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Wondisford AR, Lee J, Lu R, Schuller M, Groslambert J, Bhargava R, Schamus-Haynes S, Cespedes LC, Opresko PL, Pickett HA, Min J, Ahel I, O'Sullivan RJ. Deregulated DNA ADP-ribosylation impairs telomere replication. Nat Struct Mol Biol 2024; 31:791-800. [PMID: 38714889 PMCID: PMC11102865 DOI: 10.1038/s41594-024-01279-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/18/2024] [Indexed: 05/21/2024]
Abstract
The recognition that DNA can be ADP ribosylated provides an unexpected regulatory level of how ADP-ribosylation contributes to genome stability, epigenetics and immunity. Yet, it remains unknown whether DNA ADP-ribosylation (DNA-ADPr) promotes genome stability and how it is regulated. Here, we show that telomeres are subject to DNA-ADPr catalyzed by PARP1 and removed by TARG1. Mechanistically, we show that DNA-ADPr is coupled to lagging telomere DNA strand synthesis, forming at single-stranded DNA present at unligated Okazaki fragments and on the 3' single-stranded telomere overhang. Persistent DNA-linked ADPr, due to TARG1 deficiency, eventually leads to telomere shortening. Furthermore, using the bacterial DNA ADP-ribosyl-transferase toxin to modify DNA at telomeres directly, we demonstrate that unhydrolyzed DNA-linked ADP-ribose compromises telomere replication and telomere integrity. Thus, by identifying telomeres as chromosomal targets of PARP1 and TARG1-regulated DNA-ADPr, whose deregulation compromises telomere replication and integrity, our study highlights and establishes the critical importance of controlling DNA-ADPr turnover for sustained genome stability.
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Affiliation(s)
- Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junyeop Lee
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sandra Schamus-Haynes
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leyneir C Cespedes
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Patricia L Opresko
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Jaewon Min
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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2
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van Ipenburg JA, van den Bosch QCC, Paridaens D, Dubbink HJ, Kiliç E, Naus N, Verdijk RM. ATRX Loss in the Development and Prognosis of Conjunctival Melanoma. Int J Mol Sci 2023; 24:12988. [PMID: 37629169 PMCID: PMC10454703 DOI: 10.3390/ijms241612988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Metastatic disease is linked to TERT promoter mutations in conjunctival melanomas (CM). Both TERT promoter and ATRX mutations are associated with faulty telomere maintenance. This study aimed to determine the prognostic value of ATRX loss in conjunctival melanocytic lesions. Eighty-six conjunctival melanocytic lesions from the Rotterdam Ocular Melanoma Study group were collected. ATRX status and TERT promoter status were determined using immunohistochemical staining and molecular diagnostics, respectively. None of the nevi (n = 16) and primary acquired melanosis (PAM) without atypia (n = 6) showed ATRX loss. ATRX loss was found in 2/5 PAM with atypia without CM and in 8/59 CM. No cases with a TERT promoter mutation (n = 26) showed ATRX loss. Eight/eleven metastatic CM harbored a TERT promoter mutation, two other metastatic CM showed ATRX loss and one metastatic case showed no TERT promoter/ATRX alterations. In conclusion ATRX loss and TERT promoter mutations are only found in (pre)malignant conjunctival melanocytic lesions, with most metastatic cases harboring one of these alterations, suggesting that both alterations are associated with adverse behavior. Similar to TERT promoter mutations, ATRX loss may be used as a diagnostic tool in determining whether a conjunctival melanocytic lesion is prone to having an adverse course.
