1
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Valle-Orero J, Rieu M, Allemand JF, Bujaa D, Joubert A, Tran PLT, Croquette V, Boulé JB. Observing G4 formation and its resolution by Pif1 in real time by manipulation under magnetic tweezers. Methods Enzymol 2024; 695:119-158. [PMID: 38521583 DOI: 10.1016/bs.mie.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
G-quadruplexes (G4s) are nucleic acids secondary structures that may form in guanine-rich sequences, either intra or inter-molecularly. Ability of a primary sequence to form a G4 can be predicted computationally with an improving accuracy as well as tested in bulk using biophysical measurements. As a result, G4 density maps have been devised for a large number of genomes from all life kingdoms. Experimental validation of the formation of G4s in vivo however remains indirect and relies on their stabilization with small molecules, antibodies or proteins, or mutational studies, in order to measure downstream effects on gene expression or genome stability for example. Although numerous techniques exist to observe spontaneous formation of G4s in single-stranded DNA, observing G4 formation in double-stranded DNA (dsDNA) is more challenging. However, it is particularly relevant to understand if a given G4 sequence forms stably in a dsDNA context, if it is stable enough to dock proteins or pose a challenge to molecular motors such as helicases or polymerases. In essence, G4s can be a threat to genomic stability but carry as well as the potential to be elements of a structural language in the non-replicating genome. To study quantitatively the formation dynamics and stability of single intramolecular G4s embedded in dsDNA, we have adapted techniques of DNA manipulation under magnetic tweezers. This technique also allows to study encounters of molecular motors with G4 at a single molecule resolution, in order to gain insight into the specificity of G4 resolution by molecular motors, and its efficiency. The procedures described here include the design of the G4 substrate, the study of G4 formation probability and lifetime in dsDNA, as well as procedures to characterize the encounter between the Pif1 helicase and a G4 until G4 resolution. The procedures that we described here can easily be extended to the study of other G4s or molecular motors.
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Affiliation(s)
- Jessica Valle-Orero
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; Department of Computer Science, Mathematics and Environmental Sciences, The American University of Paris, Paris, France.
| | - Martin Rieu
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Jean-François Allemand
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France
| | - Dulamkhuu Bujaa
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France
| | - Alexandra Joubert
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France
| | - Phong Lan Thao Tran
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France; Depixus SAS, 3-5 impasse Reille, Paris, France
| | - Vincent Croquette
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; ESPCI Paris, PSL University, Paris, France.
| | - Jean-Baptiste Boulé
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France.
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2
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Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol 2024; 436:168205. [PMID: 37481156 PMCID: PMC10799177 DOI: 10.1016/j.jmb.2023.168205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Telomeres and their single stranded overhangs gradually shorten with successive cell divisions, as part of the natural aging process, but can be elongated by telomerase, a nucleoprotein complex which is activated in the majority of cancers. This prominent implication in cancer and aging has made the repetitive telomeric sequences (TTAGGG repeats) and the G-quadruplex structures that form in their overhangs the focus of intense research in the past several decades. However, until recently most in vitro efforts to understand the structure, stability, dynamics, and interactions of telomeric overhangs had been focused on short sequences that are not representative of longer sequences encountered in a physiological setting. In this review, we will provide a broad perspective about telomeres and associated factors, and introduce the agents and structural characteristics involved in organizing, maintaining, and protecting telomeric DNA. We will also present a summary of recent research performed on long telomeric sequences, nominally defined as those that can form two or more tandem G-quadruplexes, i.e., which contain eight or more TTAGGG repeats. Results of experimental studies using a broad array of experimental tools, in addition to recent computational efforts will be discussed, particularly in terms of their implications for the stability, folding topology, and compactness of the tandem G-quadruplexes that form in long telomeric overhangs.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
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3
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Chatain J, Blond A, Phan AT, Saintomé C, Alberti P. GGGCTA repeats can fold into hairpins poorly unfolded by replication protein A: a possible origin of the length-dependent instability of GGGCTA variant repeats in human telomeres. Nucleic Acids Res 2021; 49:7588-7601. [PMID: 34214172 PMCID: PMC8287962 DOI: 10.1093/nar/gkab518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/01/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022] Open
Abstract
Human telomeres are composed of GGGTTA repeats and interspersed with variant repeats. The GGGCTA variant motif was identified in the proximal regions of human telomeres about 10 years ago and was shown to display a length-dependent instability. In parallel, a structural study showed that four GGGCTA repeats folded into a non-canonical G-quadruplex (G4) comprising a Watson-Crick GCGC tetrad. It was proposed that this non-canonical G4 might be an additional obstacle for telomere replication. In the present study, we demonstrate that longer GGGCTA arrays fold into G4 and into hairpins. We also demonstrate that replication protein A (RPA) efficiently binds to GGGCTA repeats structured into G4 but poorly binds to GGGCTA repeats structured into hairpins. Our results (along with results obtained with a more stable variant motif) suggest that GGGCTA hairpins are at the origin of GGGCTA length-dependent instability. They also suggest, as working hypothesis, that failure of efficient binding of RPA to GGGCTA structured into hairpins might be involved in the mechanism of GGGCTA array instability. On the basis of our present and past studies about telomeric G4 and their interaction with RPA, we propose an original point of view about telomeric G4 and the evolution of telomeric motifs.
