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Bedet C, Quarato P, Palladino F, Cecere G, Robert VJ. The C. elegans SET1 histone methyltransferase SET-2 is not required for transgenerational memory of silencing. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001143. [PMID: 38808193 PMCID: PMC11130714 DOI: 10.17912/micropub.biology.001143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/22/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
Abstract
The SET-2 /SET1 histone H3K4 methyltransferase and RNAi pathway components are required to maintain fertility across generations in C. elegans . SET-2 preserves the germline transcriptional program transgenerationally, and RNAi pathways rely on small RNAs to establish and maintain transgenerational gene silencing. We investigated whether the functionality of RNAi-induced transgenerational silencing and the composition of pools of endogenous small RNA are affected by the absence of SET-2 . Our results suggest that defects in RNAi pathways are not responsible for the transcriptional misregulation observed in the absence of SET-2 .
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Affiliation(s)
- Cécile Bedet
- Ecole Normale Supérieure de Lyon, Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, Inserm U1293, University Claude Bernard Lyon 1, 69007 Lyon, France Auvergne-Rhône-Alpes, France
| | - Piergiuseppe Quarato
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, Paris, France
- Current address: San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Palladino
- Ecole Normale Supérieure de Lyon, Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, Inserm U1293, University Claude Bernard Lyon 1, 69007 Lyon, France Auvergne-Rhône-Alpes, France
| | - Germano Cecere
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, Paris, France
| | - Valérie J Robert
- Ecole Normale Supérieure de Lyon, Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, Inserm U1293, University Claude Bernard Lyon 1, 69007 Lyon, France Auvergne-Rhône-Alpes, France
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2
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Henriques CM, Ferreira MG. Telomere length is an epigenetic trait - Implications for the use of telomerase-deficient organisms to model human disease. Dis Model Mech 2024; 17:dmm050581. [PMID: 38441152 PMCID: PMC10941657 DOI: 10.1242/dmm.050581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Telomere length, unlike most genetic traits, is epigenetic, in the sense that it is not fully coded by the genome. Telomeres vary in length and randomly assort to the progeny leaving some individuals with longer and others with shorter telomeres. Telomerase activity counteracts this by extending telomeres in the germline and during embryogenesis but sizeable variances remain in telomere length. This effect is exacerbated by the absence of fully active telomerase. Telomerase heterozygous animals (tert+/-) have reduced telomerase activity and their telomeres fail to be elongated to wild-type average length, meaning that - with every generation - they decrease. After a given number of successive generations of telomerase-insufficient crosses, telomeres become critically short and cause organismal defects that, in humans, are known as telomere biology disorders. Importantly, these defects also occur in wild-type (tert+/+) animals derived from such tert+/- incrosses. Despite these tert+/+ animals being proficient for telomerase, they have shorter than average telomere length and, although milder, develop phenotypes that are similar to those of telomerase mutants. Here, we discuss the impact of this phenomenon on human pathologies associated with telomere length, provide a brief overview of telomere biology across species and propose specific measures for working with telomerase-deficient zebrafish.
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Affiliation(s)
- Catarina M. Henriques
- The Bateson Centre, MRC-Arthritis Research UK Centre for Integrated Research Into Musculoskeletal Ageing (CIMA) and Healthy Lifespan Institute (HELSI), School of Medicine and Population Health, University of Sheffield, Sheffield S10 2TN, UK
| | - Miguel Godinho Ferreira
- Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR7284, INSERM U1081, Université Côte d‘Azur, 06107 Nice, France
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3
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Lasho T, Patnaik MM. Adaptive and Maladaptive Clonal Hematopoiesis in Telomere Biology Disorders. Curr Hematol Malig Rep 2024; 19:35-44. [PMID: 38095828 DOI: 10.1007/s11899-023-00719-2] [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] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
PURPOSE OF REVIEW Telomere biology disorders (TBDs) are germline-inherited conditions characterized by reduction in telomerase function, accelerated shortening of telomeres, predisposition to organ-failure syndromes, and increased risk of neoplasms, especially myeloid malignancies. In normal cells, critically short telomeres trigger apoptosis and/or cellular senescence. However, the evolutionary mechanism by which TBD-related telomerase-deficient cells can overcome this fitness constraint remains elusive. RECENT FINDINGS Preliminary data suggests the existence of adaptive somatic mosaic states characterized by variants in TBD-related genes and maladaptive somatic mosaic states that attempt to overcome hematopoietic fitness constraints by alternative methods leading to clonal hematopoiesis. TBDs are both rare and highly heterogeneous in presentation, and the association of TBD with malignant transformation is unclear. Understanding the clonal complexity and mechanisms behind TBD-associated molecular signatures that lead to somatic adaptation in the setting of defective hematopoiesis will help inform therapy and treatment for this set of diseases.
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Affiliation(s)
- Terra Lasho
- Division of Hematology, Mayo Clinic Rochester, 200 First Street SW, Rochester, MN, 55905, USA
| | - Mrinal M Patnaik
- Division of Hematology, Mayo Clinic Rochester, 200 First Street SW, Rochester, MN, 55905, USA.