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Affiliation(s)
- Jolique A. van Ipenburg
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Quincy C. C. van den Bosch
- Department of Ophthalmology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
- Department of Ocular Oncology, The Rotterdam Eye Hospital, Schiedamse Vest 180, 3011 BH Rotterdam, The Netherlands
| | - Hendrikus J. Dubbink
- Department of Pathology, Section Ophthalmic Pathology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Nicole Naus
- Department of Ophthalmology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Robert M. Verdijk
- Department of Ocular Oncology, The Rotterdam Eye Hospital, Schiedamse Vest 180, 3011 BH Rotterdam, The Netherlands
- Department of Pathology, Section Ophthalmic Pathology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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3
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Gutierrez-Bayona NE, Scruggs SS, Yang HC, Chai M, Gross ML, Taylor JS. Post- and Pre-Radiolabeling Assays for anti Thymidine Cyclobutane Dimers as Intrinsic Photoprobes of Various Types of G-Quadruplexes, Reverse Hoogsteen Hairpins, and Other Non-B DNA Structures. Biochemistry 2023; 62:2269-2279. [PMID: 37459251 PMCID: PMC10474795 DOI: 10.1021/acs.biochem.3c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
G-quadruplexes are thought to play an important role in gene regulation and telomere maintenance, but developing probes for their presence and location is challenging due to their transitory and highly dynamic nature. The majority of probes for G-quadruplexes have relied on antibody or small-molecule binding agents, many of which can also alter the dynamics and relative populations of G-quadruplexes. Recently, it was discovered that ultraviolet B (UVB) irradiation of human telomeric DNA and various G-quadruplex forming sequences found in human promoters, as well as reverse Hoogsteen hairpins, produces a unique class of non-adjacent anti cyclobutane pyrimidine dimers (CPDs). Therefore, one can envision using a pulse of UVB light to irreversibly trap these non-B DNA structures via anti CPD formation without perturbing their dynamics, after which the anti CPDs can be identified and mapped. As a first step toward this goal, we report radioactive post- and pre-labeling assays for the detection of non-adjacent CPDs and illustrate their use in detecting trans,anti T=(T) CPD formation in a human telomeric DNA sequence. Both assays make use of snake venom phosphodiesterase (SVP) to degrade the trans,anti T=(T) CPD-containing DNA to the tetranucleotide pTT=(pTT) corresponding to CPD formation between the underlined T's of two separate dinucleotides while degrading the adjacent syn TT CPDs to the trinucleotide pGT=T. In the post-labeling assay, calf intestinal phosphodiesterase is used to dephosphorylate the tetranucleotides, which are then rephosphorylated with kinase and [32P]-ATP to produce radiolabeled mono- and diphosphorylated tetranucleotides. The tetranucleotides are confirmed to be non-adjacent CPDs by 254 nm photoreversion to the dinucleotide p*TT. In the pre-labeling assay, radiolabeled phosphates are introduced into non-adjacent CPD-forming sites by ligation prior to irradiation, thereby eliminating the dephosphorylation and rephosphorylation steps. The assays are also demonstrated to detect the stereoisomeric cis,anti T=(T) CPD.
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Affiliation(s)
| | - Savannah S Scruggs
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
| | - Hsin-Chieh Yang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
| | - Mengqi Chai
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
| | - John-Stephen Taylor
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
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4
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Nassar R, Thompson L, Fouquerel E. Molecular mechanisms protecting centromeres from self-sabotage and implications for cancer therapy. NAR Cancer 2023; 5:zcad019. [PMID: 37180029 PMCID: PMC10167631 DOI: 10.1093/narcan/zcad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/27/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Centromeres play a crucial role in DNA segregation by mediating the cohesion and separation of sister chromatids during cell division. Centromere dysfunction, breakage or compromised centromeric integrity can generate aneuploidies and chromosomal instability, which are cellular features associated with cancer initiation and progression. Maintaining centromere integrity is thus essential for genome stability. However, the centromere itself is prone to DNA breaks, likely due to its intrinsically fragile nature. Centromeres are complex genomic loci that are composed of highly repetitive DNA sequences and secondary structures and require the recruitment and homeostasis of a centromere-associated protein network. The molecular mechanisms engaged to preserve centromere inherent structure and respond to centromeric damage are not fully understood and remain a subject of ongoing research. In this article, we provide a review of the currently known factors that contribute to centromeric dysfunction and the molecular mechanisms that mitigate the impact of centromere damage on genome stability. Finally, we discuss the potential therapeutic strategies that could arise from a deeper understanding of the mechanisms preserving centromere integrity.