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Affiliation(s)
- Jean Chatain
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
| | - Alain Blond
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d’Histoire naturelle, CNRS, Paris 75005, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Carole Saintomé
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
- Sorbonne Université, UFR927, Paris 75005, France
| | - Patrizia Alberti
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
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4
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Tran P, Rieu M, Hodeib S, Joubert A, Ouellet J, Alberti P, Bugaut A, Allemand JF, Boulé JB, Croquette V. Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex. Nucleic Acids Res 2021; 49:5189-5201. [PMID: 34009328 PMCID: PMC8136832 DOI: 10.1093/nar/gkab306] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
G-quadruplex (G4) DNA structures have emerged as important regulatory elements during DNA metabolic transactions. While many in vitro studies have focused on the kinetics of G4 formation within DNA single-strands, G4 are found in vivo in double-stranded DNA regions, where their formation is challenged by the complementary strand. Since the energy of hybridization of Watson-Crick structures dominates the energy of G4 folding, this competition should play a critical role on G4 persistence. To address this, we designed a single-molecule assay allowing to measure G4 folding and persistence times in the presence of the complementary strand. We quantified both folding and unfolding rates of biologically relevant G4 sequences, such as the cMYC and cKIT oncogene promoters, human telomeres and an avian replication origin. We confirmed that G4s are found much more stable in tested replication origin and promoters than in human telomere repeats. In addition, we characterized how G4 dynamics was affected by G4 ligands and showed that both folding rate and persistence time increased. Our assay opens new perspectives for the measurement of G4 dynamics in double-stranded DNA mimicking a replication fork, which is important to understand their role in DNA replication and gene regulation at a mechanistic level.
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Affiliation(s)
- Phong Lan Thao Tran
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Martin Rieu
- Laboratoire de physique de L’École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Samar Hodeib
- Laboratoire de physique de L’École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alexandra Joubert
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Jimmy Ouellet
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Anthony Bugaut
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Jean-François Allemand
- Laboratoire de physique de L’École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Jean-Baptiste Boulé
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Vincent Croquette
- Laboratoire de physique de L’École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- ESPCI Paris, Université PSL, 75005 Paris, France
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5
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Shen M, Young A, Autexier C. PCNA, a focus on replication stress and the alternative lengthening of telomeres pathway. DNA Repair (Amst) 2021; 100:103055. [PMID: 33581499 DOI: 10.1016/j.dnarep.2021.103055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022]
Abstract
The maintenance of telomeres, which are specialized stretches of DNA found at the ends of linear chromosomes, is a crucial step for the immortalization of cancer cells. Approximately 10-15 % of cancer cells use a homologous recombination-based mechanism known as the Alternative Lengthening of Telomeres (ALT) pathway to maintain their telomeres. Telomeres in general pose a challenge to DNA replication owing to their repetitive nature and potential for forming secondary structures. Telomeres in ALT+ cells especially are subject to elevated levels of replication stress compared to telomeres that are maintained by the enzyme telomerase, in part due to the incorporation of telomeric variant repeats at ALT+ telomeres, their on average longer lengths, and their modified chromatin states. Many DNA metabolic strategies exist to counter replication stress and to protect stalled replication forks. The role of proliferating cell nuclear antigen (PCNA) as a platform for recruiting protein partners that participate in several of these DNA replication and repair pathways has been well-documented. We propose that many of these pathways may be active at ALT+ telomeres, either to facilitate DNA replication, to manage replication stress, or during telomere extension. Here, we summarize recent evidence detailing the role of PCNA in pathways including DNA secondary structure resolution, DNA damage bypass, replication fork restart, and DNA damage synthesis. We propose that an examination of PCNA and its post-translational modifications (PTMs) may offer a unique lens by which we might gain insight into the DNA metabolic landscape that is distinctively present at ALT+ telomeres.
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Affiliation(s)
- Michelle Shen
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Adrian Young
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada.
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6
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Wood ML, Veal CD, Neumann R, Suárez NM, Nichols J, Parker AJ, Martin D, Romaine SPR, Codd V, Samani NJ, Voors AA, Tomaszewski M, Flamand L, Davison AJ, Royle NJ. Variation in human herpesvirus 6B telomeric integration, excision, and transmission between tissues and individuals. eLife 2021; 10:70452. [PMID: 34545807 PMCID: PMC8492063 DOI: 10.7554/elife.70452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
Human herpesviruses 6A and 6B (HHV-6A/6B) are ubiquitous pathogens that persist lifelong in latent form and can cause severe conditions upon reactivation. They are spread by community-acquired infection of free virus (acqHHV6A/6B) and by germline transmission of inherited chromosomally integrated HHV-6A/6B (iciHHV-6A/6B) in telomeres. We exploited a hypervariable region of the HHV-6B genome to investigate the relationship between acquired and inherited virus and revealed predominantly maternal transmission of acqHHV-6B in families. Remarkably, we demonstrate that some copies of acqHHV-6B in saliva from healthy adults gained a telomere, indicative of integration and latency, and that the frequency of viral genome excision from telomeres in iciHHV-6B carriers is surprisingly high and varies between tissues. In addition, newly formed short telomeres generated by partial viral genome release are frequently lengthened, particularly in telomerase-expressing pluripotent cells. Consequently, iciHHV-6B carriers are mosaic for different iciHHV-6B structures, including circular extra-chromosomal forms that have the potential to reactivate. Finally, we show transmission of an HHV-6B strain from an iciHHV-6B mother to her non-iciHHV-6B son. Altogether, we demonstrate that iciHHV-6B can readily transition between telomere-integrated and free virus forms.