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4
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Lim J, Kim W, Kim J, Lee J. Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures. Genome Res 2023; 33:1947-1957. [PMID: 37918961 PMCID: PMC10760449 DOI: 10.1101/gr.278124.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Telomeres are composed of tandem arrays of telomeric-repeat motifs (TRMs) and telomere-binding proteins (TBPs), which are responsible for ensuring end-protection and end-replication of chromosomes. TRMs are highly conserved owing to the sequence specificity of TBPs, although significant alterations in TRM have been observed in several taxa, except Nematoda. We used public whole-genome sequencing data sets to analyze putative TRMs of 100 nematode species and determined that three distinct branches included specific novel TRMs, suggesting that evolutionary alterations in TRMs occurred in Nematoda. We focused on one of the three branches, the Panagrolaimidae family, and performed a de novo assembly of four high-quality draft genomes of the canonical (TTAGGC) and novel TRM (TTAGAC) isolates; the latter genomes revealed densely clustered arrays of the novel TRM. We then comprehensively analyzed the subtelomeric regions of the genomes to infer how the novel TRM evolved. We identified DNA damage-repair signatures in subtelomeric sequences that were representative of consequences of telomere maintenance mechanisms by alternative lengthening of telomeres. We propose a hypothetical scenario in which TTAGAC-containing units are clustered in subtelomeric regions and pre-existing TBPs capable of binding both canonical and novel TRMs aided the evolution of the novel TRM in the Panagrolaimidae family.
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Affiliation(s)
- Jiseon Lim
- Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Wonjoo Kim
- Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea;
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, South Korea
- Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, South Korea
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5
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Manzato C, Larini L, Oss Pegorar C, Dello Stritto MR, Jurikova K, Jantsch V, Cusanelli E. TERRA expression is regulated by the telomere-binding proteins POT-1 and POT-2 in Caenorhabditis elegans. Nucleic Acids Res 2023; 51:10681-10699. [PMID: 37713629 PMCID: PMC10602879 DOI: 10.1093/nar/gkad742] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023] Open
Abstract
Several aspects of telomere biology are regulated by the telomeric repeat-containing RNA TERRA. While TERRA expression is conserved through evolution, species-specific mechanisms regulate its biogenesis and function. Here we report on the expression of TERRA in Caenorhabditis elegans. We show that C. elegans TERRA is regulated by the telomere-binding proteins POT-1 and POT-2 which repress TERRA in a telomere-specific manner. C. elegans TERRA transcripts are heterogeneous in length and form discrete nuclear foci, as detected by RNA FISH, in both postmitotic and germline cells; a fraction of TERRA foci localizes to telomeres. Interestingly, in germ cells, TERRA is expressed in all stages of meiotic prophase I, and it increases during pachytene, a stage in meiosis when homologous recombination is ongoing. We used the MS2-GFP system to study the spatiotemporal dynamics of single-telomere TERRA molecules. Single particle tracking revealed different types of motilities, suggesting complex dynamics of TERRA transcripts. Finally, we unveiled distinctive features of C. elegans TERRA, which is regulated by telomere shortening in a telomere-specific manner, and it is upregulated in the telomerase-deficient trt-1; pot-2 double mutant prior to activation of the alternative lengthening mechanism ALT. Interestingly, in these worms TERRA displays distinct dynamics with a higher fraction of fast-moving particles.
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Affiliation(s)
- Caterina Manzato
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Luca Larini
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Claudio Oss Pegorar
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Maria Rosaria Dello Stritto
- Department of Chromosome Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter 1030, Vienna, Austria
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina 84215, Bratislava, Slovakia
| | - Verena Jantsch
- Department of Chromosome Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter 1030, Vienna, Austria
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
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6
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Lue NF, Autexier C. Orchestrating nucleic acid-protein interactions at chromosome ends: telomerase mechanisms come into focus. Nat Struct Mol Biol 2023; 30:878-890. [PMID: 37400652 PMCID: PMC10539978 DOI: 10.1038/s41594-023-01022-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 05/16/2023] [Indexed: 07/05/2023]
Abstract
Telomerase is a special reverse transcriptase ribonucleoprotein dedicated to the synthesis of telomere repeats that protect chromosome ends. Among reverse transcriptases, telomerase is unique in using a stably associated RNA with an embedded template to synthesize a specified sequence. Moreover, it is capable of iteratively copying the same template region (repeat addition processivity) through multiple rounds of RNA-DNA unpairing and reannealing, that is, the translocation reaction. Biochemical analyses of telomerase over the past 3 decades in protozoa, fungi and mammals have identified structural elements that underpin telomerase mechanisms and have led to models that account for the special attributes of telomerase. Notably, these findings and models can now be interpreted and adjudicated through recent cryo-EM structures of Tetrahymena and human telomerase holoenzyme complexes in association with substrates and regulatory proteins. Collectively, these structures reveal the intricate protein-nucleic acid interactions that potentiate telomerase's unique translocation reaction and clarify how this enzyme reconfigures the basic reverse transcriptase scaffold to craft a polymerase dedicated to the synthesis of telomere DNA. Among the many new insights is the resolution of the telomerase 'anchor site' proposed more than 3 decades ago. The structures also highlight the nearly universal conservation of a protein-protein interface between an oligonucleotide/oligosaccharide-binding (OB)-fold regulatory protein and the telomerase catalytic subunit, which enables spatial and temporal regulation of telomerase function in vivo. In this Review, we discuss key features of the structures in combination with relevant functional analyses. We also examine conserved and divergent aspects of telomerase mechanisms as gleaned from studies in different model organisms.
