C Detwiler
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA.,UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Vera Roginskaya
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marcel P Bruchez
- Departments of Biological Sciences and Chemistry and the Molecular Biosensors and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jacob Stewart-Ornstein
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA. .,UPMC Hillman Cancer Center, Pittsburgh, PA, USA. .,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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11
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Paul T, Opresko PL, Ha T, Myong S. Vectorial folding of telomere overhang promotes higher accessibility. Nucleic Acids Res 2022; 50:6271-6283. [PMID: 35687089 PMCID: PMC9226509 DOI: 10.1093/nar/gkac401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/20/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Human telomere overhang composed of tandem repeats of TTAGGG folds into G-quadruplex (G4). Unlike in an experimental setting in the test tube in which the entire length is allowed to fold at once, inside the cell, the overhang is expected to fold as it is synthesized directionally (5' to 3') and released segmentally by a specialized enzyme, the telomerase. To mimic such vectorial G4 folding process, we employed a superhelicase, Rep-X which can unwind DNA to release the TTAGGG repeats in 5' to 3' direction. We demonstrate that the folded conformation achieved by the refolding of full sequence is significantly different from that of the vectorial folding for two to eight TTAGGG repeats. Strikingly, the vectorially folded state leads to a remarkably higher accessibility to complementary C-rich strand and the telomere binding protein POT1, reflecting a less stably folded state resulting from the vectorial folding. Importantly, our study points to an inherent difference between the co-polymerizing and post-polymerized folding of telomere overhang that can impact telomere architecture and downstream processes.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, PA15213, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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12
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Abstract
Mammalian telomeres are guanine-rich sequences which cap the ends of linear chromosomes. While recognized as sites sensitive to oxidative stress, studies on the consequences of oxidative damage to telomeres have been primarily limited to experimental conditions which cause oxidative damage throughout the whole genome and cell. We developed a chemoptogenetic tool (FAP-mCER-TRF1) to specifically induce singlet oxygen at telomeres, resulting in the formation of the common oxidative lesion 8-oxo-guanine. Here, we describe this tool and detail how to generate cell lines which express FAP-mCER-TRF1 at telomeres and verify the formation of 8-oxo-guanine.
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Affiliation(s)
- Ryan P Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Sanjana A Thosar
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Elise Fouquerel
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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13
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Kumar N, Theil AF, Roginskaya V, Ali Y, Calderon M, Watkins SC, Barnes RP, Opresko PL, Pines A, Lans H, Vermeulen W, Van Houten B. Global and transcription-coupled repair of 8-oxoG is initiated by nucleotide excision repair proteins. Nat Commun 2022; 13:974. [PMID: 35190564 PMCID: PMC8861037 DOI: 10.1038/s41467-022-28642-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 02/03/2022] [Indexed: 12/17/2022] Open
Abstract
UV-DDB, consisting of subunits DDB1 and DDB2, recognizes UV-induced photoproducts during global genome nucleotide excision repair (GG-NER). We recently demonstrated a noncanonical role of UV-DDB in stimulating base excision repair (BER) which raised several questions about the timing of UV-DDB arrival at 8-oxoguanine (8-oxoG), and the dependency of UV-DDB on the recruitment of downstream BER and NER proteins. Using two different approaches to introduce 8-oxoG in cells, we show that DDB2 is recruited to 8-oxoG immediately after damage and colocalizes with 8-oxoG glycosylase (OGG1) at sites of repair. 8-oxoG removal and OGG1 recruitment is significantly reduced in the absence of DDB2. NER proteins, XPA and XPC, also accumulate at 8-oxoG. While XPC recruitment is dependent on DDB2, XPA recruitment is DDB2-independent and transcription-coupled. Finally, DDB2 accumulation at 8-oxoG induces local chromatin unfolding. We propose that DDB2-mediated chromatin decompaction facilitates the recruitment of downstream BER proteins to 8-oxoG lesions. Nucleotide excision repair proteins are involved in the repair of UV-induced DNA damage. Here, the authors show that NER proteins, DDB2, XPC, and XPA play a vital role in the 8-oxoguanine repair by coordinating with base excision repair protein OGG1.
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14
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Kaur P, Barnes R, Pan H, Detwiler AC, Liu M, Mahn C, Hall J, Messenger Z, You C, Piehler J, Smart R, Riehn R, Opresko PL, Wang H. TIN2 is an architectural protein that facilitates TRF2-mediated trans- and cis-interactions on telomeric DNA. Nucleic Acids Res 2021; 49:13000-13018. [PMID: 34883513 PMCID: PMC8682769 DOI: 10.1093/nar/gkab1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/08/2021] [Indexed: 12/23/2022] Open
Abstract
The telomere specific shelterin complex, which includes TRF1, TRF2, RAP1, TIN2, TPP1 and POT1, prevents spurious recognition of telomeres as double-strand DNA breaks and regulates telomerase and DNA repair activities at telomeres. TIN2 is a key component of the shelterin complex that directly interacts with TRF1, TRF2 and TPP1. In vivo, the large majority of TRF1 and TRF2 are in complex with TIN2 but without TPP1 and POT1. Since knockdown of TIN2 also removes TRF1 and TRF2 from telomeres, previous cell-based assays only provide information on downstream effects after the loss of TRF1/TRF2 and TIN2. Here, we investigated DNA structures promoted by TRF2-TIN2 using single-molecule imaging platforms, including tracking of compaction of long mouse telomeric DNA using fluorescence imaging, atomic force microscopy (AFM) imaging of protein-DNA structures, and monitoring of DNA-DNA and DNA-RNA bridging using the DNA tightrope assay. These techniques enabled us to uncover previously unknown unique activities of TIN2. TIN2S and TIN2L isoforms facilitate TRF2-mediated telomeric DNA compaction (cis-interactions), dsDNA-dsDNA, dsDNA-ssDNA and dsDNA-ssRNA bridging (trans-interactions). Furthermore, TIN2 facilitates TRF2-mediated T-loop formation. We propose a molecular model in which TIN2 functions as an architectural protein to promote TRF2-mediated trans and cis higher-order nucleic acid structures at telomeres.
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Affiliation(s)
- Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Ryan Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh, UPMC Hillman Cancer Center, PA 15213, USA
| | - Hai Pan
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
| | - Ariana C Detwiler
- Department of Environmental and Occupational Health, University of Pittsburgh, UPMC Hillman Cancer Center, PA 15213, USA
| | - Ming Liu
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
| | - Chelsea Mahn
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
| | - Jonathan Hall
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC27695, USA
| | - Zach Messenger
- Toxicology Program, North Carolina State University, Raleigh, NC27695, USA
| | - Changjiang You
- Department of Biology/Chemistry, Universität Osnabrück, Osnabrück 49076, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry, Universität Osnabrück, Osnabrück 49076, Germany
| | - Robert C Smart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC27695, USA
| | - Robert Riehn
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, UPMC Hillman Cancer Center, PA 15213, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC27695, USA
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15
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De Rosa M, Johnson SA, Opresko PL. Roles for the 8-Oxoguanine DNA Repair System in Protecting Telomeres From Oxidative Stress. Front Cell Dev Biol 2021; 9:758402. [PMID: 34869348 PMCID: PMC8640134 DOI: 10.3389/fcell.2021.758402] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/27/2021] [Indexed: 11/27/2022] Open
Abstract
Telomeres are protective nucleoprotein structures that cap linear chromosome ends and safeguard genome stability. Progressive telomere shortening at each somatic cell division eventually leads to critically short and dysfunctional telomeres, which can contribute to either cellular senescence and aging, or tumorigenesis. Human reproductive cells, some stem cells, and most cancer cells, express the enzyme telomerase to restore telomeric DNA. Numerous studies have shown that oxidative stress caused by excess reactive oxygen species is associated with accelerated telomere shortening and dysfunction. Telomeric repeat sequences are remarkably susceptible to oxidative damage and are preferred sites for the production of the mutagenic base lesion 8-oxoguanine, which can alter telomere length homeostasis and integrity. Therefore, knowledge of the repair pathways involved in the processing of 8-oxoguanine at telomeres is important for advancing understanding of the pathogenesis of degenerative diseases and cancer associated with telomere instability. The highly conserved guanine oxidation (GO) system involves three specialized enzymes that initiate distinct pathways to specifically mitigate the adverse effects of 8-oxoguanine. Here we introduce the GO system and review the studies focused on investigating how telomeric 8-oxoguanine processing affects telomere integrity and overall genome stability. We also discuss newly developed technologies that target oxidative damage selectively to telomeres to investigate roles for the GO system in telomere stability.