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Affiliation(s)
- Michael L Wood
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Colin D Veal
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Rita Neumann
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Andrei J Parker
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Diana Martin
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Simon PR Romaine
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom,NIHR Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUnited Kingdom
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
| | - Adriaan A Voors
- University of Groningen, Department of Cardiology, University Medical Center GroningenGroningenNetherlands
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Louis Flamand
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec CityQuébecCanada
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Nicola J Royle
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
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7
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Alhendi ASN, Royle NJ. The absence of (TCAGGG) n repeats in some telomeres, combined with variable responses to NR2F2 depletion, suggest that this nuclear receptor plays an indirect role in the alternative lengthening of telomeres. Sci Rep 2020; 10:20597. [PMID: 33244044 PMCID: PMC7691514 DOI: 10.1038/s41598-020-77606-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 11/04/2020] [Indexed: 12/26/2022] Open
Abstract
The alternative lengthening of telomeres (ALT) facilitates telomere lengthening by a DNA strand invasion and copying mechanism. The nuclear receptors (NRs), NR2F2 and NR2C2, can bind to (TCAGGG)n variant repeats within telomeres and it has been proposed that this facilitates telomere interactions in ALT+ cells. Here we show that the frequency of cells with detectable NR2F2 and NR2C2 nuclear foci varies considerably between ALT+ cell lines and does not correlate with the level of protein expression. In addition, four of five ALT+ cell lines lack (TCAGGG)n repeats in some telomeres, indicating that direct NR binding does not play a role in ALT at these telomeres. NR2F2-depletion altered the abundance of C-circles and APBs but the direction of the response was inconsistent between three ALT+ cell lines. Moreover, transcriptome analysis following NR2F2-depletion in the ALT+ cell lines revealed different very responses. For example, NR2F2-depletion down-regulated many genes in U2OS cells, consistent with the cell cycle arrest and changes to ALT markers, but these features were not shared by the other two ALT+ cell lines. Among 86 ALT-associated genes, only MND1 showed consistent down-regulation across three NR2F2-depleted ALT+ cell lines. Altogether our data suggest that NR2F2 does not play a direct role in ALT and we speculate about an alternative role for this NR in a DNA damage response at telomeres.
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Affiliation(s)
- Ahmed S N Alhendi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 3HE, UK
| | - Nicola J Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 3HE, UK.
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8
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Garrido-Navas MC, Tippins F, Barwell J, Hoffman J, Codd V, Royle NJ. Telomere Instability in Lynch Syndrome Families Leads to Some Shorter Telomeres in MSH2+/- Carriers. Life (Basel) 2020; 10:life10110265. [PMID: 33142697 PMCID: PMC7692680 DOI: 10.3390/life10110265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
Lynch syndrome (LS) is an inherited predisposition to early onset of various cancers, caused by mutation in a DNA mismatch repair (MMR) gene. In heterozygous MMR+/− carriers, somatic mutation, loss or silencing of the wild type allele increases the mutation rate, facilitating the initiation of MMR-defective cancers. These cancers are characterized by instability at short tandem repeats (STRs) and in telomeric DNA. We have investigated telomere length in saliva DNA from LS and control families, using single telomere analysis at XpYp and 12q and by qPCR to measure total telomeric DNA. Single telomere analysis showed a trend for shorter XpYp telomeres in MSH2+/− carriers compared to MLH1+/− carriers or controls, but this was masked in the comparative analysis of total telomeric DNA. Comparison of age-adjusted telomere length within families showed that neither MSH2+/− or MLH1+/− children had consistently shorter or longer telomeres than their MMR+/− parent, indicating the absence of an inter-generational effect on telomere length. Unexpectedly however, wildtype children in families with MSH2 mutations, had significantly longer XpYp telomeres than their MMR+/− parent. Altogether our data suggest that MMR insufficiency, particularly in MSH2+/− carriers, increases telomere instability and somatic cell turnover during the lifetime of LS mutation carriers but has minimal consequences for telomere length in the germline.
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Affiliation(s)
- M. Carmen Garrido-Navas
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (F.T.); (J.B.)
- Liquid Biopsies & Cancer Interception (LiqBiopCI) Group, Junta de Andalucía de Genómica Investigación Oncológica, GENYO–Centro Pfizer–Universidad de Granada, 18016 Granada, Spain
- Universidad Internacional de la Rioja, 137, 26006 Logroño, La Rioja, Spain
- Correspondence: (M.C.G.-N.); (N.J.R.)
| | - Frances Tippins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (F.T.); (J.B.)
| | - Julian Barwell
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (F.T.); (J.B.)
| | - Jonathan Hoffman
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham B15 2TG, UK;
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Leicester LE3 9QP, UK;
| | - Nicola J. Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (F.T.); (J.B.)
- Correspondence: (M.C.G.-N.); (N.J.R.)
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9
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Sommer A, Royle NJ. ALT: A Multi-Faceted Phenomenon. Genes (Basel) 2020; 11:E133. [PMID: 32012790 PMCID: PMC7073516 DOI: 10.3390/genes11020133] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 01/13/2023] Open
Abstract
One of the hallmarks of cancer cells is their indefinite replicative potential, made possible by the activation of a telomere maintenance mechanism (TMM). The majority of cancers reactivate the reverse transcriptase, telomerase, to maintain their telomere length but a minority (10% to 15%) utilize an alternative lengthening of telomeres (ALT) pathway. Here, we review the phenotypes and molecular markers specific to ALT, and investigate the significance of telomere mutations and sequence variation in ALT cell lines. We also look at the recent advancements in understanding the different mechanisms behind ALT telomere elongation and finally, the progress made in identifying potential ALT-targeted therapies, including those already in use for the treatment of both hematological and solid tumors.
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Affiliation(s)
| | - Nicola J. Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK;
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10
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Stadlbauer P, Kührová P, Vicherek L, Banáš P, Otyepka M, Trantírek L, Šponer J. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. Nucleic Acids Res 2019; 47:7276-7293. [PMID: 31318975 PMCID: PMC6698752 DOI: 10.1093/nar/gkz610] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/29/2022] Open
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lukáš Vicherek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lukáš Trantírek
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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11
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Li Y, Liu W, Zhu Y, Diao L. A fluorescence method for homogeneous detection of influenza A DNA sequence based on guanine-quadruplex-N-methylmesoporphyrin IX complex and assistance-DNA inhibition. J Med Virol 2019; 91:979-985. [PMID: 30715734 DOI: 10.1002/jmv.25422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/20/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022]
Abstract
In his study, we report a fluorescence method for homogeneous detection of influenza A (H1N1) DNA sequence based on G-quadruplex-NMM complex and assistance-DNA (A-DNA) inhibition. The quadruplex-based functional DNA (QBF-DNA), composed of a complementary probe to the target H1N1 DNA sequence and G-rich fragment, was designed as the signal DNA. The A-DNA consisted of two parts, one part was complementary to target H1N1 DNA and the other part was complementary to the signal DNA. In the absence of target H1N1 DNA, the G-rich fragment of QBF-DNA can form G-quadruplex-NMM complex, which outputted a fluorescent signal. With the presence of target H1N1 DNA, QBF-DNA, and A-DNA can simultaneously hybridize with target H1N1 DNA to form double-helix structure. In this case, the A-DNA partially hybridized with the QBF-DNA, which inhibited the formation of G-quadruplex-NMM complex, leading to the decrease of fluorescent signal. Under the optimum conditions, the fluorescence intensity was inversely proportional to the concentration of target H1N1 DNA over the range from 25 to 700 pmol/L with a detection limit of 8 pmol/L. In addition, the method is target specific and practicability, and would become a new diagnostic assay for H1N1 DNA sequence and other infectious diseases.