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Affiliation(s)
- Neal F Lue
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
| | - Chantal Autexier
- Lady Davis Institute for Medical Research, Jewish General Hospital and Department of Anatomy and Cell Biology and Department of Medicine, McGill University, Montreal, Quebec, Canada.
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7
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Cerón J. Caenorhabditis elegans for research on cancer hallmarks. Dis Model Mech 2023; 16:dmm050079. [PMID: 37278614 PMCID: PMC10259857 DOI: 10.1242/dmm.050079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023] Open
Abstract
After decades of research, our knowledge of the complexity of cancer mechanisms, elegantly summarized as 'hallmarks of cancer', is expanding, as are the therapeutic opportunities that this knowledge brings. However, cancer still needs intense research to diminish its tremendous impact. In this context, the use of simple model organisms such as Caenorhabditis elegans, in which the genetics of the apoptotic pathway was discovered, can facilitate the investigation of several cancer hallmarks. Amenable for genetic and drug screens, convenient for fast and efficient genome editing, and aligned with the 3Rs ('Replacement, Reduction and Refinement') principles for ethical animal research, C. elegans plays a significant role in unravelling the intricate network of cancer mechanisms and presents a promising option in clinical diagnosis and drug discovery.
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Affiliation(s)
- Julián Cerón
- Modeling Human Diseases in C. elegans Group – Genes, Disease and Therapy Program, Bellvitge Biomedical Research Institute – IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
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8
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Abstract
The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.
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Affiliation(s)
- Peter M Carlton
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO 80045, USA.,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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9
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Watson JM, Trieb J, Troestl M, Renfrew K, Mandakova T, Fulnecek J, Shippen DE, Riha K. A hypomorphic allele of telomerase uncovers the minimal functional length of telomeres in Arabidopsis. Genetics 2021; 219:6339584. [PMID: 34849882 DOI: 10.1093/genetics/iyab126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 07/23/2021] [Indexed: 12/23/2022] Open
Abstract
Despite the essential requirement of telomeric DNA for genome stability, the length of telomere tracts between species substantially differs, raising the question of the minimal length of telomeric DNA necessary for proper function. Here, we address this question using a hypomorphic allele of the telomerase catalytic subunit, TERT. We show that although this construct partially restored telomerase activity to a tert mutant, telomeres continued to shorten over several generations, ultimately stabilizing at a bimodal size distribution. Telomeres on two chromosome arms were maintained at a length of 1 kb, while the remaining telomeres were maintained at 400 bp. The longest telomeres identified in this background were also significantly longer in wild-type populations, suggesting cis-acting elements on these arms either promote telomerase processivity or recruitment. Genetically disrupting telomerase processivity in this background resulted in immediate lethality. Thus, telomeres of 400 bp are both necessary and sufficient for Arabidopsis viability. As this length is the estimated minimal length for t-loop formation, our data suggest that telomeres long enough to form a t-loop constitute the minimal functional length.
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Affiliation(s)
- J Matthew Watson
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Johanna Trieb
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Martina Troestl
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Kyle Renfrew
- Department of Biochemistry, Texas A&M University, College Station, TX 77840, USA
| | - Terezie Mandakova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Jaroslav Fulnecek
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Dorothy E Shippen
- Department of Biochemistry, Texas A&M University, College Station, TX 77840, USA
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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10
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The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1. Nat Commun 2021; 12:2668. [PMID: 33976151 PMCID: PMC8113555 DOI: 10.1038/s41467-021-22861-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
Telomeres are bound by dedicated proteins, which protect them from DNA damage and regulate telomere length homeostasis. In the nematode Caenorhabditis elegans, a comprehensive understanding of the proteins interacting with the telomere sequence is lacking. Here, we harnessed a quantitative proteomics approach to identify TEBP-1 and TEBP-2, two paralogs expressed in the germline and embryogenesis that associate to telomeres in vitro and in vivo. tebp-1 and tebp-2 mutants display strikingly distinct phenotypes: tebp-1 mutants have longer telomeres than wild-type animals, while tebp-2 mutants display shorter telomeres and a Mortal Germline. Notably, tebp-1;tebp-2 double mutant animals have synthetic sterility, with germlines showing signs of severe mitotic and meiotic arrest. Furthermore, we show that POT-1 forms a telomeric complex with TEBP-1 and TEBP-2, which bridges TEBP-1/-2 with POT-2/MRT-1. These results provide insights into the composition and organization of a telomeric protein complex in C. elegans.