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Affiliation(s)
- Rim Nassar
- UPMC Hillman Cancer Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
| | - Lily Thompson
- UPMC Hillman Cancer Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
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5
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Guintini L, Paillé A, Graf M, Luke B, Wellinger RJ, Conconi A. Transcription of ncRNAs promotes repair of UV induced DNA lesions in Saccharomyces cerevisiae subtelomeres. PLoS Genet 2022; 18:e1010167. [PMID: 35486666 PMCID: PMC9106180 DOI: 10.1371/journal.pgen.1010167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 05/13/2022] [Accepted: 03/25/2022] [Indexed: 11/19/2022] Open
Abstract
Ultraviolet light causes DNA lesions that are removed by nucleotide excision repair (NER). The efficiency of NER is conditional to transcription and chromatin structure. UV induced photoproducts are repaired faster in the gene transcribed strands than in the non-transcribed strands or in transcriptionally inactive regions of the genome. This specificity of NER is known as transcription-coupled repair (TCR). The discovery of pervasive non-coding RNA transcription (ncRNA) advocates for ubiquitous contribution of TCR to the repair of UV photoproducts, beyond the repair of active gene-transcribed strands. Chromatin rules transcription, and telomeres form a complex structure of proteins that silences nearby engineered ectopic genes. The essential protective function of telomeres also includes preventing unwanted repair of double-strand breaks. Thus, telomeres were thought to be transcriptionally inert, but more recently, ncRNA transcription was found to initiate in subtelomeric regions. On the other hand, induced DNA lesions like the UV photoproducts must be recognized and repaired also at the ends of chromosomes. In this study, repair of UV induced DNA lesions was analyzed in the subtelomeric regions of budding yeast. The T4-endonuclease V nicking-activity at cyclobutene pyrimidine dimer (CPD) sites was exploited to monitor CPD formation and repair. The presence of two photoproducts, CPDs and pyrimidine (6,4)-pyrimidones (6-4PPs), was verified by the effective and precise blockage of Taq DNA polymerase at these sites. The results indicate that UV photoproducts in silenced heterochromatin are slowly repaired, but that ncRNA transcription enhances NER throughout one subtelomeric element, called Y’, and in distinct short segments of the second, more conserved element, called X. Therefore, ncRNA-transcription dependent TCR assists global genome repair to remove CPDs and 6-4PPs from subtelomeric DNA. Our skin is constantly exposed to sunlight and the ultraviolet component of it can severely damage the DNA of our chromosomes. If that damage is not efficiently repaired, the cells’ physiology becomes deregulated and very often cancer ensues. The specific molecular mechanism that will remove this damage is called nucleotide excision repair or NER. NER is conserved from humans to yeast, and it is much more efficient on DNA that is transcribed into RNA. Here we report how NER acts at the very ends of the chromosomes, the telomeres. In particular, the results show that in this area of the chromosomes with very few genes and where transcription is kept very low, the remaining transcription of non-coding RNAs such as TERRAs still stimulates NER and therefore helps guarding the integrity of DNA. These findings therefore suggest that the spurious transcription of subtelomeric DNA has a very positive impact on DNA repair efficiency. Hence, in addition to the known functions of TERRA and other ncRNAs in telomere maintenance, their transcription per se can be viewed as a genome stabilizing function.
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Affiliation(s)
- Laetitia Guintini
- Department of Microbiology and Infectious Diseases at the Université de Sherbrooke, Sherbrooke, Canada
| | - Audrey Paillé
- Department of Microbiology and Infectious Diseases at the Université de Sherbrooke, Sherbrooke, Canada
| | - Marco Graf
- Institute for Developmental and Neurobiology (IDN) at the Johannes-Gutenberg-University, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases at the Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (RJW); (AC)
| | - Antonio Conconi
- Department of Microbiology and Infectious Diseases at the Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (RJW); (AC)
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6
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Wong KM, King DA, Schwartz EK, Herrera RE, Morrison AJ. Retinoblastoma protein regulates carcinogen susceptibility at heterochromatic cancer driver loci. Life Sci Alliance 2022; 5:e202101134. [PMID: 34983823 PMCID: PMC8739494 DOI: 10.26508/lsa.202101134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
Carcinogenic insult, such as UV light exposure, creates DNA lesions that evolve into mutations if left unrepaired. These resulting mutations can contribute to carcinogenesis and drive malignant phenotypes. Susceptibility to carcinogens (i.e., the propensity to form a carcinogen-induced DNA lesion) is regulated by both genetic and epigenetic factors. Importantly, carcinogen susceptibility is a critical contributor to cancer mutagenesis. It is known that mutations can be prevented by tumor suppressor regulation of DNA damage response pathways; however, their roles carcinogen susceptibility have not yet been reported. In this study, we reveal that the retinoblastoma (RB1) tumor suppressor regulates UV susceptibility across broad regions of the genome. In particular, centromere and telomere-proximal regions exhibit significant increases in UV lesion susceptibility when RB1 is deleted. Several cancer-related genes are located within genomic regions of increased susceptibility, including telomerase reverse transcriptase, TERT, thereby accelerating mutagenic potential in cancers with RB1 pathway alterations. These findings reveal novel genome stability mechanisms of a tumor suppressor and uncover new pathways to accumulate mutations during cancer evolution.