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Affiliation(s)
- Mariarosaria De Rosa
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Samuel A Johnson
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
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16
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Paul T, Liou W, Cai X, Opresko PL, Myong S. TRF2 promotes dynamic and stepwise looping of POT1 bound telomeric overhang. Nucleic Acids Res 2021; 49:12377-12393. [PMID: 34850123 PMCID: PMC8643667 DOI: 10.1093/nar/gkab1123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/20/2021] [Accepted: 11/18/2021] [Indexed: 11/12/2022] Open
Abstract
Human telomeres are protected by shelterin proteins, but how telomeres maintain a dynamic structure remains elusive. Here, we report an unexpected activity of POT1 in imparting conformational dynamics of the telomere overhang, even at a monomer level. Strikingly, such POT1-induced overhang dynamics is greatly enhanced when TRF2 engages with the telomere duplex. Interestingly, TRF2, but not TRF2ΔB, recruits POT1-bound overhangs to the telomere ds/ss junction and induces a discrete stepwise movement up and down the axis of telomere duplex. The same steps are observed regardless of the length of the POT1-bound overhang, suggesting a tightly regulated conformational dynamic coordinated by TRF2 and POT1. TPP1 and TIN2 which physically connect POT1 and TRF2 act to generate a smooth movement along the axis of the telomere duplex. Our results suggest a plausible mechanism wherein telomeres maintain a dynamic structure orchestrated by shelterin.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Wilson Liou
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xinyi Cai
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, Hillman Cancer Center, 5117 Centre Avenue, Suite 2.6a, Pittsburgh, PA 15213, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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17
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Pan H, Kaur P, Barnes R, Detwiler AC, Sanford SL, Liu M, Xu P, Mahn C, Tang Q, Hao P, Bhattaram D, You C, Gu X, Lu W, Piehler J, Xu G, Weninger K, Riehn R, Opresko PL, Wang H. Structure, dynamics, and regulation of TRF1-TIN2-mediated trans- and cis-interactions on telomeric DNA. J Biol Chem 2021; 297:101080. [PMID: 34403696 PMCID: PMC8437784 DOI: 10.1016/j.jbc.2021.101080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/30/2021] [Accepted: 08/12/2021] [Indexed: 01/17/2023] Open
Abstract
TIN2 is a core component of the shelterin complex linking double-stranded telomeric DNA-binding proteins (TRF1 and TRF2) and single-strand overhang-binding proteins (TPP1-POT1). In vivo, the large majority of TRF1 and TRF2 exist in complexes containing TIN2 but lacking TPP1/POT1; however, the role of TRF1-TIN2 interactions in mediating interactions with telomeric DNA is unclear. Here, we investigated DNA molecular structures promoted by TRF1-TIN2 interaction using atomic force microscopy (AFM), total internal reflection fluorescence microscopy (TIRFM), and the DNA tightrope assay. We demonstrate that the short (TIN2S) and long (TIN2L) isoforms of TIN2 facilitate TRF1-mediated DNA compaction (cis-interactions) and DNA-DNA bridging (trans-interactions) in a telomeric sequence- and length-dependent manner. On the short telomeric DNA substrate (six TTAGGG repeats), the majority of TRF1-mediated telomeric DNA-DNA bridging events are transient with a lifetime of ~1.95 s. On longer DNA substrates (270 TTAGGG repeats), TIN2 forms multiprotein complexes with TRF1 and stabilizes TRF1-mediated DNA-DNA bridging events that last on the order of minutes. Preincubation of TRF1 with its regulator protein Tankyrase 1 and the cofactor NAD+ significantly reduced TRF1-TIN2 mediated DNA-DNA bridging, whereas TIN2 protected the disassembly of TRF1-TIN2 mediated DNA-DNA bridging upon Tankyrase 1 addition. Furthermore, we showed that TPP1 inhibits TRF1-TIN2L-mediated DNA-DNA bridging. Our study, together with previous findings, supports a molecular model in which protein assemblies at telomeres are heterogeneous with distinct subcomplexes and full shelterin complexes playing distinct roles in telomere protection and elongation.
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Affiliation(s)
- Hai Pan
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan Barnes
- Department of Environmental and Occupational Health, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ariana C Detwiler
- Department of Environmental and Occupational Health, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Samantha Lynn Sanford
- Department of Environmental and Occupational Health, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ming Liu
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Pengning Xu
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Chelsea Mahn
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Qingyu Tang
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Pengyu Hao
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Dhruv Bhattaram
- Department of Biomedical Engineering, Georgia Institute of Technology & Emory University of Medicine, Atlanta, Georgia, USA
| | - Changjiang You
- Department of Biology/Chemistry, Universität Osnabrück, Osnabrück, Germany
| | - Xinyun Gu
- College of Art and Sciences, New York University, New York City, New York, USA
| | - Warren Lu
- Department of Pathology at NYU Grossman School of Medicine, New York University, New York City, New York, USA
| | - Jacob Piehler
- Department of Biology/Chemistry, Universität Osnabrück, Osnabrück, Germany
| | - Guozhou Xu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Keith Weninger
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert Riehn
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Molecular Biophysics and Structural Biology Graduate Program, Carnegie Mellon University and the University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA; Toxicology Program, North Carolina State University, Raleigh, North Carolina, USA.
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18
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Zhu RY, Majumdar C, Khuu C, De Rosa M, Opresko PL, David SS, Kool ET. Designer Fluorescent Adenines Enable Real-Time Monitoring of MUTYH Activity. ACS Cent Sci 2020; 6:1735-1742. [PMID: 33145410 PMCID: PMC7596860 DOI: 10.1021/acscentsci.0c00369] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Indexed: 05/04/2023]
Abstract
The human DNA base excision repair enzyme MUTYH (MutY homolog DNA glycosylase) excises undamaged adenine that has been misincorporated opposite the oxidatively damaged 8-oxoG, preventing transversion mutations and serving as an important defense against the deleterious effects of this damage. Mutations in the MUTYH gene predispose patients to MUTYH-associated polyposis and colorectal cancer, and MUTYH expression has been documented as a biomarker for pancreatic cancer. Measuring MUTYH activity is therefore critical for evaluating and diagnosing disease states as well as for testing this enzyme as a potential therapeutic target. However, current methods for measuring MUTYH activity rely on indirect electrophoresis and radioactivity assays, which are difficult to implement in biological and clinical settings. Herein, we synthesize and identify novel fluorescent adenine derivatives that can act as direct substrates for excision by MUTYH as well as bacterial MutY. When incorporated into synthetic DNAs, the resulting fluorescently modified adenine-release turn-on (FMART) probes report on enzymatic base excision activity in real time, both in vitro and in mammalian cells and human blood. We also employ the probes to identify several promising small-molecule modulators of MUTYH by employing FMART probes for in vitro screening.
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Affiliation(s)
- Ru-Yi Zhu
- Department
of Chemistry, ChEM-H Institute, and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
| | - Chandrima Majumdar
- Department
of Chemistry, and Biochemistry, Molecular, Cellular and Developmental
Biology Graduate Group, University of California
at Davis, Davis, California 95616, United States
| | - Cindy Khuu
- Department
of Chemistry, and Biochemistry, Molecular, Cellular and Developmental
Biology Graduate Group, University of California
at Davis, Davis, California 95616, United States
| | - Mariarosaria De Rosa
- Department
of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, United States
- Hillman
Cancer Center, University of Pittsburgh
Medical Center, Pittsburgh, Pennsylvania 15261, United States
| | - Patricia L. Opresko
- Department
of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, United States
- Hillman
Cancer Center, University of Pittsburgh
Medical Center, Pittsburgh, Pennsylvania 15261, United States
| | - Sheila S. David
- Department
of Chemistry, and Biochemistry, Molecular, Cellular and Developmental
Biology Graduate Group, University of California
at Davis, Davis, California 95616, United States
| | - Eric T. Kool
- Department
of Chemistry, ChEM-H Institute, and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
- E-mail:
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19
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Abstract
Telomerase is a specialized reverse transcriptase that adds GGTTAG repeats to chromosome ends and is upregulated in most human cancers to enable limitless proliferation. Here, we uncover two distinct mechanisms by which naturally occurring oxidized dNTPs and therapeutic dNTPs inhibit telomerase-mediated telomere elongation. We conduct a series of direct telomerase extension assays in the presence of modified dNTPs on various telomeric substrates. We provide direct evidence that telomerase can add the nucleotide reverse transcriptase inhibitors ddITP and AZT-TP to the telomeric end, causing chain termination. In contrast, telomerase continues elongation after inserting oxidized 2-OH-dATP or therapeutic 6-thio-dGTP, but insertion disrupts translocation and inhibits further repeat addition. Kinetics reveal that telomerase poorly selects against 6-thio-dGTP, inserting with similar catalytic efficiency as dGTP. Furthermore, telomerase processivity factor POT1-TPP1 fails to restore processive elongation in the presence of inhibitory dNTPs. These findings reveal mechanisms for targeting telomerase with modified dNTPs in cancer therapy.
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Affiliation(s)
- Samantha L Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Griffin A Welfer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, USA.