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11
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Spichal M, Heestand B, Billmyre KK, Frenk S, Mello CC, Ahmed S. Germ granule dysfunction is a hallmark and mirror of Piwi mutant sterility. Nat Commun 2021; 12:1420. [PMID: 33658512 PMCID: PMC7930041 DOI: 10.1038/s41467-021-21635-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/29/2021] [Indexed: 01/31/2023] Open
Abstract
In several species, Piwi/piRNA genome silencing defects cause immediate sterility that correlates with transposon expression and transposon-induced genomic instability. In C. elegans, mutations in the Piwi-related gene (prg-1) and other piRNA deficient mutants cause a transgenerational decline in fertility over a period of several generations. Here we show that the sterility of late generation piRNA mutants correlates poorly with increases in DNA damage signaling. Instead, sterile individuals consistently exhibit altered perinuclear germ granules. We show that disruption of germ granules does not activate transposon expression but induces multiple phenotypes found in sterile prg-1 pathway mutants. Furthermore, loss of the germ granule component pgl-1 enhances prg-1 mutant infertility. Environmental restoration of germ granule function for sterile pgl-1 mutants restores their fertility. We propose that Piwi mutant sterility is a reproductive arrest phenotype that is characterized by perturbed germ granule structure and is phenocopied by germ granule dysfunction, independent of genomic instability.
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Affiliation(s)
- Maya Spichal
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA
| | - Bree Heestand
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA
| | - Katherine Kretovich Billmyre
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.250820.d0000 0000 9420 1591Present Address: Stowers Institute for Medical Research, Kansas City, MO USA
| | - Stephen Frenk
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,Present Address: Achilles Therapeutics Limited, London, UK
| | - Craig C. Mello
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Worcester, MA USA
| | - Shawn Ahmed
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC USA
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12
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Gartner A, Engebrecht J. DNA repair, recombination, and damage signaling. Genetics 2021; 220:6522877. [PMID: 35137093 PMCID: PMC9097270 DOI: 10.1093/genetics/iyab178] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
DNA must be accurately copied and propagated from one cell division to the next, and from one generation to the next. To ensure the faithful transmission of the genome, a plethora of distinct as well as overlapping DNA repair and recombination pathways have evolved. These pathways repair a large variety of lesions, including alterations to single nucleotides and DNA single and double-strand breaks, that are generated as a consequence of normal cellular function or by external DNA damaging agents. In addition to the proteins that mediate DNA repair, checkpoint pathways have also evolved to monitor the genome and coordinate the action of various repair pathways. Checkpoints facilitate repair by mediating a transient cell cycle arrest, or through initiation of cell suicide if DNA damage has overwhelmed repair capacity. In this chapter, we describe the attributes of Caenorhabditis elegans that facilitate analyses of DNA repair, recombination, and checkpoint signaling in the context of a whole animal. We review the current knowledge of C. elegans DNA repair, recombination, and DNA damage response pathways, and their role during development, growth, and in the germ line. We also discuss how the analysis of mutational signatures in C. elegans is helping to inform cancer mutational signatures in humans.
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Affiliation(s)
- Anton Gartner
- Department for Biological Sciences, IBS Center for Genomic Integrity, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea,Corresponding author: (A.G.); (J.E.)
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA,Corresponding author: (A.G.); (J.E.)
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13
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Yamamoto I, Zhang K, Zhang J, Vorontsov E, Shibuya H. Telomeric double-strand DNA-binding proteins DTN-1 and DTN-2 ensure germline immortality in Caenorhabditis elegans. eLife 2021; 10:64104. [PMID: 33476260 PMCID: PMC7819708 DOI: 10.7554/elife.64104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
Telomeres are nucleoprotein complexes at the ends of chromosomes and are indispensable for the protection and lengthening of terminal DNA. Despite the evolutionarily conserved roles of telomeres, the telomeric double-strand DNA (dsDNA)-binding proteins have evolved rapidly. Here, we identified double-strand telomeric DNA-binding proteins (DTN-1 and DTN-2) in Caenorhabditis elegans as non-canonical telomeric dsDNA-binding proteins. DTN-1 and DTN-2 are paralogous proteins that have three putative MYB-like DNA-binding domains and bind to telomeric dsDNA in a sequence-specific manner. DTN-1 and DTN-2 form complexes with the single-strand telomeric DNA-binding proteins POT-1 and POT-2 and constitutively localize to telomeres. The dtn-1 and dtn-2 genes function redundantly, and their simultaneous deletion results in progressive germline mortality, which accompanies telomere hyper-elongation and chromosomal bridges. Our study suggests that DTN-1 and DTN-2 are core shelterin components in C. elegans telomeres that act as negative regulators of telomere length and are essential for germline immortality.