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Affiliation(s)
- Ka Man Wong
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Devin A King
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Erin K Schwartz
- Department of Biology, Stanford University, Stanford, CA, USA
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7
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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: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [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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8
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Stefos GC, Szantai E, Konstantopoulos D, Samiotaki M, Fousteri M. aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin. Nucleic Acids Res 2021; 49:e64. [PMID: 33693861 DOI: 10.1093/nar/gkab144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Specific capture of chromatin fractions with distinct and well-defined features has emerged as both challenging and a key strategy towards a comprehensive understanding of genome biology. In this context, we developed aniFOUND (accelerated native isolation of factors on unscheduled nascent DNA), an antibody-free method, which can label, capture, map and characterise nascent chromatin fragments that are synthesized in response to specific cues outside S-phase. We used the 'unscheduled' DNA synthesis (UDS) that takes place during the repair of UV-induced DNA lesions and coupled the captured chromatin to high-throughput analytical technologies. By mass-spectrometry we identified several factors with no previously known role in UVC-DNA damage response (DDR) as well as known DDR proteins. We experimentally validated the repair-dependent recruitment of the chromatin remodeller RSF1 and the cohesin-loader NIPBL at sites of UVC-induced photolesions. Developing aniFOUND-seq, a protocol for mapping UDS activity with high resolution, allowed us to monitor the landscape of UVC repair-synthesis events genome wide. We further resolved repair efficacy of the rather unexplored repeated genome, in particular rDNA and telomeres. In summary, aniFOUND delineates the proteome composition and genomic landscape of chromatin loci with specific features by integrating state-of-the-art 'omics' technologies to promote a comprehensive view of their function.
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Affiliation(s)
- Georgios C Stefos
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
| | - Eszter Szantai
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
| | | | | | - Maria Fousteri
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
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9
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Kychygina A, Dall'Osto M, Allen JAM, Cadoret JC, Piras V, Pickett HA, Crabbe L. Progerin impairs 3D genome organization and induces fragile telomeres by limiting the dNTP pools. Sci Rep 2021; 11:13195. [PMID: 34162976 PMCID: PMC8222272 DOI: 10.1038/s41598-021-92631-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/11/2021] [Indexed: 11/09/2022] Open
Abstract
Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity. A key player in this spatial scattering of chromosomes is the nuclear envelope (NE). The NE tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins. This organization is perturbed in cells from Hutchinson–Gilford progeria syndrome (HGPS), a genetic disorder characterized by premature aging features. Here, we show that HGPS-related lamina defects trigger an altered 3D telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state. The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late. As a consequence, we detected a higher density of replication forks traveling simultaneously on DNA fibers, which relies on limiting cellular dNTP pools to support processive DNA synthesis. Remarkably, increasing dNTP levels in HGPS cells rescued fragile telomeres, and improved the replicative capacity of the cells. Our work highlights a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.
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Affiliation(s)
- Anna Kychygina
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.,INSERM UMR1291, CNRS UMR5051, UT3, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), 31059, Toulouse, France
| | - Marina Dall'Osto
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | - Vincent Piras
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.
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10
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The Power of Stress: The Telo-Hormesis Hypothesis. Cells 2021; 10:cells10051156. [PMID: 34064566 PMCID: PMC8151059 DOI: 10.3390/cells10051156] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Adaptative response to stress is a strategy conserved across evolution to promote survival. In this context, the groundbreaking findings of Miroslav Radman on the adaptative value of changing mutation rates opened new avenues in our understanding of stress response. Inspired by this work, we explore here the putative beneficial effects of changing the ends of eukaryotic chromosomes, the telomeres, in response to stress. We first summarize basic principles in telomere biology and then describe how various types of stress can alter telomere structure and functions. Finally, we discuss the hypothesis of stress-induced telomere signaling with hormetic effects.
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11
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Tomasova K, Kroupa M, Forsti A, Vodicka P, Vodickova L. Telomere maintenance in interplay with DNA repair in pathogenesis and treatment of colorectal cancer. Mutagenesis 2021; 35:261-271. [PMID: 32083302 DOI: 10.1093/mutage/geaa005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/29/2020] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) continues to be one of the leading malignancies and causes of tumour-related deaths worldwide. Both impaired DNA repair mechanisms and disrupted telomere length homeostasis represent key culprits in CRC initiation, progression and prognosis. Mechanistically, altered DNA repair results in the accumulation of mutations in the genome and, ultimately, in genomic instability. DNA repair also determines the response to chemotherapeutics in CRC treatment, suggesting its utilisation in the prediction of therapy response and individual approach to patients. Telomere attrition resulting in replicative senescence, simultaneously by-passing cell cycle checkpoints, is a hallmark of malignant transformation of the cell. Telomerase is almost ubiquitous in advanced solid cancers, including CRC, and its expression is fundamental to cell immortalisation. Therefore, there is a persistent effort to develop therapeutics, which are telomerase-specific and gentle to non-malignant tissues. However, in practice, we are still at the level of clinical trials. The current state of knowledge and the route, which the research takes, gives us a positive perspective that the problem of molecular models of telomerase activation and telomere length stabilisation will finally be solved. We summarise the current literature herein, by pointing out the crosstalk between proteins involved in DNA repair and telomere length homeostasis in relation to CRC.