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20
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Lee HT, Sanford S, Paul T, Choe J, Bose A, Opresko PL, Myong S. Position-Dependent Effect of Guanine Base Damage and Mutations on Telomeric G-Quadruplex and Telomerase Extension. Biochemistry 2020; 59:2627-2639. [PMID: 32578995 DOI: 10.1021/acs.biochem.0c00434] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Telomeres are hot spots for mutagenic oxidative and methylation base damage due to their high guanine content. We used single-molecule fluorescence resonance energy transfer detection and biochemical assays to determine how different positions and types of guanine damage and mutations alter telomeric G-quadruplex structure and telomerase activity. We compared 15 modifications, including 8-oxoguanine (8oxoG), O-6-methylguanine (O6mG), and all three possible point mutations (G to A, T, and C) at the 3' three terminal guanine positions of a telomeric G-quadruplex, which is the critical access point for telomerase. We found that G-quadruplex structural instability was induced in the order C < T < A ≤ 8oxoG < O6mG, with the perturbation caused by O6mG far exceeding the perturbation caused by other base alterations. For all base modifications, the central G position was the most destabilizing among the three terminal guanines. While the structural disruption by 8oxoG and O6mG led to concomitant increases in telomerase binding and extension activity, the structural perturbation by point mutations (A, T, and C) did not, due to disrupted annealing between the telomeric overhang and the telomerase RNA template. Repositioning the same mutations away from the terminal guanines caused both G-quadruplex structural instability and elevated telomerase activity. Our findings demonstrate how a single-base modification drives structural alterations and telomere lengthening in a position-dependent manner. Furthermore, our results suggest a long-term and inheritable effect of telomeric DNA damage that can lead to telomere lengthening, which potentially contributes to oncogenesis.
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Affiliation(s)
- Hui-Ting Lee
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Samantha Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania 15261, United States
| | - Tapas Paul
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joshua Choe
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania 15261, United States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania 15261, United States
| | - Sua Myong
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, United States
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21
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Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang TH, Opresko PL, Freudenthal BD. Mechanisms of nucleotide selection by telomerase. eLife 2020; 9:55438. [PMID: 32501800 PMCID: PMC7274783 DOI: 10.7554/elife.55438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/18/2020] [Indexed: 01/31/2023] Open
Abstract
Telomerase extends telomere sequences at chromosomal ends to protect genomic DNA. During this process it must select the correct nucleotide from a pool of nucleotides with various sugars and base pairing properties, which is critically important for the proper capping of telomeric sequences by shelterin. Unfortunately, how telomerase selects correct nucleotides is unknown. Here, we determined structures of Tribolium castaneum telomerase reverse transcriptase (TERT) throughout its catalytic cycle and mapped the active site residues responsible for nucleoside selection, metal coordination, triphosphate binding, and RNA template stabilization. We found that TERT inserts a mismatch or ribonucleotide ~1 in 10,000 and ~1 in 14,000 insertion events, respectively. At biological ribonucleotide concentrations, these rates translate to ~40 ribonucleotides inserted per 10 kilobases. Human telomerase assays determined a conserved tyrosine steric gate regulates ribonucleotide insertion into telomeres. Cumulatively, our work provides insight into how telomerase selects the proper nucleotide to maintain telomere integrity.
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Affiliation(s)
- Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Samantha L Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Griffin A Welfer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Samuel A Johnson
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Thu H Khoang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, United States
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22
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Xie W, Jiao B, Bai Q, Ilin VA, Sun M, Burton CE, Kolodieznyi D, Calderon MJ, Stolz DB, Opresko PL, St Croix CM, Watkins S, Van Houten B, Bruchez MP, Burton EA. Chemoptogenetic ablation of neuronal mitochondria in vivo with spatiotemporal precision and controllable severity. eLife 2020; 9:e51845. [PMID: 32180546 PMCID: PMC7077989 DOI: 10.7554/elife.51845] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial dysfunction is implicated in the pathogenesis of multiple neurological diseases, but elucidation of underlying mechanisms is limited experimentally by the inability to damage specific mitochondria in defined neuronal groups. We developed a precision chemoptogenetic approach to target neuronal mitochondria in the intact nervous system in vivo. MG2I, a chemical fluorogen, produces singlet oxygen when bound to the fluorogen-activating protein dL5** and exposed to far-red light. Transgenic zebrafish expressing dL5** within neuronal mitochondria showed dramatic MG2I- and light-dependent neurobehavioral deficits, caused by neuronal bioenergetic crisis and acute neuronal depolarization. These abnormalities resulted from loss of neuronal respiration, associated with mitochondrial fragmentation, swelling and elimination of cristae. Remaining cellular ultrastructure was preserved initially, but cellular pathology downstream of mitochondrial damage eventually culminated in neuronal death. Our work provides powerful new chemoptogenetic tools for investigating mitochondrial homeostasis and pathophysiology and shows a direct relationship between mitochondrial function, neuronal biogenetics and whole-animal behavior.
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Affiliation(s)
- Wenting Xie
- Department of Neurology, University of PittsburghPittsburghUnited States
- Pittsburgh Institute for Neurodegenerative Diseases, University of PittsburghPittsburghUnited States
- Tsinghua University Medical SchoolBeijingChina
| | - Binxuan Jiao
- Department of Neurology, University of PittsburghPittsburghUnited States
- Pittsburgh Institute for Neurodegenerative Diseases, University of PittsburghPittsburghUnited States
- Tsinghua University Medical SchoolBeijingChina
| | - Qing Bai
- Department of Neurology, University of PittsburghPittsburghUnited States
- Pittsburgh Institute for Neurodegenerative Diseases, University of PittsburghPittsburghUnited States
| | - Vladimir A Ilin
- Department of Neurology, University of PittsburghPittsburghUnited States
- Pittsburgh Institute for Neurodegenerative Diseases, University of PittsburghPittsburghUnited States
| | - Ming Sun
- Center for Biologic Imaging, University of PittsburghPittsburghUnited States
| | | | - Dmytro Kolodieznyi
- Departments of Biological Sciences and Chemistry, Carnegie Mellon UniversityPittsburghUnited States
| | - Michael J Calderon
- Center for Biologic Imaging, University of PittsburghPittsburghUnited States
- Department of Cell Biology, University of PittsburghPittsburghUnited States
| | - Donna B Stolz
- Center for Biologic Imaging, University of PittsburghPittsburghUnited States
- Department of Cell Biology, University of PittsburghPittsburghUnited States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of PittsburghPittsburghUnited States
- Genome Stability Program, UPMC Hillman Cancer CenterPittsburghUnited States
| | - Claudette M St Croix
- Center for Biologic Imaging, University of PittsburghPittsburghUnited States
- Department of Cell Biology, University of PittsburghPittsburghUnited States
| | - Simon Watkins
- Center for Biologic Imaging, University of PittsburghPittsburghUnited States
- Department of Cell Biology, University of PittsburghPittsburghUnited States
| | - Bennett Van Houten
- Genome Stability Program, UPMC Hillman Cancer CenterPittsburghUnited States
- Department of Pharmacology and Chemical Biology, University of PittsburghPittsburghUnited States
| | - Marcel P Bruchez
- Departments of Biological Sciences and Chemistry, Carnegie Mellon UniversityPittsburghUnited States
- Molecular Biosensors and Imaging Center, Carnegie Mellon UniversityPittsburghUnited States
| | - Edward A Burton
- Department of Neurology, University of PittsburghPittsburghUnited States
- Pittsburgh Institute for Neurodegenerative Diseases, University of PittsburghPittsburghUnited States
- Geriatric Research, Education and Clinical Center, Pittsburgh VA Healthcare SystemPittsburghUnited States
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23
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Lee HT, Paul T, Choe J, Sanford S, Opresko PL, Myong S. DNA Base Damage and Consequential Point Mutation Controls Telomere Conformation and Elaborates Telomerase Extension Activity. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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24
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Barnes RP, Fouquerel E, Opresko PL. The impact of oxidative DNA damage and stress on telomere homeostasis. Mech Ageing Dev 2019; 177:37-45. [PMID: 29604323 PMCID: PMC6162185 DOI: 10.1016/j.mad.2018.03.013] [Citation(s) in RCA: 252] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Telomeres are dynamic nucleoprotein-DNA structures that cap and protect linear chromosome ends. Because telomeres shorten progressively with each replication, they impose a functional limit on the number of times a cell can divide. Critically short telomeres trigger cellular senescence in normal cells, or genomic instability in pre-malignant cells, which contribute to numerous degenerative and aging-related diseases including cancer. Therefore, a detailed understanding of the mechanisms of telomere loss and preservation is important for human health. Numerous studies have shown that oxidative stress is associated with accelerated telomere shortening and dysfunction. Oxidative stress caused by inflammation, intrinsic cell factors or environmental exposures, contributes to the pathogenesis of many degenerative diseases and cancer. Here we review the studies demonstrating associations between oxidative stress and accelerated telomere attrition in human tissue, mice and cell culture, and discuss possible mechanisms and cellular pathways that protect telomeres from oxidative damage.