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Affiliation(s)
- Io Yamamoto
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Kexin Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jingjing Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Egor Vorontsov
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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14
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Harnessing the power of genetics: fast forward genetics in Caenorhabditis elegans. Mol Genet Genomics 2020; 296:1-20. [PMID: 32888055 DOI: 10.1007/s00438-020-01721-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022]
Abstract
Forward genetics is a powerful tool to unravel molecular mechanisms of diverse biological processes. The success of genetic screens primarily relies on the ease of genetic manipulation of an organism and the availability of a plethora of genetic tools. The roundworm Caenorhabditis elegans has been one of the favorite models for genetic studies due to its hermaphroditic lifestyle, ease of maintenance, and availability of various genetic manipulation tools. The strength of C. elegans genetics is highlighted by the leading role of this organism in the discovery of several conserved biological processes. In this review, the principles and strategies for forward genetics in C. elegans are discussed. Further, the recent advancements that have drastically accelerated the otherwise time-consuming process of mutation identification, making forward genetic screens a method of choice for understanding biological functions, are discussed. The emphasis of the review has been on providing practical and conceptual pointers for designing genetic screens that will identify mutations, specifically disrupting the biological processes of interest.
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15
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Meier B, Volkova NV, Gerstung M, Gartner A. Analysis of mutational signatures in C. elegans: Implications for cancer genome analysis. DNA Repair (Amst) 2020; 95:102957. [PMID: 32980770 DOI: 10.1016/j.dnarep.2020.102957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/19/2020] [Accepted: 08/22/2020] [Indexed: 01/02/2023]
Abstract
Genome integrity is constantly challenged by exogenous and endogenous insults, and mutations are associated with inherited disease and cancer. Here we summarize recent studies that utilized C. elegans whole genome next generation sequencing to experimentally determine mutational signatures associated with mutagen exposure, DNA repair deficiency or a combination of both and discuss the implications of these results for the understanding of cancer genome evolution. The experimental analysis of wild-type and DNA repair deficient nematodes propagated under unchallenged conditions over many generations revealed increased mutagenesis in approximately half of all DNA repair deficient strains, its rate, except for DNA mismatch repair, only being moderately increased. The exposure of wild-type and DNA repair defective strains to selected genotoxins, including UV-B and ionizing radiation, alkylating compounds, aristolochic acid, aflatoxin-B1, and cisplatin enabled the systematic analysis of the relative contributions of redundant repair modalities that mend DNA damage. Combining genotoxin exposure with DNA repair deficiency can manifest as altered mutation rates and/or as a change in mutational profiles, and reveals how different DNA alterations induced by one genotoxin are repaired by separate DNA repair pathways, often in a highly redundant way. Cancer genomes provide a snapshot of all mutational events that happened prior to cancer detection and sequencing, necessitating computational models to deduce mutational signatures using mathematical best fit approaches. While computationally deducing signatures from cancer genomes has been tremendously successful in associating some signatures to known mutagenic causes, many inferred signatures lack a clear link to a known mutagenic process. Moreover, analytical signatures might not reflect any distinct mutagenic processes. Nonetheless, combined effects of mutagen exposure and DNA damage-repair deficiency are also present in cancer genomes, but cannot be as easily detected owing to the unknown histories of genotoxic exposures and because biallelic in contrast to monoallelic DNA repair deficiency is rare. The impact of damage-repair interactions also manifests through selective pressure for DNA repair gene inactivation during cancer evolution. Using these considerations, we discuss a theoretical framework that explains why minute mutagenic changes, possibly too small to manifest as change in a signature, can have major effects in oncogenesis. Overall, the experimental analysis of mutational processes underscores that the interpretation of mutational signatures requires considering both the primary DNA lesion and repair status and imply that mutational signatures derived from cancer genomes may be more variable than currently anticipated.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Scotland, UK
| | - Nadezda V Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anton Gartner
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea.
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16
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Roake CM, Artandi SE. Regulation of human telomerase in homeostasis and disease. Nat Rev Mol Cell Biol 2020; 21:384-397. [PMID: 32242127 DOI: 10.1038/s41580-020-0234-z] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2020] [Indexed: 12/14/2022]
Abstract
Telomerase is a ribonucleoprotein complex, the catalytic core of which includes the telomerase reverse transcriptase (TERT) and the non-coding human telomerase RNA (hTR), which serves as a template for the addition of telomeric repeats to chromosome ends. Telomerase expression is restricted in humans to certain cell types, and telomerase levels are tightly controlled in normal conditions. Increased levels of telomerase are found in the vast majority of human cancers, and we have recently begun to understand the mechanisms by which cancer cells increase telomerase activity. Conversely, germline mutations in telomerase-relevant genes that decrease telomerase function cause a range of genetic disorders, including dyskeratosis congenita, idiopathic pulmonary fibrosis and bone marrow failure. In this Review, we discuss the transcriptional regulation of human TERT, hTR processing, assembly of the telomerase complex, the cellular localization of telomerase and its recruitment to telomeres, and the regulation of telomerase activity. We also discuss the disease relevance of each of these steps of telomerase biogenesis.