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Affiliation(s)
- Yubin Li
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
| | - Wanshan Liu
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
| | - Yinling Zhu
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
| | - Liping Diao
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
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12
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Inherited Chromosomally Integrated Human Herpesvirus 6 Genomes Are Ancient, Intact, and Potentially Able To Reactivate from Telomeres. J Virol 2017; 91:JVI.01137-17. [PMID: 28835501 PMCID: PMC5660504 DOI: 10.1128/jvi.01137-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/15/2017] [Indexed: 01/31/2023] Open
Abstract
The genomes of human herpesvirus 6A (HHV-6A) and HHV-6B have the capacity to integrate into telomeres, the essential capping structures of chromosomes that play roles in cancer and ageing. About 1% of people worldwide are carriers of chromosomally integrated HHV-6 (ciHHV-6), which is inherited as a genetic trait. Understanding the consequences of integration for the evolution of the viral genome, for the telomere, and for the risk of disease associated with carrier status is hampered by a lack of knowledge about ciHHV-6 genomes. Here, we report an analysis of 28 ciHHV-6 genomes and show that they are significantly divergent from the few modern nonintegrated HHV-6 strains for which complete sequences are currently available. In addition, ciHHV-6B genomes in Europeans are more closely related to each other than to ciHHV-6B genomes from China and Pakistan, suggesting regional variation of the trait. Remarkably, at least one group of European ciHHV-6B carriers has inherited the same ciHHV-6B genome, integrated in the same telomere allele, from a common ancestor estimated to have existed 24,500 ± 10,600 years ago. Despite the antiquity of some, and possibly most, germ line HHV-6 integrations, the majority of ciHHV-6B (95%) and ciHHV-6A (72%) genomes contain a full set of intact viral genes and therefore appear to have the capacity for viral gene expression and full reactivation. IMPORTANCE Inheritance of HHV-6A or HHV-6B integrated into a telomere occurs at a low frequency in most populations studied to date, but its characteristics are poorly understood. However, stratification of ciHHV-6 carriers in modern populations due to common ancestry is an important consideration for genome-wide association studies that aim to identify disease risks for these people. Here, we present full sequence analysis of 28 ciHHV-6 genomes and show that ciHHV-6B in many carriers with European ancestry most likely originated from ancient integration events in a small number of ancestors. We propose that ancient ancestral origins for ciHHV-6A and ciHHV-6B are also likely in other populations. Moreover, despite their antiquity, all of the ciHHV-6 genomes appear to retain the capacity to express viral genes, and most are predicted to be capable of full viral reactivation. These discoveries represent potentially important considerations in immunocompromised patients, in particular in organ transplantation and in stem cell therapy.
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13
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Wand T, Fang M, Chen C, Hardy N, McCoy JP, Dumitriu B, Young NS, Biancotto A. Telomere content measurement in human hematopoietic cells: Comparative analysis of qPCR and Flow-FISH techniques. Cytometry A 2016; 89:914-921. [PMID: 27717244 PMCID: PMC6482817 DOI: 10.1002/cyto.a.22982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 05/13/2016] [Accepted: 08/31/2016] [Indexed: 12/30/2022]
Abstract
Abnormal telomere lengths have been linked to cancer and other hematologic disorders. Determination of mean telomere content (MTC) is traditionally performed by Southern blotting and densitometry, giving a mean telomere restriction fragment (TRF) value for the total cell population studied. Here, we compared a quantitative Polymerase Chain Reaction approach (qPCR) and a flow cytometric approach, fluorescence in situ hybridization (Flow-FISH), to evaluate telomere content distribution in total patient peripheral blood mononuclear cells or specific cell populations. Flow-FISH is based on in situ hybridization using a fluorescein-labeled peptide nucleic acid (PNA) (CCCTAA)3 probe and DNA staining with propidium iodide. We showed that both qPCR and Flow-FISH provide a robust measurement, with Flow-FISH measuring a relative content longer than qPCR at a single cell approach and that TRF2 fluorescence intensity did not correlate with MTC. Both methods showed comparable telomere content reduction with age, and the rate of relative telomere loss was similar. Published 2016 Wiley Periodicals Inc. This article is a US government work and, as such, is in the public domain in the United States of America.
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Affiliation(s)
- Taylor Wand
- Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, Maryland, 28092
| | - Mike Fang
- Hematology Branch, National Heart Lung and Blood Institute National Institutes of Health, Bethesda, Maryland, 28092
| | - Christina Chen
- Hematology Branch, National Heart Lung and Blood Institute National Institutes of Health, Bethesda, Maryland, 28092
| | - Nathan Hardy
- Hematology Branch, National Heart Lung and Blood Institute National Institutes of Health, Bethesda, Maryland, 28092
| | - J Philip McCoy
- Flow Cytometry Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 28092
| | - Bogdan Dumitriu
- Hematology Branch, National Heart Lung and Blood Institute National Institutes of Health, Bethesda, Maryland, 28092
| | - Neal S Young
- Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, Maryland, 28092
- Hematology Branch, National Heart Lung and Blood Institute National Institutes of Health, Bethesda, Maryland, 28092
| | - Angélique Biancotto
- Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, Maryland, 28092.