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25
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Robinson AR, Yousefzadeh MJ, Rozgaja TA, Wang J, Li X, Tilstra JS, Feldman CH, Gregg SQ, Johnson CH, Skoda EM, Frantz MC, Bell-Temin H, Pope-Varsalona H, Gurkar AU, Nasto LA, Robinson RAS, Fuhrmann-Stroissnigg H, Czerwinska J, McGowan SJ, Cantu-Medellin N, Harris JB, Maniar S, Ross MA, Trussoni CE, LaRusso NF, Cifuentes-Pagano E, Pagano PJ, Tudek B, Vo NV, Rigatti LH, Opresko PL, Stolz DB, Watkins SC, Burd CE, Croix CMS, Siuzdak G, Yates NA, Robbins PD, Wang Y, Wipf P, Kelley EE, Niedernhofer LJ. Spontaneous DNA damage to the nuclear genome promotes senescence, redox imbalance and aging. Redox Biol 2018; 17:259-273. [PMID: 29747066 PMCID: PMC6006678 DOI: 10.1016/j.redox.2018.04.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 11/20/2022] Open
Abstract
Accumulation of senescent cells over time contributes to aging and age-related diseases. However, what drives senescence in vivo is not clear. Here we used a genetic approach to determine if spontaneous nuclear DNA damage is sufficient to initiate senescence in mammals. Ercc1-/∆ mice with reduced expression of ERCC1-XPF endonuclease have impaired capacity to repair the nuclear genome. Ercc1-/∆ mice accumulated spontaneous, oxidative DNA damage more rapidly than wild-type (WT) mice. As a consequence, senescent cells accumulated more rapidly in Ercc1-/∆ mice compared to repair-competent animals. However, the levels of DNA damage and senescent cells in Ercc1-/∆ mice never exceeded that observed in old WT mice. Surprisingly, levels of reactive oxygen species (ROS) were increased in tissues of Ercc1-/∆ mice to an extent identical to naturally-aged WT mice. Increased enzymatic production of ROS and decreased antioxidants contributed to the elevation in oxidative stress in both Ercc1-/∆ and aged WT mice. Chronic treatment of Ercc1-/∆ mice with the mitochondrial-targeted radical scavenger XJB-5-131 attenuated oxidative DNA damage, senescence and age-related pathology. Our findings indicate that nuclear genotoxic stress arises, at least in part, due to mitochondrial-derived ROS, and this spontaneous DNA damage is sufficient to drive increased levels of ROS, cellular senescence, and the consequent age-related physiological decline.
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Affiliation(s)
- Andria R Robinson
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA; University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Matthew J Yousefzadeh
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tania A Rozgaja
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jin Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Xuesen Li
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeremy S Tilstra
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Chelsea H Feldman
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Siobhán Q Gregg
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | - Erin M Skoda
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Marie-Céline Frantz
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Harris Bell-Temin
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Hannah Pope-Varsalona
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Aditi U Gurkar
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Luigi A Nasto
- Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Paediatric Orthopaedics, G. Gaslini Children's Hospital, Genoa, Italy
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Heike Fuhrmann-Stroissnigg
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jolanta Czerwinska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Sara J McGowan
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Jamie B Harris
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Salony Maniar
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Mark A Ross
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Christy E Trussoni
- Division of Gastroenterology and Center for Cell Signaling in Gastroenterology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas F LaRusso
- Division of Gastroenterology and Center for Cell Signaling in Gastroenterology, Mayo Clinic, Rochester, MN 55905, USA
| | - Eugenia Cifuentes-Pagano
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Patrick J Pagano
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nam V Vo
- Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lora H Rigatti
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Patricia L Opresko
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Donna B Stolz
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Christin E Burd
- Department of Molecular Genetics, Cancer Biology and Genetics, The Ohio State University, Columbus OH 43210 USA
| | - Claudette M St Croix
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Gary Siuzdak
- The Scripps Research Institute California, La Jolla, CA 92037, USA
| | - Nathan A Yates
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Biomedical Mass Spectrometry Center, Schools of the Health Sciences University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Paul D Robbins
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Eric E Kelley
- Department of Physiology & Pharmacology, West Virginia University, Morgantown, WV 26506, USA.
| | - Laura J Niedernhofer
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA.
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26
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Zhou J, Chan J, Lambelé M, Yusufzai T, Stumpff J, Opresko PL, Thali M, Wallace SS. NEIL3 Repairs Telomere Damage during S Phase to Secure Chromosome Segregation at Mitosis. Cell Rep 2018; 20:2044-2056. [PMID: 28854357 DOI: 10.1016/j.celrep.2017.08.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/05/2017] [Accepted: 08/01/2017] [Indexed: 12/28/2022] Open
Abstract
Oxidative damage to telomere DNA compromises telomere integrity. We recently reported that the DNA glycosylase NEIL3 preferentially repairs oxidative lesions in telomere sequences in vitro. Here, we show that loss of NEIL3 causes anaphase DNA bridging because of telomere dysfunction. NEIL3 expression increases during S phase and reaches maximal levels in late S/G2. NEIL3 co-localizes with TRF2 and associates with telomeres during S phase, and this association increases upon oxidative stress. Mechanistic studies reveal that NEIL3 binds to single-stranded DNA via its intrinsically disordered C terminus in a telomere-sequence-independent manner. Moreover, NEIL3 is recruited to telomeres through its interaction with TRF1, and this interaction enhances the enzymatic activity of purified NEIL3. Finally, we show that NEIL3 interacts with AP Endonuclease 1 (APE1) and the long-patch base excision repair proteins PCNA and FEN1. Taken together, we propose that NEIL3 protects genome stability through targeted repair of oxidative damage in telomeres during S/G2 phase.
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Affiliation(s)
- Jia Zhou
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jany Chan
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Marie Lambelé
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, College of Medicine, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Markus Thali
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA.
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA.
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27
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Lee HT, Bose A, Lee CY, Opresko PL, Myong S. Molecular mechanisms by which oxidative DNA damage promotes telomerase activity. Nucleic Acids Res 2017; 45:11752-11765. [PMID: 28981887 PMCID: PMC5714237 DOI: 10.1093/nar/gkx789] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/14/2017] [Indexed: 11/13/2022] Open
Abstract
Telomeres are highly susceptible to oxidative DNA damage, which if left unrepaired can lead to dysregulation of telomere length homeostasis. Here we employed single molecule FRET, single molecule pull-down and biochemical analysis to investigate how the most common oxidative DNA lesions, 8-oxoguanine (8oxoG) and thymine glycol (Tg), regulate the structural properties of telomeric DNA and telomerase extension activity. In contrast to 8oxoG which disrupts the telomeric DNA structure, Tg exhibits substantially reduced perturbation of G-quadruplex folding. As a result, 8oxoG induces high accessibility, whereas Tg retains limited accessibility, of telomeric G-quadruplex DNA to complementary single stranded DNA and to telomere binding protein POT1. Surprisingly, the Tg lesion stimulates telomerase loading and activity to a similar degree as an 8oxoG lesion. We demonstrate that this unexpected stimulation arises from Tg-induced conformational alterations and dynamics in telomeric DNA. Despite impacting structure by different mechanisms, both 8oxoG and Tg enhance telomerase binding and extension activity to the same degree, potentially contributing to oncogenesis.
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Affiliation(s)
- Hui-Ting Lee
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA 15261, USA
| | - Chun-Ying Lee
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA 15261, USA
| | - Sua Myong
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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28
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Garcia-Exposito L, Bournique E, Bergoglio V, Bose A, Barroso-Gonzalez J, Zhang S, Roncaioli JL, Lee M, Wallace CT, Watkins SC, Opresko PL, Hoffmann JS, O'Sullivan RJ. Proteomic Profiling Reveals a Specific Role for Translesion DNA Polymerase η in the Alternative Lengthening of Telomeres. Cell Rep 2017; 17:1858-1871. [PMID: 27829156 PMCID: PMC5406014 DOI: 10.1016/j.celrep.2016.10.048] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/18/2016] [Accepted: 10/14/2016] [Indexed: 11/22/2022] Open
Abstract
Cancer cells rely on the activation of telomerase or the alternative lengthening of telomeres (ALT) pathways for telomere maintenance and survival. ALT involves homologous recombination (HR)-dependent exchange and/or HR-associated synthesis of telomeric DNA. Utilizing proximity-dependent biotinylation (BioID), we sought to determine the proteome of telomeres in cancer cells that employ these distinct telomere elongation mechanisms. Our analysis reveals that multiple DNA repair networks converge at ALT telomeres. These include the specialized translesion DNA synthesis (TLS) proteins FANCJ-RAD18-PCNA and, most notably, DNA polymerase eta (Polη). We observe that the depletion of Polη leads to increased ALT activity and late DNA polymerase δ (Polδ)-dependent synthesis of telomeric DNA in mitosis. We propose that Polη fulfills an important role in managing replicative stress at ALT telomeres, maintaining telomere recombination at tolerable levels and stimulating DNA synthesis by Polδ.