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Affiliation(s)
- Caitlin M Roake
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven E Artandi
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Bayat M, Tanny RE, Wang Y, Herden C, Daniel J, Andersen EC, Liebau E, Waschk DE. Effects of telomerase overexpression in the model organism Caenorhabditis elegans. Gene X 2020; 732:144367. [DOI: 10.1016/j.gene.2020.144367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 11/30/2022] Open
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18
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Dokshin GA, Davis GM, Sawle AD, Eldridge MD, Nicholls PK, Gourley TE, Romer KA, Molesworth LW, Tatnell HR, Ozturk AR, de Rooij DG, Hannon GJ, Page DC, Mello CC, Carmell MA. GCNA Interacts with Spartan and Topoisomerase II to Regulate Genome Stability. Dev Cell 2020; 52:53-68.e6. [PMID: 31839538 PMCID: PMC7227305 DOI: 10.1016/j.devcel.2019.11.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/14/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Abstract
GCNA proteins are expressed across eukarya in pluripotent cells and have conserved functions in fertility. GCNA homologs Spartan (DVC-1) and Wss1 resolve DNA-protein crosslinks (DPCs), including Topoisomerase-DNA adducts, during DNA replication. Here, we show that GCNA mutants in mouse and C. elegans display defects in genome maintenance including DNA damage, aberrant chromosome condensation, and crossover defects in mouse spermatocytes and spontaneous genomic rearrangements in C. elegans. We show that GCNA and topoisomerase II (TOP2) physically interact in both mice and worms and colocalize on condensed chromosomes during mitosis in C. elegans embryos. Moreover, C. elegans gcna-1 mutants are hypersensitive to TOP2 poison. Together, our findings support a model in which GCNA provides genome maintenance functions in the germline and may do so, in part, by promoting the resolution of TOP2 DPCs.
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Affiliation(s)
- Gregoriy A Dokshin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gregory M Davis
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Ashley D Sawle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Taylin E Gourley
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Katherine A Romer
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Luke W Molesworth
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Hannah R Tatnell
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Ahmet R Ozturk
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dirk G de Rooij
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584, the Netherlands; Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam 1105, the Netherlands
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Michelle A Carmell
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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19
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Heestand B, Simon M, Frenk S, Titov D, Ahmed S. Transgenerational Sterility of Piwi Mutants Represents a Dynamic Form of Adult Reproductive Diapause. Cell Rep 2019; 23:156-171. [PMID: 29617657 PMCID: PMC5918633 DOI: 10.1016/j.celrep.2018.03.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 01/24/2018] [Accepted: 03/05/2018] [Indexed: 01/17/2023] Open
Abstract
Environmental stress can induce adult reproductive diapause, a state of developmental arrest that temporarily suspends reproduction. Deficiency for C. elegans Piwi protein PRG-1 results in strains that reproduce for many generations but then become sterile. We found that sterile-generation prg-1/Piwi mutants typically displayed pronounced germ cell atrophy as L4 larvae matured into 1-day-old adults. Atrophied germlines spontaneously reproliferated across the first days of adulthood, and this was accompanied by fertility for day 2–4 adults. Sterile day 5 prg-1 mutant adults remained sterile indefinitely, but providing an alternative food source could restore their fertility. Our data imply that late-generation prg-1 mutants experience a dynamic form of adult reproductive diapause, promoted by stress response, cell death, and RNAi pathways, where delayed fertility and reproductive quiescence represent parallel adaptive developmental outcomes. This may occur in response to a form of “heritable stress” that is transmitted by gametes and epigenetic in nature.
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Affiliation(s)
- Bree Heestand
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matt Simon
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Stephen Frenk
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Denis Titov
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA.
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20
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Kim C, Kim J, Kim S, Cook DE, Evans KS, Andersen EC, Lee J. Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans. Genome Res 2019; 29:1023-1035. [PMID: 31123081 PMCID: PMC6581047 DOI: 10.1101/gr.246082.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/22/2019] [Indexed: 12/05/2022]
Abstract
Long-read sequencing technologies have contributed greatly to comparative genomics among species and can also be applied to study genomics within a species. In this study, to determine how substantial genomic changes are generated and tolerated within a species, we sequenced a C. elegans strain, CB4856, which is one of the most genetically divergent strains compared to the N2 reference strain. For this comparison, we used the Pacific Biosciences (PacBio) RSII platform (80×, N50 read length 11.8 kb) and generated de novo genome assembly to the level of pseudochromosomes containing 76 contigs (N50 contig = 2.8 Mb). We identified structural variations that affected as many as 2694 genes, most of which are at chromosome arms. Subtelomeric regions contained the most extensive genomic rearrangements, which even created new subtelomeres in some cases. The subtelomere structure of Chromosome VR implies that ancestral telomere damage was repaired by alternative lengthening of telomeres even in the presence of a functional telomerase gene and that a new subtelomere was formed by break-induced replication. Our study demonstrates that substantial genomic changes including structural variations and new subtelomeres can be tolerated within a species, and that these changes may accumulate genetic diversity within a species.
