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Prušáková D, Peska V, Pekár S, Bubeník M, Čížek L, Bezděk A, Čapková Frydrychová R. Telomeric DNA sequences in beetle taxa vary with species richness. Sci Rep 2021; 11:13319. [PMID: 34172809 PMCID: PMC8233369 DOI: 10.1038/s41598-021-92705-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Telomeres are protective structures at the ends of eukaryotic chromosomes, and disruption of their nucleoprotein composition usually results in genome instability and cell death. Telomeric DNA sequences have generally been found to be exceptionally conserved in evolution, and the most common pattern of telomeric sequences across eukaryotes is (TxAyGz)n maintained by telomerase. However, telomerase-added DNA repeats in some insect taxa frequently vary, show unusual features, and can even be absent. It has been speculated about factors that might allow frequent changes in telomere composition in Insecta. Coleoptera (beetles) is the largest of all insect orders and based on previously available data, it seemed that the telomeric sequence of beetles varies to a great extent. We performed an extensive mapping of the (TTAGG)n sequence, the ancestral telomeric sequence in Insects, across the main branches of Coleoptera. Our study indicates that the (TTAGG)n sequence has been repeatedly or completely lost in more than half of the tested beetle superfamilies. Although the exact telomeric motif in most of the (TTAGG)n-negative beetles is unknown, we found that the (TTAGG)n sequence has been replaced by two alternative telomeric motifs, the (TCAGG)n and (TTAGGG)n, in at least three superfamilies of Coleoptera. The diversity of the telomeric motifs was positively related to the species richness of taxa, regardless of the age of the taxa. The presence/absence of the (TTAGG)n sequence highly varied within the Curculionoidea, Chrysomeloidea, and Staphylinoidea, which are the three most diverse superfamilies within Metazoa. Our data supports the hypothesis that telomere dysfunctions can initiate rapid genomic changes that lead to reproductive isolation and speciation.
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Affiliation(s)
- Daniela Prušáková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Michal Bubeník
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Lukáš Čížek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Bezděk
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Radmila Čapková Frydrychová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
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2
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Regulated expression of the lncRNA TERRA and its impact on telomere biology. Mech Ageing Dev 2017; 167:16-23. [PMID: 28888705 DOI: 10.1016/j.mad.2017.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/21/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022]
Abstract
The telomere protects against genomic instability by minimizing the accelerated end resection of the genetic material, a phenomenon that results in severe chromosome instability that could favor the transformation of a cell by enabling the emergence of tumor-promoting mutations. Some mechanisms that avoid this fate, such as capping and loop formation, have been very well characterized; however, telomeric non-coding transcripts, such as long non-coding RNAs (lncRNAs), should also be considered in this context because they play roles in the organization of telomere dynamics, involving processes such as replication, degradation, extension, and heterochromatin stabilization. Although the mechanism through which the expression of telomeric transcripts regulates telomere dynamics is not yet clear, a non-coding RNA component opens the research options in telomere biology and the impact that it can have on telomere-associated diseases such as cancer.
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Paudyal SC, You Z. Sharpening the ends for repair: mechanisms and regulation of DNA resection. Acta Biochim Biophys Sin (Shanghai) 2016; 48:647-57. [PMID: 27174871 DOI: 10.1093/abbs/gmw043] [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: 01/31/2016] [Accepted: 04/12/2016] [Indexed: 12/23/2022] Open
Abstract
DNA end resection is a key process in the cellular response to DNA double-strand break damage that is essential for genome maintenance and cell survival. Resection involves selective processing of 5' ends of broken DNA to generate ssDNA overhangs, which in turn control both DNA repair and checkpoint signaling. DNA resection is the first step in homologous recombination-mediated repair and a prerequisite for the activation of the ataxia telangiectasia mutated and Rad3-related (ATR)-dependent checkpoint that coordinates repair with cell cycle progression and other cellular processes. Resection occurs in a cell cycle-dependent manner and is regulated by multiple factors to ensure an optimal amount of ssDNA required for proper repair and genome stability. Here, we review the latest findings on the molecular mechanisms and regulation of the DNA end resection process and their implications for cancer formation and treatment.