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Affiliation(s)
- Laura Garcia-Exposito
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Elodie Bournique
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jonathan Barroso-Gonzalez
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Justin L Roncaioli
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Callen T Wallace
- Department of Cell Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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29
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Jenkins FJ, Kerr CM, Fouquerel E, Bovbjerg DH, Opresko PL. Modified Terminal Restriction Fragment Analysis for Quantifying Telomere Length Using In-gel Hybridization. J Vis Exp 2017. [PMID: 28715381 DOI: 10.3791/56001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There are several different techniques for measuring telomere length, each with their own advantages and disadvantages. The traditional approach, Telomere Restriction Fragment (TRF) analysis, utilizes a DNA hybridization technique whereby genomic DNA samples are digested with restriction enzymes, leaving behind telomere DNA repeats and some sub-telomeric DNA. These are separated by agarose gel electrophoresis, transferred to a filter membrane and hybridized to oligonucleotide probes tagged with either chemiluminescence or radioactivity to visualize telomere restriction fragments. This approach, while requiring a larger quantity of DNA than other techniques such as PCR, can measure the telomere length distribution of a population of cells and allows measurement expressed in absolute kilobases. This manuscript demonstrates a modified DNA hybridization procedure for determining telomere length. Genomic DNA is first digested with restriction enzymes (that do not cut telomeres) and separated by agarose gel electrophoresis. The gel is then dried and the DNA is denatured and hybridized in situ to a radiolabeled oligonucleotide probe. This in situ hybridization avoids loss of telomere DNA and improves signal intensity. Following hybridization, the gels are imaged utilizing phosphor screens and the telomere length is quantified using a graphing program. This procedure was developed by the laboratories of Drs. Woodring Wright and Jerry Shay at the University of Texas Southwestern1,2. Here, we present a detailed description of this procedure, with some modifications.
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Affiliation(s)
- Frank J Jenkins
- Departments of Pathology and Infectious Diseases and Microbiology, University of Pittsburgh; University of Pittsburgh Cancer Institute;
| | | | - Elise Fouquerel
- University of Pittsburgh Cancer Institute; Department of Environmental and Occupational Health, University of Pittsburgh
| | - Dana H Bovbjerg
- University of Pittsburgh Cancer Institute; Departments of Psychiatry, Psychology, Behavioral & Community Health Sciences, University of Pittsburgh
| | - Patricia L Opresko
- University of Pittsburgh Cancer Institute; Department of Environmental and Occupational Health, University of Pittsburgh
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30
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Fouquerel E, Opresko PL. Convergence of The Nobel Fields of Telomere Biology and DNA Repair. Photochem Photobiol 2017; 93:229-237. [PMID: 27861975 DOI: 10.1111/php.12672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/26/2016] [Indexed: 02/02/2023]
Abstract
The fields of telomere biology and DNA repair have enjoyed a great deal of cross-fertilization and convergence in recent years. Telomeres function at chromosome ends to prevent them from being falsely recognized as chromosome breaks by the DNA damage response and repair machineries. Conversely, both canonical and nonconical functions of numerous DNA repair proteins have been found to be critical for preserving telomere structure and function. In 2009, Elizabeth Blackburn, Carol Greider and Jack Szostak were awarded the Nobel prize in Physiology or Medicine for the discovery of telomeres and telomerase. Four years later, pioneers in the field of DNA repair, Aziz Sancar, Tomas Lindahl and Paul Modrich were recognized for their seminal contributions by being awarded the Nobel Prize in Chemistry. This review is part of a special issue meant to celebrate this amazing achievement, and will focus in particular on the convergence of nucleotide excision repair and telomere biology, and will discuss the profound implications for human health.
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Affiliation(s)
- Elise Fouquerel
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh Cancer Institute Research Pavilion, University of Pittsburgh, Pittsburgh, PA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh Cancer Institute Research Pavilion, University of Pittsburgh, Pittsburgh, PA
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31
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Fouquerel E, Lormand J, Bose A, Lee HT, Kim GS, Li J, Sobol RW, Freudenthal BD, Myong S, Opresko PL. Oxidative guanine base damage regulates human telomerase activity. Nat Struct Mol Biol 2016; 23:1092-1100. [PMID: 27820808 PMCID: PMC5140714 DOI: 10.1038/nsmb.3319] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/11/2016] [Indexed: 12/19/2022]
Abstract
Changes in telomere length are associated with degenerative diseases and cancer. Oxidative stress and DNA damage have been linked to both positive and negative alterations in telomere length and integrity. Here we examined how the common oxidative lesion 8-oxo-7,8-dihydro-2′-deoxyguanine (8-oxoG) regulates telomere elongation by telomerase. When present in the deoxynucleoside triphosphate pool as 8-oxodGTP, telomerase utilization of the oxidized nucleotide during telomere extension is mutagenic and terminates further elongation. Depletion of the enzyme that removes oxidized dNTPs, MTH1, increases telomere dysfunction and cell death in telomerase positive cancer cells harboring shortened telomeres. In contrast, a pre-existing 8-oxoG within the telomeric DNA sequence promotes telomerase activity by destabilizing G-quadruplex structure in the DNA. We show that the mechanism by which 8-oxoG arises in the telomere, either by insertion of oxidized nucleotides or by direct reaction with free radicals, dictates whether telomerase is inhibited or stimulated and thereby, mediates the biological outcome.
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Affiliation(s)
- Elise Fouquerel
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Justin Lormand
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Hui-Ting Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Grace S Kim
- Department of Bioengineering, University of Illinois, Urbana, IL, USA
| | - Jianfeng Li
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Robert W Sobol
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.,Department of Bioengineering, University of Illinois, Urbana, IL, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.,Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, USA
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32
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Lin J, Countryman P, Chen H, Pan H, Fan Y, Jiang Y, Kaur P, Miao W, Gurgel G, You C, Piehler J, Kad NM, Riehn R, Opresko PL, Smith S, Tao YJ, Wang H. Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA-DNA pairing. Nucleic Acids Res 2016; 44:6363-76. [PMID: 27298259 PMCID: PMC5291270 DOI: 10.1093/nar/gkw518] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/30/2016] [Indexed: 12/23/2022] Open
Abstract
Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids. Cohesion is thought to occur through the entrapment of DNA within the tripartite ring (Smc1, Smc3 and Rad21) with enforcement from a fourth subunit (SA1/SA2). Surprisingly, cohesin rings do not play a major role in sister telomere cohesion. Instead, this role is replaced by SA1 and telomere binding proteins (TRF1 and TIN2). Neither the DNA binding property of SA1 nor this unique telomere cohesion mechanism is understood. Here, using single-molecule fluorescence imaging, we discover that SA1 displays two-state binding on DNA: searching by one-dimensional (1D) free diffusion versus recognition through subdiffusive sliding at telomeric regions. The AT-hook motif in SA1 plays dual roles in modulating non-specific DNA binding and subdiffusive dynamics over telomeric regions. TRF1 tethers SA1 within telomeric regions that SA1 transiently interacts with. SA1 and TRF1 together form longer DNA–DNA pairing tracts than with TRF1 alone, as revealed by atomic force microscopy imaging. These results suggest that at telomeres cohesion relies on the molecular interplay between TRF1 and SA1 to promote DNA–DNA pairing, while along chromosomal arms the core cohesin assembly might also depend on SA1 1D diffusion on DNA and sequence-specific DNA binding.
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Affiliation(s)
- Jiangguo Lin
- School of Bioscience and Engineering, South China University of Technology, Guangzhou, Guangdong 510006, P.R. China Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Preston Countryman
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Haijiang Chen
- Department of BioSciences, Rice University, Houston, TX 77005, USA Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Hai Pan
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Yanlin Fan
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Yunyun Jiang
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Wang Miao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
| | - Gisele Gurgel
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Changjiang You
- Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Robert Riehn
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, PA 15213, USA
| | - Susan Smith
- Kimmel Center for Biology and Medicine at the Skirball Institute, Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
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33
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Kaur P, Wu D, Lin J, Countryman P, Bradford KC, Erie DA, Riehn R, Opresko PL, Wang H. Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2. Sci Rep 2016; 6:20513. [PMID: 26856421 PMCID: PMC4746636 DOI: 10.1038/srep20513] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 01/04/2016] [Indexed: 12/19/2022] Open
Abstract
Shelterin protein TRF2 modulates telomere structures by promoting dsDNA compaction and T-loop formation. Advancement of our understanding of the mechanism underlying TRF2-mediated DNA compaction requires additional information regarding DNA paths in TRF2-DNA complexes. To uncover the location of DNA inside protein-DNA complexes, we recently developed the Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy (DREEM) imaging technique. DREEM imaging shows that in contrast to chromatin with DNA wrapping around histones, large TRF2-DNA complexes (with volumes larger than TRF2 tetramers) compact DNA inside TRF2 with portions of folded DNA appearing at the edge of these complexes. Supporting coarse-grained molecular dynamics simulations uncover the structural requirement and sequential steps during TRF2-mediated DNA compaction and result in folded DNA structures with protruding DNA loops as seen in DREEM imaging. Revealing DNA paths in TRF2 complexes provides new mechanistic insights into structure-function relationships underlying telomere maintenance pathways.