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Affiliation(s)
- Chuna Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826
| | - Sunghyun Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Junho Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826
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21
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Fischer KE, Riddle NC. Sex Differences in Aging: Genomic Instability. J Gerontol A Biol Sci Med Sci 2019; 73:166-174. [PMID: 28575157 DOI: 10.1093/gerona/glx105] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/26/2017] [Indexed: 11/13/2022] Open
Abstract
Aging is characterized by decreasing physiological integration, reduced function, loss of resilience, and increased risk of death. Paradoxically, although women live longer, they suffer greater morbidity particularly late in life. These sex differences in human lifespan and healthspan are consistently observed in all countries and during every era for which reliable data exist. While these differences are ubiquitous in humans, evidence of sex differences in longevity and health for other species is more equivocal. Among fruit flies, nematodes, and mice, sex differences in lifespan vary depending on strain and treatment. In this review, we focus on sex differences in age-related alterations in DNA damage and mutation rates, telomere attrition, epigenetics, and nuclear architecture. We find that robust sex differences exist, eg, the higher incidence of DNA damage in men compared to women, but sex differences are not often conserved between species. For most mechanisms reviewed here, there are insufficient data to make a clear determination regarding the impact of sex, largely because sex differences have not been analyzed. Overall, our findings reveal an urgent need for well-designed studies that explicitly examine sex differences in molecular drivers of aging.
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Affiliation(s)
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham
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22
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Billmyre KK, Doebley AL, Spichal M, Heestand B, Belicard T, Sato-Carlton A, Flibotte S, Simon M, Gnazzo M, Skop A, Moerman D, Carlton PM, Sarkies P, Ahmed S. The meiotic phosphatase GSP-2/PP1 promotes germline immortality and small RNA-mediated genome silencing. PLoS Genet 2019; 15:e1008004. [PMID: 30921322 PMCID: PMC6456222 DOI: 10.1371/journal.pgen.1008004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/09/2019] [Accepted: 02/05/2019] [Indexed: 12/21/2022] Open
Abstract
Germ cell immortality, or transgenerational maintenance of the germ line, could be promoted by mechanisms that could occur in either mitotic or meiotic germ cells. Here we report for the first time that the GSP-2 PP1/Glc7 phosphatase promotes germ cell immortality. Small RNA-induced genome silencing is known to promote germ cell immortality, and we identified a separation-of-function allele of C. elegans gsp-2 that is compromised for germ cell immortality and is also defective for small RNA-induced genome silencing and meiotic but not mitotic chromosome segregation. Previous work has shown that GSP-2 is recruited to meiotic chromosomes by LAB-1, which also promoted germ cell immortality. At the generation of sterility, gsp-2 and lab-1 mutant adults displayed germline degeneration, univalents, histone methylation and histone phosphorylation defects in oocytes, phenotypes that mirror those observed in sterile small RNA-mediated genome silencing mutants. Our data suggest that a meiosis-specific function of GSP-2 ties small RNA-mediated silencing of the epigenome to germ cell immortality. We also show that transgenerational epigenomic silencing at hemizygous genetic elements requires the GSP-2 phosphatase, suggesting a functional link to small RNAs. Given that LAB-1 localizes to the interface between homologous chromosomes during pachytene, we hypothesize that small localized discontinuities at this interface could promote genomic silencing in a manner that depends on small RNAs and the GSP-2 phosphatase.
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Affiliation(s)
- Katherine Kretovich Billmyre
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Anna-Lisa Doebley
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Maya Spichal
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Bree Heestand
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tony Belicard
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute for Clinical Sciences, Imperial College London, London, United Kingdom
| | | | - Stephane Flibotte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Simon
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Megan Gnazzo
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ahna Skop
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Donald Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Peter Sarkies
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute for Clinical Sciences, Imperial College London, London, United Kingdom
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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Frézal L, Demoinet E, Braendle C, Miska E, Félix MA. Natural Genetic Variation in a Multigenerational Phenotype in C. elegans. Curr Biol 2018; 28:2588-2596.e8. [PMID: 30078564 PMCID: PMC6984962 DOI: 10.1016/j.cub.2018.05.091] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/16/2018] [Accepted: 05/31/2018] [Indexed: 10/28/2022]
Abstract
Although heredity mostly relies on the transmission of DNA sequence, additional molecular and cellular features are heritable across several generations. In the nematode Caenorhabditis elegans, insights into such unconventional inheritance result from two lines of work. First, the mortal germline (Mrt) phenotype was defined as a multigenerational phenotype whereby a selfing lineage becomes sterile after several generations, implying multigenerational memory [1, 2]. Second, certain RNAi effects are heritable over several generations in the absence of the initial trigger [3-5]. Both lines of work converged when the subset of Mrt mutants that are heat sensitive were found to closely correspond to mutants defective in the RNAi-inheritance machinery, including histone modifiers [6-9]. Here, we report the surprising finding that several C. elegans wild isolates display a heat-sensitive mortal germline phenotype in laboratory conditions: upon chronic exposure to higher temperatures, such as 25°C, lines reproducibly become sterile after several generations. This phenomenon is reversible, as it can be suppressed by temperature alternations at each generation, suggesting a non-genetic basis for the sterility. We tested whether natural variation in the temperature-induced Mrt phenotype was of genetic nature by building recombinant inbred lines between the isolates MY10 (Mrt) and JU1395 (non-Mrt). Using bulk segregant analysis, we detected two quantitative trait loci. After further recombinant mapping and genome editing, we identified the major causal locus as a polymorphism in the set-24 gene, encoding a SET- and SPK-domain protein. We conclude that C. elegans natural populations may harbor natural genetic variation in epigenetic inheritance phenomena.