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Affiliation(s)
- Sharad C Paudyal
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO 63110, USA
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4
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Rice C, Skordalakes E. Structure and function of the telomeric CST complex. Comput Struct Biotechnol J 2016; 14:161-7. [PMID: 27239262 PMCID: PMC4872678 DOI: 10.1016/j.csbj.2016.04.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 11/25/2022] Open
Abstract
Telomeres comprise the ends of eukaryotic chromosomes and are essential for cell proliferation and genome maintenance. Telomeres are replicated by telomerase, a ribonucleoprotein (RNP) reverse transcriptase, and are maintained primarily by nucleoprotein complexes such as shelterin (TRF1, TRF2, TIN2, RAP1, POT1, TPP1) and CST (Cdc13/Ctc1, Stn1, Ten1). The focus of this review is on the CST complex and its role in telomere maintenance. Although initially thought to be unique to yeast, it is now evident that the CST complex is present in a diverse range of organisms where it contributes to genome maintenance. The CST accomplishes these tasks via telomere capping and by regulating telomerase and DNA polymerase alpha-primase (polα-primase) access to telomeres, a process closely coordinated with the shelterin complex in most organisms. The goal of this review is to provide a brief but comprehensive account of the diverse, and in some cases organism-dependent, functions of the CST complex and how it contributes to telomere maintenance and cell proliferation.
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Fission Yeast Exo1 and Rqh1-Dna2 Redundantly Contribute to Resection of Uncapped Telomeres. PLoS One 2015; 10:e0140456. [PMID: 26465752 PMCID: PMC4605587 DOI: 10.1371/journal.pone.0140456] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 09/25/2015] [Indexed: 01/01/2023] Open
Abstract
The uncapping of telomeres induces a DNA damage response. In Schizosaccharomyces pombe, deletion of pot1+ causes telomere uncapping and rapid telomere resection, resulting in chromosome fusion. Using the nmt-pot1-aid strain, we previously reported that Pot1 shut-off causes telomere loss and chromosome fusion in S. pombe. However, the factors responsible for the resection of uncapped telomeres remain unknown. In this study, we investigated these factors and found that concomitant deletion of rqh1+ and exo1+ alleviated the loss of telomeres following Pot1 shut-off, suggesting that Rqh1 and Exo1 are redundantly involved in the resection of uncapped telomeres. We also investigated the role of Rqh1 helicase activity and found it to be essential for the resection of uncapped telomeres. Moreover, we found that Dna2 and Exo1 function redundantly in the resection of uncapped telomeres. Taken together, these results suggest that Exo1 and Rqh1-Dna2 redundantly contribute to the resection of uncapped telomeres. Therefore, our results demonstrate that nmt-pot1-aid is an important model strain to study the role of helicases and nucleases in the resection of uncapped telomeres and to improve our understanding of DNA double-strand break repair.
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6
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Mind the gap; seven reasons to close fragmented genome assemblies. Fungal Genet Biol 2015; 90:24-30. [PMID: 26342853 DOI: 10.1016/j.fgb.2015.08.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions.
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Gobbini E, Trovesi C, Cassani C, Longhese MP. Telomere uncapping at the crossroad between cell cycle arrest and carcinogenesis. Mol Cell Oncol 2014; 1:e29901. [PMID: 27308311 PMCID: PMC4905175 DOI: 10.4161/mco.29901] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/24/2014] [Accepted: 06/30/2014] [Indexed: 01/24/2023]
Abstract
Telomeres are nucleoprotein complexes that protect the natural ends of chromosomes from fusion and degradation and prevent them eliciting a checkpoint response. This protective function, which is called telomere capping, is largely mediated by telomere-binding proteins that suppress checkpoint activation and DNA repair activities. Telomere dysfunction through progressive shortening or removal of capping proteins leads to a checkpoint-mediated block of cell proliferation, which acts as a cancer-suppressor mechanism. However, genetic alterations that inactivate the checkpoint can lead to further telomere erosion and increased genomic instability that, coupled with the activation of mechanisms to restabilize telomeres, can drive the oncogenic process.