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Affiliation(s)
- Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Dong Wu
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Jiangguo Lin
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,School of Bioscience and Engineering, South China University of Technology, Guangzhou, Guangdong 510006, P.R. China
| | - Preston Countryman
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Kira C Bradford
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599.,Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599
| | - Robert Riehn
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15219, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
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Parikh D, Fouquerel E, Murphy CT, Wang H, Opresko PL. Telomeres are partly shielded from ultraviolet-induced damage and proficient for nucleotide excision repair of photoproducts. Nat Commun 2015; 6:8214. [PMID: 26351258 PMCID: PMC4566151 DOI: 10.1038/ncomms9214] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/29/2015] [Indexed: 12/12/2022] Open
Abstract
Ultraviolet light induces cyclobutane pyrimidine dimers (CPD) and pyrimidine(6–4)pyrimidone photoproducts, which interfere with DNA replication and transcription. Nucleotide excision repair (NER) removes these photoproducts, but whether NER functions at telomeres is unresolved. Here we use immunospot blotting to examine the efficiency of photoproduct formation and removal at telomeres purified from UVC irradiated cells at various recovery times. Telomeres exhibit approximately twofold fewer photoproducts compared with the bulk genome in cells, and telomere-binding protein TRF1 significantly reduces photoproduct formation in telomeric fragments in vitro. CPD removal from telomeres occurs 1.5-fold faster than the bulk genome, and is completed by 48 h. 6–4PP removal is rapidly completed by 6 h in both telomeres and the overall genome. A requirement for XPA protein indicates the mechanism of telomeric photoproduct removal is NER. These data provide new evidence that telomeres are partially protected from ultraviolet irradiation and that NER preserves telomere integrity. DNA damage caused by ultraviolet irradiation is removed from the genome by nucleotide excision repair; however, it is unclear if this occurs at chromosome ends. Here the authors provide evidence indicating that telomeres are partially shielded from damage and that repair is fully functional.
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Affiliation(s)
- Dhvani Parikh
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Elise Fouquerel
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.,University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213, USA
| | - Connor T Murphy
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.,Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Hong Wang
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.,University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213, USA.,Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.,Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
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Abstract
Telomeres at chromosome ends are normally masked from proteins that signal and repair DNA double strand breaks (DSBs). Bulky DNA lesions can cause DSBs if they block DNA replication, unless they are bypassed by translesion (TLS) DNA polymerases. Here, we investigated roles for TLS polymerase η, (polη) in preserving telomeres following acute physical UVC exposure and chronic chemical Cr(VI) exposure, which both induce blocking lesions. We report that polη protects against cytotoxicity and replication stress caused by Cr(VI), similar to results with ultraviolet C light (UVC). Both exposures induce ataxia telangiectasia and Rad3-related (ATR) kinase and polη accumulation into nuclear foci and localization to individual telomeres, consistent with replication fork stalling at DNA lesions. Polη-deficient cells exhibited greater numbers of telomeres that co-localized with DSB response proteins after exposures. Furthermore, the genotoxic exposures induced telomere aberrations associated with failures in telomere replication that were suppressed by polη. We propose that polη's ability to bypass bulky DNA lesions at telomeres is critical for proper telomere replication following genotoxic exposures.
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Affiliation(s)
- Hannah Pope-Varsalona
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Fu-Jun Liu
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Lynda Guzik
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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36
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Pham HH, Murphy CT, Sureshkumar G, Ly DH, Opresko PL, Armitage BA. Cooperative hybridization of γPNA miniprobes to a repeating sequence motif and application to telomere analysis. Org Biomol Chem 2014; 12:7345-7354. [PMID: 25115693 PMCID: PMC4162129 DOI: 10.1039/c4ob00953c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
GammaPNA oligomers having one or two repeats of the sequence AATCCC were designed to hybridize to DNA having one or more repeats of the complementary TTAGGG sequence found in the human telomere. UV melting curves and surface plasmon resonance experiments demonstrate high affinity and cooperativity for hybridization of these miniprobes to DNA having multiple complementary repeats. Fluorescence spectroscopy for Cy3-labeled miniprobes demonstrate increases in fluorescence intensity for assembling multiple short probes on a DNA target compared with fewer longer probes. The fluorescent γPNA miniprobes were then used to stain telomeres in metaphase chromosomes derived from U2OS cells possessing heterogeneous long telomeres and Jurkat cells harboring homogenous short telomeres. The miniprobes yielded comparable fluorescence intensity to a commercially available PNA 18mer probe in U2OS cells, but significantly brighter fluorescence was observed for telomeres in Jurkat cells. These results suggest that γPNA miniprobes can be effective telomere-staining reagents with applications toward analysis of critically short telomeres, which have been implicated in a range of human diseases.
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Affiliation(s)
- Ha H. Pham
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Connor T. Murphy
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Environmental and Occupational Health, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15219
| | - Gopalsamy Sureshkumar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Danith H. Ly
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Patricia L. Opresko
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Environmental and Occupational Health, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15219
| | - Bruce A. Armitage
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
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37
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Murphy CT, Gupta A, Armitage BA, Opresko PL. Hybridization of G-quadruplex-forming peptide nucleic acids to guanine-rich DNA templates inhibits DNA polymerase η extension. Biochemistry 2014; 53:5315-22. [PMID: 25068499 DOI: 10.1021/bi5006859] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The guanine quadruplex (G-quadruplex) is a highly stable secondary structure that forms in G-rich repeats of DNA, which can interfere with DNA processes, including DNA replication and transcription. We showed previously that short guanine-rich peptide nucleic acids (PNAs) can form highly stable hybrid quadruplexes with DNA. We hypothesized that such structures would provide a stronger block to polymerase extension on G-rich templates than a native DNA homoquadruplex because of the greater thermodynamic stability of the PNA-DNA hybrid structures. To test this, we analyzed the DNA primer extension activity of polymerase η, a translesion polymerase implicated in synthesis past G-quadruplex blocks, on DNA templates containing guanine repeats. We observed a PNA concentration-dependent decrease in the level of polymerase η extension to the end of the template and an increase in the level of polymerase η inhibition at the sequence prior to the G-rich repeats. In contrast, the addition of a complementary C-rich PNA that hybridizes to the G-rich repeats by Watson-Crick base pairing led to a decrease in the level of polymerase inhibition and an increase in the level of full-length extension products. The G-quadruplex-forming PNA exhibited inhibition (IC50=16.2±3.3 nM) of polymerase η DNA synthesis on the G-rich templates stronger than that of the established G-quadruplex-stabilizing ligand BRACO-19 (IC50=42.5±4.8 nM). Our results indicate that homologous PNA targeting of G-rich sequences creates stable PNA-DNA heteroquadruplexes that inhibit polymerase η extension more effectively than a DNA homoquadruplex. The implications of these results for the potential development of homologous PNAs as therapeutics for halting proliferating cancer cells are discussed.
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Affiliation(s)
- Connor T Murphy
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health , Pittsburgh, Pennsylvania 15219, United States
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38
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Hwang H, Kreig A, Calvert J, Lormand J, Kwon Y, Daley JM, Sung P, Opresko PL, Myong S. Telomeric overhang length determines structural dynamics and accessibility to telomerase and ALT-associated proteins. Structure 2014; 22:842-53. [PMID: 24836024 DOI: 10.1016/j.str.2014.03.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/07/2014] [Accepted: 03/04/2014] [Indexed: 02/03/2023]
Abstract
The G-rich single-stranded DNA at the 3' end of human telomeres can self-fold into G-quaduplex (GQ). However, telomere lengthening by telomerase or the recombination-based alternative lengthening of telomere (ALT) mechanism requires protein loading on the overhang. Using single-molecule fluorescence spectroscopy, we discovered that lengthening the telomeric overhang also increased the rate of dynamic exchanges between structural conformations. Overhangs with five to seven TTAGGG repeats, compared with four repeats, showed much greater dynamics and accessibility to telomerase binding and activity and loading of the ALT-associated proteins RAD51, WRN, and BLM. Although the eight repeats are highly dynamic, they can fold into two GQs, which limited protein accessibility. In contrast, the telomere-specific protein POT1 is unique in that it binds independently of repeat number. Our results suggest that the telomeric overhang length and dynamics may contribute to the regulation of telomere extension via telomerase action and the ALT mechanism.