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14
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Wang M, Wang W, Kang TS, Leung CH, Ma DL. Development of an Iridium(III) Complex as a G-Quadruplex Probe and Its Application for the G-Quadruplex-Based Luminescent Detection of Picomolar Insulin. Anal Chem 2015; 88:981-7. [DOI: 10.1021/acs.analchem.5b04064] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Modi Wang
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Wanhe Wang
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Tian-Shu Kang
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chung-Hang Leung
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macao, China
| | - Dik-Lung Ma
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- Partner
State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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15
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Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. Biochimie 2014; 105:22-35. [DOI: 10.1016/j.biochi.2014.07.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/01/2014] [Indexed: 11/23/2022]
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16
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Parrotta L, Ortuso F, Moraca F, Rocca R, Costa G, Alcaro S, Artese A. Targeting unimolecular G-quadruplex nucleic acids: a new paradigm for the drug discovery? Expert Opin Drug Discov 2014; 9:1167-87. [PMID: 25109710 DOI: 10.1517/17460441.2014.941353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION G-quadruplexes (G4s) are targets of great interest because of their roles in crucial biological processes, such as aging and cancer. G4s are based on the formation of G-quartets, stabilised by Hoogsteen-type hydrogen bonds and by interaction with cations between the tetrads. These biologically relevant conformations were first discovered in eukaryotic chromosomal telomeric DNA, but have also been found in the proximal location of promoters in a number of human genes. Therefore, the extensive analysis of an intriguing target could move towards the rational drug design of new selective anticancer agents. AREAS COVERED The authors review G4 structural characterisation, with detailed insight related to the polymorphism issue. The authors describe the topologically distinct G4 structural forms and the factors involved in their interconversion mechanisms, such as the sequence of the oligonucleotides, the strand stoichiometry and orientation, the syn-anti conformation of the guanine glycosidic bonds and the G4 loop types and the environmental factors. Furthermore, the authors report several studies related to folding and unfolding kinetic profiles in order to understand the conformational view of monomolecular G4 formations. EXPERT OPINION G4 unimolecular nucleic acids can be considered as valid targets for the rational drug development of novel anticancer agents. Structural biology represents an essential link between the biology and medicinal chemistry knowledge in this field. In silico methods have already been demonstrated to be useful, especially if well integrated with biophysical tests. If this proves successful, the G4-targeting paradigm could also be extended to drug discovery beyond neoplastic pathologies.
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Affiliation(s)
- Lucia Parrotta
- Università degli Studi "Magna Græcia", Dipartimento di Scienze della Salute , Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro , Italy
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17
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Martinerie L, Manterola M, Chung SSW, Panigrahi SK, Weisbach M, Vasileva A, Geng Y, Sicinski P, Wolgemuth DJ. Mammalian E-type cyclins control chromosome pairing, telomere stability and CDK2 localization in male meiosis. PLoS Genet 2014; 10:e1004165. [PMID: 24586195 PMCID: PMC3937215 DOI: 10.1371/journal.pgen.1004165] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 12/22/2013] [Indexed: 11/24/2022] Open
Abstract
Loss of function of cyclin E1 or E2, important regulators of the mitotic cell cycle, yields viable mice, but E2-deficient males display reduced fertility. To elucidate the role of E-type cyclins during spermatogenesis, we characterized their expression patterns and produced additional deletions of Ccne1 and Ccne2 alleles in the germline, revealing unexpected meiotic functions. While Ccne2 mRNA and protein are abundantly expressed in spermatocytes, Ccne1 mRNA is present but its protein is detected only at low levels. However, abundant levels of cyclin E1 protein are detected in spermatocytes deficient in cyclin E2 protein. Additional depletion of E-type cyclins in the germline resulted in increasingly enhanced spermatogenic abnormalities and corresponding decreased fertility and loss of germ cells by apoptosis. Profound meiotic defects were observed in spermatocytes, including abnormal pairing and synapsis of homologous chromosomes, heterologous chromosome associations, unrepaired double-strand DNA breaks, disruptions in telomeric structure and defects in cyclin-dependent-kinase 2 localization. These results highlight a new role for E-type cyclins as important regulators of male meiosis. Understanding the control of meiosis is fundamental to deciphering the origin of male infertility. Although the mechanisms controlling meiosis are poorly understood, key regulators of mitosis, such as cyclins, appear to be critical. In this regard, male mice deficient for cyclin E2 exhibit subfertility and defects in spermatogenesis; however, neither the stages of germ cell differentiation affected nor the responsible mechanisms are known. We investigated how E-type cyclins control male meiosis by examining their expression in spermatogenesis and the consequences that multiple deletions of Ccne1 and Ccne2 alleles produce. Loss of Ccne2 expression increases cyclin E1 levels as a compensatory effect, but there are still meiotic defects and subfertility. Further, loss of one Ccne1 allele in the absence of cyclin E2 results in infertility as does loss of the remaining Ccne1 allele, but with even more severe meiotic abnormalities. We further found that cyclin E1 is involved in sex chromosome synapsis while E2 is involved with homologous pairing and chromosome and telomere integrity. These processes and structures were severely disrupted in absence of both cyclin E1 and E2, uncovering new roles for the E-type cyclins in regulating male meiosis.