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Affiliation(s)
- Kristyna Tomasova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Vídeňská, Praha, Czech Republic.,Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Alej Svobody, Plzeň, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Vídeňská, Praha, Czech Republic.,Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Alej Svobody, Plzeň, Czech Republic
| | - Asta Forsti
- Hopp Children's Cancer Center (KiTZ), Im Neuenheimer Feld, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld, Heidelberg, Germany
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Vídeňská, Praha, Czech Republic.,Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Alej Svobody, Plzeň, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov, Praha, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Vídeňská, Praha, Czech Republic.,Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Alej Svobody, Plzeň, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov, Praha, Czech Republic
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12
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Abstract
Telomere repeats at chromosomal ends are essential for genome stability and sustained cellular proliferation but are susceptible to DNA damage. Repair of damage at telomeres is influenced by numerous factors including telomeric binding proteins, sequence and structure. Ultraviolet (UV) light irradiation induces DNA photoproducts at telomeres that can interfere with telomere maintenance. Here we describe a highly sensitive method for quantifying the formation and removal of UV photoproducts in telomeres isolated from UV irradiated cultured human cells. Damage is detected by immunospot blotting of telomeres with highly specific antibodies against UV photoproducts. This method is adaptable for measuring other types of DNA damage at telomeres as well.
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13
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Victorelli S, Passos JF. Telomeres: beacons of autocrine and paracrine DNA damage during skin aging. Cell Cycle 2020; 19:532-540. [PMID: 32065062 DOI: 10.1080/15384101.2020.1728016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cellular senescence is an irreversible cell cycle arrest, which can be triggered by a number of stressors, including telomere damage. Among many other phenotypic changes, senescence is accompanied by increased secretion of pro-inflammatory molecules, also known as the senescence-associated secretory phenotype (SASP). It is thought that accumulation of senescent cells contributes to age-associated tissue dysfunction partly by inducing senescence in neighboring cells through mechanisms involving SASP factors. Here, we will review evidence suggesting that telomeres can become dysfunctional irrespectively of shortening, and that this may be a mechanism-driving senescence in post-mitotic or slow dividing cells. Furthermore, we review recent evidence that supports that senescent melanocytes induce paracrine telomere damage during skin aging, which may be the mechanism responsible for propagation of senescent cells. We propose that telomeres are sensors of imbalances in the cellular milieu and act as beacons of stress, contributing to autocrine and paracrine senescence.
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Affiliation(s)
- Stella Victorelli
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, USA
| | - João F Passos
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, USA.,Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
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14
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Sobecki M, Souaid C, Boulay J, Guerineau V, Noordermeer D, Crabbe L. MadID, a Versatile Approach to Map Protein-DNA Interactions, Highlights Telomere-Nuclear Envelope Contact Sites in Human Cells. Cell Rep 2019; 25:2891-2903.e5. [PMID: 30517874 PMCID: PMC6293860 DOI: 10.1016/j.celrep.2018.11.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/26/2018] [Accepted: 11/04/2018] [Indexed: 11/19/2022] Open
Abstract
Mapping the binding sites of DNA- or chromatin-interacting proteins is essential to understanding biological processes. DNA adenine methyltransferase identification (DamID) has emerged as a comprehensive method to map genome-wide occupancy of proteins of interest. A caveat of DamID is the specificity of Dam methyltransferase for GATC motifs that are not homogenously distributed in the genome. Here, we developed an optimized method named MadID, using proximity labeling of DNA by the methyltransferase M.EcoGII. M.EcoGII mediates N6-adenosine methylation in any DNA sequence context, resulting in deeper and unbiased coverage of the genome. We demonstrate, using m6A-specific immunoprecipitation and deep sequencing, that MadID is a robust method to identify protein-DNA interactions at the whole-genome level. Using MadID, we revealed contact sites between human telomeres, repetitive sequences devoid of GATC sites, and the nuclear envelope. Overall, MadID opens the way to identification of binding sites in genomic regions that were largely inaccessible. MadID: mapping of protein-DNA interactions in vivo using proximity labeling Deeper and unbiased genome-wide coverage using M.EcoGII, a methyltransferase Identification of binding sites in previously inaccessible regions of the genome Identification of telomere-nuclear envelope contact sites
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Affiliation(s)
- Michal Sobecki
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Charbel Souaid
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Jocelyne Boulay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Vincent Guerineau
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Laure Crabbe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France; LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 31062 Toulouse Cedex, France.