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Affiliation(s)
- Helen Hwang
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA; Medical Scholars Program, University of Illinois, 506 South Matthews Avenue, Urbana, IL 61801, USA
| | - Alex Kreig
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA
| | - Jacob Calvert
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA
| | - Justin Lormand
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Drive, Suite 326, BRIDG, Pittsburgh, PA 15219, USA
| | - Yongho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - James M Daley
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Drive, Suite 326, BRIDG, Pittsburgh, PA 15219, USA
| | - Sua Myong
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois, 1206 West Gregory Street, Urbana, IL 61801, USA; Physics Frontier Center (Center of Physics for Living Cells), University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA.
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39
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Abstract
RecQ helicases are an important family of genome surveillance proteins conserved from bacteria to humans. Each of the five human RecQ helicases plays critical roles in genome maintenance and stability, and the RecQ protein family members are often referred to as guardians of the genome. The importance of these proteins in cellular homeostasis is underscored by the fact that defects in BLM, WRN, and RECQL4 are linked to distinct heritable human disease syndromes. Each human RecQ helicase has a unique set of protein-interacting partners, and these interactions dictate its specialized functions in genome maintenance, including DNA repair, recombination, replication, and transcription. Human RecQ helicases also interact with each other, and these interactions have significant impact on enzyme function. Future research goals in this field include a better understanding of the division of labor among the human RecQ helicases and learning how human RecQ helicases collaborate and cooperate to enhance genome stability.
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Affiliation(s)
- Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, Maryland 21224;
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40
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Lin J, Kaur P, Countryman P, Opresko PL, Wang H. Unraveling secrets of telomeres: one molecule at a time. DNA Repair (Amst) 2014; 20:142-153. [PMID: 24569170 DOI: 10.1016/j.dnarep.2014.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 01/03/2014] [Accepted: 01/13/2014] [Indexed: 01/23/2023]
Abstract
Telomeres play important roles in maintaining the stability of linear chromosomes. Telomere maintenance involves dynamic actions of multiple proteins interacting with long repetitive sequences and complex dynamic DNA structures, such as G-quadruplexes, T-loops and t-circles. Given the heterogeneity and complexity of telomeres, single-molecule approaches are essential to fully understand the structure-function relationships that govern telomere maintenance. In this review, we present a brief overview of the principles of single-molecule imaging and manipulation techniques. We then highlight results obtained from applying these single-molecule techniques for studying structure, dynamics and functions of G-quadruplexes, telomerase, and shelterin proteins.
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Affiliation(s)
- Jiangguo Lin
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Preston Countryman
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA.
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41
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Lin J, Countryman P, Buncher N, Kaur P, E L, Zhang Y, Gibson G, You C, Watkins SC, Piehler J, Opresko PL, Kad NM, Wang H. TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres. Nucleic Acids Res 2013; 42:2493-504. [PMID: 24271387 PMCID: PMC3936710 DOI: 10.1093/nar/gkt1132] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Human telomeres are maintained by the shelterin protein complex in which TRF1 and TRF2 bind directly to duplex telomeric DNA. How these proteins find telomeric sequences among a genome of billions of base pairs and how they find protein partners to form the shelterin complex remains uncertain. Using single-molecule fluorescence imaging of quantum dot-labeled TRF1 and TRF2, we study how these proteins locate TTAGGG repeats on DNA tightropes. By virtue of its basic domain TRF2 performs an extensive 1D search on nontelomeric DNA, whereas TRF1’s 1D search is limited. Unlike the stable and static associations observed for other proteins at specific binding sites, TRF proteins possess reduced binding stability marked by transient binding (∼9–17 s) and slow 1D diffusion on specific telomeric regions. These slow diffusion constants yield activation energy barriers to sliding ∼2.8–3.6 κBT greater than those for nontelomeric DNA. We propose that the TRF proteins use 1D sliding to find protein partners and assemble the shelterin complex, which in turn stabilizes the interaction with specific telomeric DNA. This ‘tag-team proofreading’ represents a more general mechanism to ensure a specific set of proteins interact with each other on long repetitive specific DNA sequences without requiring external energy sources.
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Affiliation(s)
- Jiangguo Lin
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA, Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA, Electric and Computer Engineering Department, University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Department of Industrial and System Engineering, North Carolina State University, Raleigh, NC 27695, USA, Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA, Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076, Osnabrück, Germany and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ UK
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42
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Lormand JD, Buncher N, Murphy CT, Kaur P, Lee MY, Burgers P, Wang H, Kunkel TA, Opresko PL. DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation. Nucleic Acids Res 2013; 41:10323-33. [PMID: 24038470 PMCID: PMC3905856 DOI: 10.1093/nar/gkt813] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Previous evidence indicates that telomeres resemble common fragile sites and present a challenge for DNA replication. The precise impediments to replication fork progression at telomeric TTAGGG repeats are unknown, but are proposed to include G-quadruplexes (G4) on the G-rich strand. Here we examined DNA synthesis and progression by the replicative DNA polymerase δ/proliferating cell nuclear antigen/replication factor C complex on telomeric templates that mimic the leading C-rich and lagging G-rich strands. Increased polymerase stalling occurred on the G-rich template, compared with the C-rich and nontelomeric templates. Suppression of G4 formation by substituting Li+ for K+ as the cation, or by using templates with 7-deaza-G residues, did not alleviate Pol δ pause sites within the G residues. Furthermore, we provide evidence that G4 folding is less stable on single-stranded circular TTAGGG templates where ends are constrained, compared with linear oligonucleotides. Artificially stabilizing G4 structures on the circular templates with the G4 ligand BRACO-19 inhibited Pol δ progression into the G-rich repeats. Similar results were obtained for yeast and human Pol δ complexes. Our data indicate that G4 formation is not required for polymerase stalling on telomeric lagging strands and suggest that an alternative mechanism, in addition to stable G4s, contributes to replication stalling at telomeres.
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Affiliation(s)
- Justin D Lormand
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, 100 Technology Drive, Pittsburgh, PA 15219, USA, Department of Physics, North Carolina State University, 2401 Stinson Drive, Raleigh, NC, 27695, USA, Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA, Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA and Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
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43
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Hwang H, Buncher N, Opresko PL, Myong S. POT1-TPP1 regulates telomeric overhang structural dynamics. Structure 2012; 20:1872-80. [PMID: 22981946 DOI: 10.1016/j.str.2012.08.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 02/05/2023]
Abstract
Human telomeres possess a single-stranded DNA (ssDNA) overhang of TTAGGG repeats, which can self-fold into a G-quadruplex structure. POT1 binds specifically to the telomeric overhang and partners with TPP1 to regulate telomere lengthening and capping, although the mechanism remains elusive. Here, we show that POT1 binds stably to folded telomeric G-quadruplex DNA in a sequential manner, one oligonucleotide/oligosaccharide binding fold at a time. POT1 binds from 3' to 5', thereby unfolding the G-quadruplex in a stepwise manner. In contrast, the POT1-TPP1 complex induces a continuous folding and unfolding of the G-quadruplex. We demonstrate that POT1-TPP1 slides back and forth on telomeric DNA and also on a mutant telomeric DNA to which POT1 cannot bind alone. The sliding motion is specific to POT1-TPP1, as POT1 and ssDNA binding protein gp32 cannot recapitulate this activity. Our results reveal fundamental molecular steps and dynamics involved in telomere structure regulation.
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Affiliation(s)
- Helen Hwang
- Bioengineering Department, University of Illinois, Urbana, IL 61801, USA
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Damerla RR, Knickelbein KE, Strutt S, Liu FJ, Wang H, Opresko PL. Werner syndrome protein suppresses the formation of large deletions during the replication of human telomeric sequences. Cell Cycle 2012; 11:3036-44. [PMID: 22871734 DOI: 10.4161/cc.21399] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Werner syndrome (WS) is a disorder characterized by features of premature aging and increased cancer that is caused by loss of the RecQ helicase WRN. Telomeres consisting of duplex TTAGGG repeats in humans protect chromosome ends and sustain cellular proliferation. WRN prevents the loss of telomeres replicated from the G-rich strand, which can form secondary G-quadruplex (G4) structures. Here, we dissected WRN roles in the replication of telomeric sequences by examining factors inherent to telomeric repeats, such as G4 DNA, independently from other factors at chromosome ends that can also impede replication. For this we used the supF shuttle vector (SV) mutagenesis assay. We demonstrate that SVs with [TTAGGG]6 sequences are stably replicated in human cells, and that the repeats suppress the frequency of large deletions despite G4 folding potential. WRN depletion increased the supF mutant frequency for both the telomeric and non-telomeric SVs, compared with the control cells, but this increase was much greater (27-fold) for telomeric SVs. The higher SV mutant frequencies in WRN-deficient cells were primarily due to an increase in large sequence deletions and rearrangements. However, WRN depletion caused a more dramatic increase in deletions and rearrangements arising within the telomeric SV (70-fold), compared with non-telomeric SV (8-fold). Our results indicate that WRN prevents large deletions and rearrangements during replication, and that this role is particularly important in templates with telomeric sequence. This provides a possible explanation for increased telomere loss in WS cells.