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Affiliation(s)
- Laetitia Martinerie
- Departments of Genetics & Development, Columbia University Medical Center, New York, New York, United States of America
| | - Marcia Manterola
- Departments of Genetics & Development, Columbia University Medical Center, New York, New York, United States of America
| | - Sanny S W Chung
- Departments of Genetics & Development, Columbia University Medical Center, New York, New York, United States of America
| | - Sunil K Panigrahi
- Center for Radiological Research, Columbia University Medical Center, New York, New York, United States of America
| | - Melissa Weisbach
- Departments of Genetics & Development, Columbia University Medical Center, New York, New York, United States of America
| | - Ana Vasileva
- Departments of Genetics & Development, Columbia University Medical Center, New York, New York, United States of America ; Center for Radiological Research, Columbia University Medical Center, New York, New York, United States of America
| | - Yan Geng
- Department of Genetics, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Peter Sicinski
- Department of Genetics, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Debra J Wolgemuth
- Departments of Genetics & Development, Columbia University Medical Center, New York, New York, United States of America ; Obstetrics & Gynecology, Columbia University Medical Center, New York, New York, United States of America ; Institute of Human Nutrition, Columbia University Medical Center, New York, New York, United States of America
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18
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Sattin G, Artese A, Nadai M, Costa G, Parrotta L, Alcaro S, Palumbo M, Richter SN. Conformation and stability of intramolecular telomeric G-quadruplexes: sequence effects in the loops. PLoS One 2013; 8:e84113. [PMID: 24367632 PMCID: PMC3867476 DOI: 10.1371/journal.pone.0084113] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 11/12/2013] [Indexed: 01/15/2023] Open
Abstract
Telomeres are guanine-rich sequences that protect the ends of chromosomes. These regions can fold into G-quadruplex structures and their stabilization by G-quadruplex ligands has been employed as an anticancer strategy. Genetic analysis in human telomeres revealed extensive allelic variation restricted to loop bases, indicating that the variant telomeric sequences maintain the ability to fold into G-quadruplex. To assess the effect of mutations in loop bases on G-quadruplex folding and stability, we performed a comprehensive analysis of mutant telomeric sequences by spectroscopic techniques, molecular dynamics simulations and gel electrophoresis. We found that when the first position in the loop was mutated from T to C or A the resulting structure adopted a less stable antiparallel topology; when the second position was mutated to C or A, lower thermal stability and no evident conformational change were observed; in contrast, substitution of the third position from A to C induced a more stable and original hybrid conformation, while mutation to T did not significantly affect G-quadruplex topology and stability. Our results indicate that allelic variations generate G-quadruplex telomeric structures with variable conformation and stability. This aspect needs to be taken into account when designing new potential anticancer molecules.
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Affiliation(s)
- Giovanna Sattin
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Catanzaro, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Catanzaro, Italy
| | - Lucia Parrotta
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Catanzaro, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy
- * E-mail:
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19
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Lee M, Hills M, Conomos D, Stutz MD, Dagg RA, Lau LMS, Reddel RR, Pickett HA. Telomere extension by telomerase and ALT generates variant repeats by mechanistically distinct processes. Nucleic Acids Res 2013; 42:1733-46. [PMID: 24225324 PMCID: PMC3919612 DOI: 10.1093/nar/gkt1117] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Telomeres are terminal repetitive DNA sequences on chromosomes, and are considered to comprise almost exclusively hexameric TTAGGG repeats. We have evaluated telomere sequence content in human cells using whole-genome sequencing followed by telomere read extraction in a panel of mortal cell strains and immortal cell lines. We identified a wide range of telomere variant repeats in human cells, and found evidence that variant repeats are generated by mechanistically distinct processes during telomerase- and ALT-mediated telomere lengthening. Telomerase-mediated telomere extension resulted in biased repeat synthesis of variant repeats that differed from the canonical sequence at positions 1 and 3, but not at positions 2, 4, 5 or 6. This indicates that telomerase is most likely an error-prone reverse transcriptase that misincorporates nucleotides at specific positions on the telomerase RNA template. In contrast, cell lines that use the ALT pathway contained a large range of variant repeats that varied greatly between lines. This is consistent with variant repeats spreading from proximal telomeric regions throughout telomeres in a stochastic manner by recombination-mediated templating of DNA synthesis. The presence of unexpectedly large numbers of variant repeats in cells utilizing either telomere maintenance mechanism suggests a conserved role for variant sequences at human telomeres.
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Affiliation(s)
- Michael Lee
- Telomere Length Regulation Group, Children's Medical Research Institute, Westmead NSW 2145, Australia, Cancer Research Unit, Children's Medical Research Institute, Westmead NSW 2145, Australia, Terry Fox Laboratory, BC Cancer Agency, Vancouver V5Z 1L3, Canada, Sydney Medical School, University of Sydney, Sydney NSW 2006, Australia and Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead NSW 2145, Australia
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20
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Seguí N, Pineda M, Guinó E, Borràs E, Navarro M, Bellido F, Moreno V, Lázaro C, Blanco I, Capellá G, Valle L. Telomere length and genetic anticipation in Lynch syndrome. PLoS One 2013; 8:e61286. [PMID: 23637804 PMCID: PMC3634050 DOI: 10.1371/journal.pone.0061286] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/08/2013] [Indexed: 02/02/2023] Open
Abstract
Telomere length variation has been associated with increased risk of several types of tumors, and telomere shortening, with genetic anticipation in a number of genetic diseases including hereditary cancer syndromes. No conclusive studies have been performed for Lynch syndrome, a hereditary colorectal cancer syndrome caused by germline mutations in the DNA mismatch repair genes. Here we evaluate telomere length in Lynch syndrome, both as a cancer risk factor and as a mechanism associated with anticipation in the age of cancer onset observed in successive generations of Lynch syndrome families. Leukocyte telomere length was measured in 244 mismatch repair gene mutation carriers from 96 Lynch syndrome families and in 234 controls using a monochrome multiplex quantitative PCR method. Cancer-affected mutation carriers showed significantly shorter telomeres than cancer-free mutation carriers. In addition, cancer-affected carriers showed the most pronounced shortening of telomere length with age, compared with unaffected carriers. The anticipation in the age of cancer onset observed in successive generations was not associated with telomere shortening, although, interestingly, all mother-son pairs showed telomere shortening. In conclusion, cancer-affected mismatch repair gene mutation carriers have distinct telomere-length pattern and dynamics. However, anticipation in the age of onset is not explained by telomere shortening. Pending further study, our findings suggest that telomere attrition might explain the previously reported dependence of cancer risk on the parent-of-origin of mismatch repair gene mutations.