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15
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Abstract
Reactive oxygen species (ROS) play important roles in aging, inflammation, and cancer. Mitochondria are an important source of ROS; however, the spatiotemporal ROS events underlying oxidative cellular damage from dysfunctional mitochondria remain unresolved. To this end, we have developed and validated a chemoptogenetic approach that uses a mitochondrially targeted fluorogen-activating peptide (Mito-FAP) to deliver a photosensitizer MG-2I dye exclusively to this organelle. Light-mediated activation (660 nm) of the Mito-FAP-MG-2I complex led to a rapid loss of mitochondrial respiration, decreased electron transport chain complex activity, and mitochondrial fragmentation. Importantly, one round of singlet oxygen produced a persistent secondary wave of mitochondrial superoxide and hydrogen peroxide lasting for over 48 h after the initial insult. By following ROS intermediates, we were able to detect hydrogen peroxide in the nucleus through ratiometric analysis of the oxidation of nuclear cysteine residues. Despite mitochondrial DNA (mtDNA) damage and nuclear oxidative stress induced by dysfunctional mitochondria, there was a lack of gross nuclear DNA strand breaks and apoptosis. Targeted telomere analysis revealed fragile telomeres and telomere loss as well as 53BP1-positive telomere dysfunction-induced foci (TIFs), indicating that DNA double-strand breaks occurred exclusively in telomeres as a direct consequence of mitochondrial dysfunction. These telomere defects activated ataxia-telangiectasia mutated (ATM)-mediated DNA damage repair signaling. Furthermore, ATM inhibition exacerbated the Mito-FAP-induced mitochondrial dysfunction and sensitized cells to apoptotic cell death. This profound sensitivity of telomeres through hydrogen peroxide induced by dysregulated mitochondria reveals a crucial mechanism of telomere-mitochondria communication underlying the pathophysiological role of mitochondrial ROS in human diseases.
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16
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Saker L, Ali S, Masserot C, Kellermann G, Poupon J, Teulade-Fichou MP, Ségal-Bendirdjian E, Bombard S. Platinum Complexes Can Bind to Telomeres by Coordination. Int J Mol Sci 2018; 19:E1951. [PMID: 29970863 PMCID: PMC6073198 DOI: 10.3390/ijms19071951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 01/07/2023] Open
Abstract
It is suggested that several compounds, including G-quadruplex ligands, can target telomeres, inducing their uncapping and, ultimately, cell death. However, it has never been demonstrated whether such ligands can bind directly and quantitatively to telomeres. Here, we employed the property of platinum and platinum-G-quadruplex complexes to target G-rich sequences to investigate and quantify their covalent binding to telomeres. Using inductively coupled plasma mass spectrometry, surprisingly, we found that, in cellulo, in the presence of cisplatin, a di-functional platinum complex, telomeric DNA was platinated 13-times less than genomic DNA in cellulo, as compared to in vitro data. On the contrary, the amount of mono-functional platinum complexes (Pt-ttpy and Pt-tpy) bound either to telomeric or to genomic DNA was similar and occurred in a G-quadruplex independent-manner. Importantly, the quantification revealed that the low level of cisplatin bound to telomeric DNA could not be the direct physical cause of TRF2 displacement from telomeres. Altogether, our data suggest that platinum complexes can affect telomeres both directly and indirectly.
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Affiliation(s)
- Lina Saker
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, 75006 Paris, France.
- Paris Descartes University, Paris Sorbonne Cité, 75006 Paris, France.
| | - Samar Ali
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, 75006 Paris, France.
- Paris Sud University, Paris-Saclay University, 91405 Orsay, France.
| | - Caroline Masserot
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, 75006 Paris, France.
- Paris Sud University, Paris-Saclay University, 91405 Orsay, France.
| | - Guillaume Kellermann
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, 75006 Paris, France.
- Paris Descartes University, Paris Sorbonne Cité, 75006 Paris, France.
| | - Joel Poupon
- Laboratoire de Toxicologie-Biologique, Hôpital Lariboisière, 2 rue Ambroise Paré, 75475 Paris, France.
| | - Marie-Paule Teulade-Fichou
- Paris Sud University, Paris-Saclay University, 91405 Orsay, France.
- Institut Curie-Recherche, Bât. 112, Centre Universitaire, 91405 Orsay, France.
- CNRS UMR918, Centre Universitaire, 91405 Orsay, France.