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Affiliation(s)
- Rama Rao Damerla
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
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Miller AS, Balakrishnan L, Buncher NA, Opresko PL, Bambara RA. Telomere proteins POT1, TRF1 and TRF2 augment long-patch base excision repair in vitro. Cell Cycle 2012; 11:998-1007. [PMID: 22336916 PMCID: PMC3323798 DOI: 10.4161/cc.11.5.19483] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 01/24/2012] [Accepted: 01/25/2012] [Indexed: 12/13/2022] Open
Abstract
Human telomeres consist of multiple tandem hexameric repeats, each containing a guanine triplet. Guanosine-rich clusters are highly susceptible to oxidative base damage, necessitating base excision repair (BER). Previous demonstration of enhanced strand displacement synthesis by the BER component DNA polymerase β in the presence of telomere protein TRF2 suggests that telomeres employ long-patch (LP) BER. Earlier analyses in vitro showed that efficiency of BER reactions is reduced in the DNA-histone environment of chromatin. Evidence presented here indicates that BER is promoted at telomeres. We found that the three proteins that contact telomere DNA, POT1, TRF1 and TRF2, enhance the rate of individual steps of LP-BER and stimulate the complete reconstituted LP-BER pathway. Thought to protect telomere DNA from degradation, these proteins still apparently evolved to allow selective access of repair proteins.
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Affiliation(s)
- Adam S Miller
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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Choi S, Wang W, Ribeiro AJS, Kalinowski A, Gregg SQ, Opresko PL, Niedernhofer LJ, Rohde GK, Dahl KN. Computational image analysis of nuclear morphology associated with various nuclear-specific aging disorders. Nucleus 2011; 2:570-9. [PMID: 22127259 DOI: 10.4161/nucl.2.6.17798] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Computational image analysis is used in many areas of biological and medical research, but advanced techniques including machine learning remain underutilized. Here, we used automated segmentation and shape analyses, with pre-defined features and with computer generated components, to compare nuclei from various premature aging disorders caused by alterations in nuclear proteins. We considered cells from patients with Hutchinson-Gilford progeria syndrome (HGPS) with an altered nucleoskeletal protein; a mouse model of XFE progeroid syndrome caused by a deficiency of ERCC1-XPF DNA repair nuclease; and patients with Werner syndrome (WS) lacking a functional WRN exonuclease and helicase protein. Using feature space analysis, including circularity, eccentricity, and solidity, we found that XFE nuclei were larger and significantly more elongated than control nuclei. HGPS nuclei were smaller and rounder than the control nuclei with features suggesting small bumps. WS nuclei did not show any significant shape changes from control. We also performed principle component analysis (PCA) and a geometric, contour based metric. PCA allowed direct visualization of morphological changes in diseased nuclei, whereas standard, feature-based approaches required pre-defined parameters and indirect interpretation of multiple parameters. Both methods yielded similar results, but PCA proves to be a powerful pre-analysis methodology for unknown systems.
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Affiliation(s)
- Siwon Choi
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
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Sanders JL, Iannaccone A, Boudreau RM, Conley YP, Opresko PL, Hsueh WC, Cummings SR, Cawthon RM, Harris TB, Nalls MA, Kritchevsky SB, Newman AB. The association of cataract with leukocyte telomere length in older adults: defining a new marker of aging. J Gerontol A Biol Sci Med Sci 2011; 66:639-45. [PMID: 21382885 DOI: 10.1093/gerona/glr034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lens transparency, or the magnitude of cataract severity, is a potential in vivo marker of aging distinguishable from diagnosed cataract. To explore lens transparency as a marker of aging, we determined its association with leukocyte telomere length (LTL) measured with quantitative polymerase chain reaction. Cataract severity was directly measured in 259 participants, and prevalent cataract and incident cataract surgery were ascertained in 2,750 participants of the Health, Aging, and Body Composition Study. LTL was unassociated with clinical cataract outcomes. Six of 259 had successfully aged lenses and a mean LTL of 5,700 bp, whereas 253/259 with poorly aged lenses had a mean LTL of 4,770 bp. Participants with a 1,000 bp greater mean LTL had nearly half the odds of any cataract (odds ratio = 0.47, 95% confidence interval 0.22-1.02) after adjustment. Lens transparency might be associated with longer LTL in community-dwelling older adults and should be investigated further as a possible biomarker of aging.
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Affiliation(s)
- Jason L Sanders
- Medical Scientist Training Program, School of Medicine, University of Pittsburgh, Pennsylvania, USA.
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Wang H, Nora GJ, Ghodke H, Opresko PL. Single molecule studies of physiologically relevant telomeric tails reveal POT1 mechanism for promoting G-quadruplex unfolding. J Biol Chem 2010; 286:7479-89. [PMID: 21183684 DOI: 10.1074/jbc.m110.205641] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human telomeres are composed of duplex TTAGGG repeats and a 3' single-stranded DNA tail. The telomeric DNA is protected and regulated by the shelterin proteins, including the protection of telomeres 1 (POT1) protein that binds telomeric single-stranded DNA. The single-stranded tail can fold into G-quadruplex (G4) DNA. Both POT1 and G4 DNA play important roles in regulating telomere length homeostasis. To date, most studies have focused on individual quadruplexes formed by four TTAGGG repeats. Telomeric tails in human cells have on average six times as many repeats, and no structural studies have examined POT1 binding in competition with G4 DNA folding. Using single molecule atomic force microscopy imaging, we observed that the majority of the telomeric tails of 16 repeats formed two quadruplexes even though four were possible. The result that physiological telomeric tails rarely form the maximum potential number of G4 units provides a structural basis for the coexistence of G4 and POT1 on the same DNA molecule, which is observed directly in the captured atomic force microscopy images. We further observed that POT1 is significantly more effective in disrupting quadruplex DNA on long telomeric tails than an antisense oligonucleotide, indicating a novel POT1 activity beyond simply preventing quadruplex folding.
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Affiliation(s)
- Hong Wang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA.
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Abstract
Werner syndrome
is an inherited human progeriod syndrome caused by mutations in the gene
encoding the Werner Syndrome protein, WRN. It has both 3'-5' DNA
helicase and exonuclease activities, and is
suggested to have roles in many aspects of DNA metabolism, including DNA
repair and telomere maintenance. The DNA-PK complex also functions in both
DNA double strand break repair and telomere maintenance. Interaction
between WRN and the DNA-PK complex has been reported in DNA double strand
break repair, but their possible cooperation at telomeres has not been
reported. This study analyzes thein vitro and in vivo
interaction at the telomere between WRN and DNA-PKcs, the catalytic subunit
of DNA-PK. The results show that DNA-PKcs selectively stimulates WRN
helicase but not WRN exonuclease in vitro, affecting that WRN
helicase unwinds and promotes the release of the full-length invading strand
of a telomere D-loop model substrate. In addition, the length of telomeric
G-tails decreases in DNA-PKcs knockdown cells, and this phenotype is
reversed by overexpression of WRN helicase. These results suggest that WRN
and DNA-PKcs may cooperatively prevent G-tail shortening in vivo.
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Affiliation(s)
- Rika Kusumoto-Matsuo
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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Nora GJ, Buncher NA, Opresko PL. Telomeric protein TRF2 protects Holliday junctions with telomeric arms from displacement by the Werner syndrome helicase. Nucleic Acids Res 2010; 38:3984-98. [PMID: 20215438 PMCID: PMC2896529 DOI: 10.1093/nar/gkq144] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
WRN protein loss causes Werner syndrome (WS), which is characterized by premature aging as well as genomic and telomeric instability. WRN prevents telomere loss, but the telomeric protein complex must regulate WRN activities to prevent aberrant telomere processing. Telomere-binding TRF2 protein inhibits telomere t-loop deletion by blocking Holliday junction (HJ) resolvase cleavage activity, but whether TRF2 also modulates HJ displacement at t-loops is unknown. In this study, we used multiplex fluorophore imaging to track the fate of individual strands of HJ substrates. We report the novel finding that TRF2 inhibits WRN helicase strand displacement of HJs with telomeric repeats in duplex arms, but unwinding of HJs with a telomeric center or lacking telomeric sequence is unaffected. These data, together with results using TRF2 fragments and TRF2 HJ binding assays, indicate that both the TRF2 B- and Myb domains are required to inhibit WRN HJ activity. We propose a novel model whereby simultaneous binding of the TRF2 B-domain to the HJ core and the Myb domain to telomeric arms promote and stabilize HJs in a stacked arm conformation that is unfavorable for unwinding. Our biochemical study provides a mechanistic basis for the cellular findings that TRF2 regulates WRN activity at telomeres.
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Affiliation(s)
- Gerald J Nora
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
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