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Affiliation(s)
- Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze; Università degli Studi di Milano-Bicocca; Milano, Italia
| | - Camilla Trovesi
- Dipartimento di Biotecnologie e Bioscienze; Università degli Studi di Milano-Bicocca; Milano, Italia
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze; Università degli Studi di Milano-Bicocca; Milano, Italia
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze; Università degli Studi di Milano-Bicocca; Milano, Italia
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8
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Telomere recombination preferentially occurs at short telomeres in telomerase-null type II survivors. PLoS One 2014; 9:e90644. [PMID: 24594632 PMCID: PMC3940914 DOI: 10.1371/journal.pone.0090644] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 02/03/2014] [Indexed: 01/17/2023] Open
Abstract
In telomerase negative yeast cells, Rad52-dependent recombination is activated to maintain telomeres. This recombination-mediated telomere elongation usually involves two independent pathways, type I and type II, and leads to generation of type I and type II survivors. It remains elusive whether the recombination-mediated telomere elongation prefers to take place on shorter or longer telomeres. In this study, we exploited the de novo telomere addition system to examine the telomere recombination event in telomerase negative cells. We show that recombination preferentially occurs on shorter rather than longer telomeres in both pre-survivors and established type II survivors. In type II survivors, the short VII–L telomeres could invade either terminal TG1–3 sequence or short tracts of TG1–3 sequence in subtelomeric Y′-X and Y′-Y′ junction to initiate recombination. Unexpectedly, short VII–L telomere recombination still takes place in type II survivors lacking either Rad50 or Rad59, which are required for type II survivor generation in senescing telomerase-null cells. Our results support the notion that Rad50 and Rad59 are not essential for the maintenance of type II survivors once established.
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Ribeyre C, Shore D. Regulation of telomere addition at DNA double-strand breaks. Chromosoma 2013; 122:159-73. [DOI: 10.1007/s00412-013-0404-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/28/2013] [Accepted: 03/04/2013] [Indexed: 12/11/2022]
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Nelson ADL, Shippen DE. Surprises from the chromosome front: lessons from Arabidopsis on telomeres and telomerase. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2013; 77:7-15. [PMID: 23460576 DOI: 10.1101/sqb.2013.77.017053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Telomeres serve two vital functions: They act as a buffer against the end-replication problem, and they prevent chromosome ends from being recognized as double-strand DNA (dsDNA) breaks. These functions are orchestrated by the telomerase reverse transcriptase and a variety of telomere protein complexes. Here, we discuss our recent studies with Arabidopsis thaliana that uncovered a new and highly conserved telomere complex called CST (Cdc13/CTC1, STN1, TEN1). Formerly believed to be yeast specific, CST has now been identified as a key component of both plant and vertebrate telomeres, which is essential for genome integrity and stem cell viability. We also describe the unexpected discovery of alternative telomerase ribonucleoprotein complexes in Arabidopsis. Fueled by duplication and diversification of the telomerase RNA subunit and telomerase accessory proteins, these telomerase complexes act in concert to maintain genome stability. In addition to the canonical telomerase enzyme, one of two alternative telomerase ribonucleoprotein (RNP) complexes functions as a novel negative regulator of enzyme activity in response to genotoxic stress. These contributions highlight the immense potential of Arabidopsis in probing the depths of the chromosome end.
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Affiliation(s)
- A D L Nelson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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11
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Londoño-Vallejo JA, Wellinger RJ. Telomeres and telomerase dance to the rhythm of the cell cycle. Trends Biochem Sci 2012; 37:391-9. [PMID: 22727244 DOI: 10.1016/j.tibs.2012.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Revised: 05/21/2012] [Accepted: 05/25/2012] [Indexed: 11/27/2022]
Abstract
The stability of the ends of linear eukaryotic chromosomes is ensured by functional telomeres, which are composed of short, species-specific direct repeat sequences. The maintenance of telomeres depends on a specialized ribonucleoprotein (RNP) called telomerase. Both telomeres and telomerase are dynamic entities with different physical behaviors and, given their substrate-enzyme relation, they must establish a productive interaction. Regulatory mechanisms controlling this interaction are key missing elements in our understanding of telomere functions. Here, we review the dynamic properties of telomeres and the maturing telomerase RNPs, and summarize how tracking the timing of their dance during the cell cycle will yield insights into chromosome stability mechanisms. Cancer cells often display loss of genome integrity; therefore, these issues are of particular interest for our understanding of cancer initiation or progression.