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Affiliation(s)
- Nuria Seguí
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology, IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain
| | - Ester Borràs
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Fernando Bellido
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology, IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- * E-mail:
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21
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Genetic variant in the telomerase gene modifies cancer risk in Lynch syndrome. Eur J Hum Genet 2012; 21:511-6. [PMID: 22948024 DOI: 10.1038/ejhg.2012.204] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lynch syndrome (LS) is an inherited cancer-predisposing disorder caused by germline mutations in the mismatch repair (MMR) genes. The high variability in individual cancer risk observed among LS patients suggests the existence of modifying factors. Identifying genetic modifiers of risk could help implement personalized surveillance programs based on predicted cancer risks. Here we evaluate the role of the telomerase (hTERT) rs2075786 SNP as a cancer-risk modifier in LS, studying 255 and 675 MMR gene mutation carriers from Spain and the Netherlands, respectively. The study of the Spanish sample revealed that the minor allele (A) confers increased cancer risk at an early age. The analysis of the Dutch sample confirmed the association of the A allele, especially in homozygosity, with increased cancer risk in mutation carriers under the age of 45 (relative riskLSca<45_AA=2.90; 95% confidence interval=1.02-8.26). Rs2075786 is associated with colorectal cancer (CRC) risk neither in the general population nor in non-Lynch CRC families. In silico studies predicted that the SNP causes the disruption of a transcription binding site for a retinoid receptor, retinoid X receptor alpha, probably causing early telomerase activation and therefore accelerated carcinogenesis. Notably, cancer-affected LS patients with the AA genotype have shorter telomeres than those with GG. In conclusion, MMR gene mutation carriers with hTERT rs2075786 are at high risk to develop a LS-related tumor at an early age. Cancer-preventive measures and stricter cancer surveillance at early ages might help prevent or early detect cancer in these mutation carriers.
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Mendez-Bermudez A, Royle NJ. Deficiency in DNA mismatch repair increases the rate of telomere shortening in normal human cells. Hum Mutat 2011; 32:939-46. [PMID: 21538690 DOI: 10.1002/humu.21522] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA mismatch repair (MMR) is essential for genome stability and inheritance of a mutated MMR gene, most frequently MSH2 or MLH1, results in cancer predisposition known as Lynch syndrome or hereditary nonpolyposis colorectal cancer (HNPCC). Tumors that arise through MMR deficiency show instability at simple tandem repeat loci (STRs) throughout the genome, known as microsatellite instability (MSI). The STR instability is dominated by errors that accumulate during replication in the absence of effective MMR. In this study we show that there is a high level of instability within telomeric DNA with a tendency toward deletions in tumor-derived MMR defective cell lines. We downregulated MSH2 expression in a normal fibroblast cell line and isolated four clones, with differing levels of MSH2 depletion. The telomere-shortening rate was measured at the Xp/Yp, 12q, and 17p telomeres in the MSH2 depleted and three control clones. Interestingly the mean telomere-shortening rate in the clones with MSH2 depletion was significantly greater than in the control clones. This is the first demonstration that MSH2 deficiency alone can lead to accelerated telomere shortening in normal human cells.
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23
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Wu X, Xu Y, Chai W, Her C. Causal link between microsatellite instability and hMRE11 dysfunction in human cancers. Mol Cancer Res 2011; 9:1443-8. [PMID: 21849470 DOI: 10.1158/1541-7786.mcr-11-0322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Maintenance of genomic integrity is essential for cell survival, and genomic instability is a commonly recognized intrinsic property of all cancers. Microsatellite instability (MSI) represents a frequently occurring and easily traceable simple form of sequence variation, signified by the contraction or expansion of specific DNA sequences containing short tandem repeats. MSI is frequently detected in tumor cells with DNA mismatch repair (MMR) deficiency. It is commonly conceived that instability at individual microsatellite loci can arise spontaneously in cells independent of MMR status, and different microsatellite loci are generally not affected uniformly by MMR deficiency. It is well recognized that MMR deficiency per se is not sufficient to initiate tumorigenesis; rather, the biological effects have to be exerted by mutations in genes controlling cell survival, DNA damage response, and apoptosis. Recently, shortening of an intronic hMRE11 poly(T)11 tract has been associated with MMR deficiency, raising the possibility that hMRE11 may be inactivated by defective MMR. However, the molecular nature underlying this association is presently unknown, and review of the current literature suggests that hMRE11 is most likely involved with the MMR pathway in a more complex fashion than simply being a MMR target gene. An alternative scenario is proposed to better reconcile the differences among various studies. The potential role of hMRE11 in telomere repeats stability is also discussed.
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Affiliation(s)
- Xiling Wu
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
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Telomere length measurement-caveats and a critical assessment of the available technologies and tools. Mutat Res 2011; 730:59-67. [PMID: 21663926 DOI: 10.1016/j.mrfmmm.2011.04.003] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/15/2011] [Accepted: 04/06/2011] [Indexed: 12/19/2022]
Abstract
Studies of telomeres and telomere biology often critically rely on the detection of telomeric DNA and measurements of the length of telomere repeats in either single cells or populations of cells. Several methods are available that provide this type of information and it is often not clear what method is most appropriate to address a specific research question. The major variables that need to be considered are the material that is or can be made available and the accuracy of measurements that is required. The goal of this review is to provide a comprehensive summary of the most commonly used methods and discuss the advantages and disadvantages of each. Methods that start with genomic DNA include telomere restriction fragment (TRF) length analysis, PCR amplification of telomere repeats relative to a single copy gene by Q-PCR or MMQPCR and single telomere length analysis (STELA), a PCR-based approach that accurately measures the full spectrum of telomere lengths from individual chromosomes. A different set of methods relies on fluorescent in situ hybridization (FISH) to detect telomere repeats in individual cells or chromosomes. By including essential calibration steps and appropriate controls these methods can be used to measure telomere repeat length or content in chromosomes and cells. Such methods include quantitative FISH (Q-FISH) and flow FISH which are based on digital microscopy and flow cytometry, respectively. Here the basic principles of various telomere length measurement methods are described and their strengths and weaknesses are highlighted. Some recent developments in telomere length analysis are also discussed. The information in this review should facilitate the selection of the most suitable method to address specific research question about telomeres in either model organisms or human subjects.