- INSERM U1196, Centre Universitaire, 91405 Orsay, France.
| | - Evelyne Ségal-Bendirdjian
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, 75006 Paris, France.
- Paris Descartes University, Paris Sorbonne Cité, 75006 Paris, France.
- Paris Sud University, Paris-Saclay University, 91405 Orsay, France.
| | - Sophie Bombard
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, 75006 Paris, France.
- Paris Descartes University, Paris Sorbonne Cité, 75006 Paris, France.
- Paris Sud University, Paris-Saclay University, 91405 Orsay, France.
- Institut Curie-Recherche, Bât. 112, Centre Universitaire, 91405 Orsay, France.
- CNRS UMR918, Centre Universitaire, 91405 Orsay, France.
- INSERM U1196, Centre Universitaire, 91405 Orsay, France.
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17
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Trajano LADSN, Trajano ETL, Silva MADS, Stumbo AC, Mencalha AL, Fonseca ADSD. Genomic stability and telomere regulation in skeletal muscle tissue. Biomed Pharmacother 2018; 98:907-915. [DOI: 10.1016/j.biopha.2018.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 02/07/2023] Open
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18
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Impact of oxidative stress on telomere biology. Differentiation 2018; 99:21-27. [DOI: 10.1016/j.diff.2017.12.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 12/12/2022]
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19
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Third EU-US workshop on “Nucleotide excision repair and crosslink repair—From molecules to mankind”, Smolenice Castle, Slovak Republic, May 7th–11th 2017. DNA Repair (Amst) 2017. [DOI: 10.1016/j.dnarep.2017.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Guintini L, Tremblay M, Toussaint M, D'Amours A, Wellinger RE, Wellinger RJ, Conconi A. Repair of UV-induced DNA lesions in natural Saccharomyces cerevisiae telomeres is moderated by Sir2 and Sir3, and inhibited by yKu-Sir4 interaction. Nucleic Acids Res 2017; 45:4577-4589. [PMID: 28334768 PMCID: PMC5416773 DOI: 10.1093/nar/gkx123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 02/10/2017] [Indexed: 01/28/2023] Open
Abstract
Ultraviolet light (UV) causes DNA damage that is removed by nucleotide excision repair (NER). UV-induced DNA lesions must be recognized and repaired in nucleosomal DNA, higher order structures of chromatin and within different nuclear sub-compartments. Telomeric DNA is made of short tandem repeats located at the ends of chromosomes and their maintenance is critical to prevent genome instability. In Saccharomyces cerevisiae the chromatin structure of natural telomeres is distinctive and contingent to telomeric DNA sequences. Namely, nucleosomes and Sir proteins form the heterochromatin like structure of X-type telomeres, whereas a more open conformation is present at Y’-type telomeres. It is proposed that there are no nucleosomes on the most distal telomeric repeat DNA, which is bound by a complex of proteins and folded into higher order structure. How these structures affect NER is poorly understood. Our data indicate that the X-type, but not the Y’-type, sub-telomeric chromatin modulates NER, a consequence of Sir protein-dependent nucleosome stability. The telomere terminal complex also prevents NER, however, this effect is largely dependent on the yKu–Sir4 interaction, but Sir2 and Sir3 independent.
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Affiliation(s)
- Laetitia Guintini
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Maxime Tremblay
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Martin Toussaint
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Annie D'Amours
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Ralf E Wellinger
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, CSIC, Avda Américo Vespucio s/n, Sevilla 41092, Spain
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Antonio Conconi
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
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21
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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] [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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22
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Telomere-associated aging disorders. Ageing Res Rev 2017; 33:52-66. [PMID: 27215853 PMCID: PMC9926533 DOI: 10.1016/j.arr.2016.05.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 01/25/2023]
Abstract
Telomeres are dynamic nucleoprotein-DNA structures that cap and protect linear chromosome ends. Several monogenic inherited diseases that display features of human premature aging correlate with shortened telomeres, and are referred to collectively as telomeropathies. These disorders have overlapping symptoms and a common underlying mechanism of telomere dysfunction, but also exhibit variable symptoms and age of onset, suggesting they fall along a spectrum of disorders. Primary telomeropathies are caused by defects in the telomere maintenance machinery, whereas secondary telomeropathies have some overlapping symptoms with primary telomeropathies, but are generally caused by mutations in DNA repair proteins that contribute to telomere preservation. Here we review both the primary and secondary telomeropathies, discuss potential mechanisms for tissue specificity and age of onset, and highlight outstanding questions in the field and future directions toward elucidating disease etiology and developing therapeutic strategies.