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Affiliation(s)
- J Arturo Londoño-Vallejo
- Laboratoire Télomères et Cancer, UMR3244, Institut Curie, 26 rue d'Ulm, 75248 Paris, France; UPMC Université Paris 06, F-75005 Paris, France
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12
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Ribaud V, Ribeyre C, Damay P, Shore D. DNA-end capping by the budding yeast transcription factor and subtelomeric binding protein Tbf1. EMBO J 2011; 31:138-49. [PMID: 21952045 DOI: 10.1038/emboj.2011.349] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 09/01/2011] [Indexed: 11/09/2022] Open
Abstract
Telomere repeats in budding yeast are maintained at a constant average length and protected ('capped'), in part, by mechanisms involving the TG(1-3) repeat-binding protein Rap1. However, metazoan telomere repeats (T(2)AG(3)) can be maintained in yeast through a Rap1-independent mechanism. Here, we examine the dynamics of capping and telomere formation at an induced DNA double-strand break flanked by varying lengths of T(2)AG(3) repeats. We show that a 60-bp T(2)AG(3) repeat array induces a transient G2/M checkpoint arrest, but is rapidly elongated by telomerase to generate a stable T(2)AG(3)/TG(1-3) hybrid telomere. In contrast, a 230-bp T(2)AG(3) array induces neither G2/M arrest nor telomerase elongation. This capped state requires the T(2)AG(3)-binding protein Tbf1, but is independent of two Tbf1-interacting factors, Vid22 and Ygr071c. Arrays of binding sites for three other subtelomeric or Myb/SANT domain-containing proteins fail to display a similar end-protection effect, indicating that Tbf1 capping is an evolved function. Unexpectedly, we observed strong telomerase association with non-telomeric ends, whose elongation is blocked by a Mec1-dependent mechanism, apparently acting at the level of Cdc13 binding.
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Affiliation(s)
- Virginie Ribaud
- Department of Molecular Biology, NCCR Program Frontiers in Genetics, University of Geneva, Geneva, Switzerland
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Recombination can either help maintain very short telomeres or generate longer telomeres in yeast cells with weak telomerase activity. EUKARYOTIC CELL 2011; 10:1131-42. [PMID: 21666075 DOI: 10.1128/ec.05079-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Yeast mutants lacking telomerase are able to elongate their telomeres through processes involving homologous recombination. In this study, we investigated telomeric recombination in several mutants that normally maintain very short telomeres due to the presence of a partially functional telomerase. The abnormal colony morphology present in some mutants was correlated with especially short average telomere length and with a requirement for RAD52 for indefinite growth. Better-growing derivatives of some of the mutants were occasionally observed and were found to have substantially elongated telomeres. These telomeres were composed of alternating patterns of mutationally tagged telomeric repeats and wild-type repeats, an outcome consistent with amplification occurring via recombination rather than telomerase. Our results suggest that recombination at telomeres can produce two distinct outcomes in the mutants we studied. In occasional cells, recombination generates substantially longer telomeres, apparently through the roll-and-spread mechanism. However, in most cells, recombination appears limited to helping to maintain very short telomeres. The latter outcome likely represents a simplified form of recombinational telomere maintenance that is independent of the generation and copying of telomeric circles.
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Polo SE, Jackson SP. Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev 2011; 25:409-33. [PMID: 21363960 DOI: 10.1101/gad.2021311] [Citation(s) in RCA: 837] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genome integrity is constantly monitored by sophisticated cellular networks, collectively termed the DNA damage response (DDR). A common feature of DDR proteins is their mobilization in response to genotoxic stress. Here, we outline how the development of various complementary methodologies has provided valuable insights into the spatiotemporal dynamics of DDR protein assembly/disassembly at sites of DNA strand breaks in eukaryotic cells. Considerable advances have also been made in understanding the underlying molecular mechanisms for these events, with post-translational modifications of DDR factors being shown to play prominent roles in controlling the formation of foci in response to DNA-damaging agents. We review these regulatory mechanisms and discuss their biological significance to the DDR.
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Affiliation(s)
- Sophie E Polo
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB21QN, United Kingdom
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