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Abstract
G-quadruplex structures formed by DNA at the human telomeres are attractive anticancer targets. Human telomeric sequences can adopt a diverse range of intramolecular G-quadruplex conformations: a parallel-stranded conformation was observed in the crystalline state, while at least four other forms were seen in K(+) solution, raising the question of which conformation is favored in crowded cellular environment. Here, we report the first NMR structure of a human telomeric G-quadruplex in crowded solution. We show that four different G-quadruplex conformations are converted to a propeller-type parallel-stranded G-quadruplex in K(+)-containing crowded solution due to water depletion. This study also reveals the formation of a new higher-order G-quadruplex structure under molecular crowding conditions. Our molecular dynamics simulations of solvent distribution provide insights at molecular level on the formation of parallel-stranded G-quadruplex in environment depleted of water. These results regarding human telomeric DNA can be extended to oncogenic promoters and other genomic G-rich sequences.
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Affiliation(s)
- Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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TCAGG, an alternative telomeric sequence in insects. Chromosoma 2011; 120:367-76. [PMID: 21499744 DOI: 10.1007/s00412-011-0317-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 03/06/2011] [Accepted: 03/06/2011] [Indexed: 10/18/2022]
Abstract
The TTAGG repeat, the only determined telomerase-dependent sequence in the Insecta, is generally reputed to be the canonical telomeric motif within the class. By studying the distribution of telomeric DNAs in 30 coleopteran beetles using Southern hybridization, BAL 31 DNA end-degradation assay and fluorescence in situ hybridization, we showed that arrays built of a TCAGG repeat substitute for (TTAGG)n sequences in all tested species within the superfamily Tenebrionoidea. We also provided the experimental evidence that (TCAGG)n repeats represent the terminal sequences on all chromosomes of the model species Tribolium castaneum. (TCAGG)n repeats are therefore promoted as the first sequence-motif alternative to TTAGG-type chromosome ends in insects. Detection of species negative for both TTAGG and TCAGG reveals that, although widespread, these motifs are not ubiquitous telomeric sequences within the order Coleoptera. In addition, Timarcha balearica proved to be a species that harbors (TTAGG)n repeats, but not at telomeric positions, thus further increasing the complexity of telomeric DNAs. Our experiments discarded CTAGG, CTGGG, TTGGG, and TTAGGG variants as potential replacements in TTAGG/TCAGG-negative species, indicating that chromosome termini of these beetles comprise other form(s) of telomeric sequences and telomere maintenance mechanisms.
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Bertrand H, Granzhan A, Monchaud D, Saettel N, Guillot R, Clifford S, Guédin A, Mergny J, Teulade‐Fichou M. Recognition of G‐Quadruplex DNA by Triangular Star‐Shaped Compounds: With or Without Side Chains? Chemistry 2011; 17:4529-39. [DOI: 10.1002/chem.201002810] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 01/03/2011] [Indexed: 12/12/2022]
Affiliation(s)
- Hélène Bertrand
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
| | - Anton Granzhan
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
| | - David Monchaud
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
- Current address: Institut de Chimie Moléculaire, CNRS UMR5260, Université de Bourgogne (ICMUB), Faculté des Sciences Mirande, 9, Avenue Alain Savary, 21000 Dijon (France)
| | - Nicolas Saettel
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, CNRS UMR8182, Université Paris Sud XI, Bât. 420, 91405 Orsay (France)
| | - Sarah Clifford
- Département de chimie minérale, analytique et appliquée Université de Genève, quai Ernest‐Ansermet 30, 1211 Genève 4 (Switzerland)
| | - Aurore Guédin
- Laboratoire des Régulations et Dynamique du Génome, INSERM U565, CNRS UMR5153, Muséum National d'Histoire Naturelle, 43, Rue Cuvier, 75005 Paris (France)
- INSERM U869, Université de Bordeaux, Institut Européen de Chimie et Biologie, 2, Rue Robert Escarpit, 33607 Pessac (France)
| | - Jean‐Louis Mergny
- Laboratoire des Régulations et Dynamique du Génome, INSERM U565, CNRS UMR5153, Muséum National d'Histoire Naturelle, 43, Rue Cuvier, 75005 Paris (France)
- INSERM U869, Université de Bordeaux, Institut Européen de Chimie et Biologie, 2, Rue Robert Escarpit, 33607 Pessac (France)
| | - Marie‐Paule Teulade‐Fichou
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
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28
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Abstract
Telomeres play an important role in cellular aging and cancer. Human telomeric DNA and RNA G-rich sequences are capable of forming a four-stranded structure, known as the G-quadruplex. Such a structure might be important for telomere biology and a good target for drug design. This minireview describes the structural diversity or conservation of DNA and RNA human telomeric G-quadruplexes, discusses structural views on targeting these G-quadruplexes and presents some future challenges for structural studies.
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Affiliation(s)
- Anh Tuân Phan
- Division of Physics & Applied Physics, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore.
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Lim KW, Alberti P, Guédin A, Lacroix L, Riou JF, Royle NJ, Mergny JL, Phan AT. Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G.C.G.C tetrad. Nucleic Acids Res 2009; 37:6239-48. [PMID: 19692585 PMCID: PMC2764449 DOI: 10.1093/nar/gkp630] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Short contiguous arrays of variant CTAGGG repeats in the human telomere are unstable in the male germline and somatic cells, suggesting formation of unusual structures by this repeat type. Here, we report on the structure of an intramolecular G-quadruplex formed by DNA sequences containing four human telomeric variant CTAGGG repeats in potassium solution. Our results reveal a new robust antiparallel G-quadruplex fold involving two G-tetrads sandwiched between a G.C base pair and a G.C.G.C tetrad, which could represent a new platform for drug design targeted to human telomeric DNA.
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Affiliation(s)
- Kah Wai Lim
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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