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23
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Fouquerel E, Opresko P. Convergence of The Nobel Fields of Telomere Biology and DNA Repair. Photochem Photobiol 2017; 93:229-237. [PMID: 27861975 PMCID: PMC5315637 DOI: 10.1111/php.12672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [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, 5117 Centre Avenue, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Patricia Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh Cancer Institute Research Pavilion, 5117 Centre Avenue, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
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24
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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: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [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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25
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Lee JR, Xie X, Yang K, Zhang J, Lee SY, Shippen DE. Dynamic Interactions of Arabidopsis TEN1: Stabilizing Telomeres in Response to Heat Stress. THE PLANT CELL 2016; 28:2212-2224. [PMID: 27609839 PMCID: PMC5059806 DOI: 10.1105/tpc.16.00408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 05/15/2023]
Abstract
Telomeres are the essential nucleoprotein structures that provide a physical cap for the ends of linear chromosomes. The highly conserved CST (CTC1/STN1/TEN1) protein complex facilitates telomeric DNA replication and promotes telomere stability. Here we report three unexpected properties of Arabidopsis thaliana TEN1 that indicate it possesses functions distinct from other previously characterized telomere proteins. First, we show that telomeres in ten1 mutants are highly sensitive to thermal stress. Heat shock causes abrupt and dramatic loss of telomeric DNA in ten1 plants, likely via deletional recombination. Second, we show that AtTEN1 has the properties of a heat-shock induced molecular chaperone. At elevated temperature, AtTEN1 rapidly assembles into high molecular weight homo-oligomeric complexes that efficiently suppress heat-induced aggregation of model protein substrates in vitro. Finally, we report that AtTEN1 specifically protects CTC1 from heat-induced aggregation in vitro, and from heat-induced protein degradation and loss of telomere association in vivo. Collectively, these observations define Arabidopsis TEN1 as a highly dynamic protein that works in concert with CTC1 to preserve telomere integrity in response to environmental stress.
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Affiliation(s)
- Jung Ro Lee
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Xiaoyuan Xie
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Kailu Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Sang Yeol Lee
- Division of Applied Life Sciences (BK21) and PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
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26
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Abstract
Telomeres at chromosome ends are nucleoprotein structures consisting of tandem TTAGGG repeats and a complex of proteins termed shelterin. DNA damage and repair at telomeres is uniquely influenced by the ability of telomeric DNA to form alternate structures including loops and G-quadruplexes, coupled with the ability of shelterin proteins to interact with and regulate enzymes in every known DNA repair pathway. The role of shelterin proteins in preventing telomeric ends from being falsely recognized and processed as DNA double strand breaks is well established. Here we focus instead on recent developments in understanding the roles of shelterin proteins and telomeric DNA sequence and structure in processing genuine damage at telomeres induced by endogenous and exogenous DNA damage agents. We will highlight advances in double strand break repair, base excision repair and nucleotide excision repair at telomeres, and will discuss important questions remaining in the field.
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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, 5117 Centre Avenue, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Dhvani Parikh
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh Cancer Institute Research Pavilion, 5117 Centre Avenue, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Patricia Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh Cancer Institute Research Pavilion, 5117 Centre Avenue, University of Pittsburgh, Pittsburgh, PA 15213, United States.
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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] [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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28
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Abstract
DNA damage is caused by either endogenous cellular metabolic processes such as hydrolysis, oxidation, alkylation, and DNA base mismatches, or exogenous sources including ultraviolet (UV) light, ionizing radiation, and chemical agents. Damaged DNA that is not properly repaired can lead to genomic instability, driving tumorigenesis. To protect genomic stability, mammalian cells have evolved highly conserved DNA repair mechanisms to remove and repair DNA lesions. Telomeres are composed of long tandem TTAGGG repeats located at the ends of chromosomes. Maintenance of functional telomeres is critical for preventing genome instability. The telomeric sequence possesses unique features that predispose telomeres to a variety of DNA damage induced by environmental genotoxins. This review briefly describes the relevance of excision repair pathways in telomere maintenance, with the focus on base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). By summarizing current knowledge on excision repair of telomere damage and outlining many unanswered questions, it is our hope to stimulate further interest in a better understanding of excision repair processes at telomeres and in how these processes contribute to telomere maintenance.
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Affiliation(s)
- Pingping Jia
- Elson S. Floyd College of Medicine, United States
| | - Chengtao Her
- School of Molecular Biosciences, Washington State University, United States
| | - Weihang Chai
- Elson S. Floyd College of Medicine, United States; School of Molecular Biosciences, Washington State University, United States.
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