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Affiliation(s)
- Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, INSERM, École Normale Supérieure, Paris Sciences et Lettres, Paris, France; Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | | | | | - Eric Miska
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, INSERM, École Normale Supérieure, Paris Sciences et Lettres, Paris, France.
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Lidzbarsky G, Gutman D, Shekhidem HA, Sharvit L, Atzmon G. Genomic Instabilities, Cellular Senescence, and Aging: In Vitro, In Vivo and Aging-Like Human Syndromes. Front Med (Lausanne) 2018; 5:104. [PMID: 29719834 PMCID: PMC5913290 DOI: 10.3389/fmed.2018.00104] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
As average life span and elderly people prevalence in the western world population is gradually increasing, the incidence of age-related diseases such as cancer, heart diseases, diabetes, and dementia is increasing, bearing social and economic consequences worldwide. Understanding the molecular basis of aging-related processes can help extend the organism’s health span, i.e., the life period in which the organism is free of chronic diseases or decrease in basic body functions. During the last few decades, immense progress was made in the understanding of major components of aging and healthy aging biology, including genomic instability, telomere attrition, epigenetic changes, proteostasis, nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and intracellular communications. This progress has been made by three spear-headed strategies: in vitro (cell and tissue culture from various sources), in vivo (includes diverse model and non-model organisms), both can be manipulated and translated to human biology, and the study of aging-like human syndromes and human populations. Herein, we will focus on current repository of genomic “senescence” stage of aging, which includes health decline, structural changes of the genome, faulty DNA damage response and DNA damage, telomere shortening, and epigenetic alterations. Although aging is a complex process, many of the “hallmarks” of aging are directly related to DNA structure and function. This review will illustrate the variety of these studies, done in in vitro, in vivo and human levels, and highlight the unique potential and contribution of each research level and eventually the link between them.
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Affiliation(s)
| | - Danielle Gutman
- Department of Human Biology, University of Haifa, Haifa, Israel
| | | | - Lital Sharvit
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Gil Atzmon
- Department of Human Biology, University of Haifa, Haifa, Israel
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25
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Telomeres, Aging and Exercise: Guilty by Association? Int J Mol Sci 2017; 18:ijms18122573. [PMID: 29186077 PMCID: PMC5751176 DOI: 10.3390/ijms18122573] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 02/07/2023] Open
Abstract
Telomeres are repetitive tandem DNA sequences that cap chromosomal ends protecting genomic DNA from enzymatic degradation. Telomeres progressively shorten with cellular replication and are therefore assumed to correlate with biological and chronological age. An expanding body of evidence suggests (i) a predictable inverse association between telomere length, aging and age-related diseases and (ii) a positive association between physical activity and telomere length. Both hypotheses have garnered tremendous research attention and broad consensus; however, the evidence for each proposition is inconsistent and equivocal at best. Telomere length does not meet the basic criteria for an aging biomarker and at least 50% of key studies fail to find associations with physical activity. In this review, we address the evidence in support and refutation of the putative associations between telomere length, aging and physical activity. We finish with a brief review of plausible mechanisms and potential future research directions.
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Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F, Gunsalus KC. Genome Architecture and Evolution of a Unichromosomal Asexual Nematode. Curr Biol 2017; 27:2928-2939.e6. [PMID: 28943090 PMCID: PMC5659720 DOI: 10.1016/j.cub.2017.08.038] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 10/24/2022]
Abstract
Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture, and cellular processes. Here we report the genome sequence of the parthenogenetic nematode Diploscapter pachys with only one chromosome pair. We show that this unichromosomal architecture is shared by a long-lived clade of asexual nematodes closely related to the genetic model organism Caenorhabditis elegans. Analysis of the genome assembly reveals that the unitary chromosome arose through fusion of six ancestral chromosomes, with extensive rearrangement among neighboring regions. Typical nematode telomeres and telomeric protection-encoding genes are lacking. Most regions show significant heterozygosity; homozygosity is largely concentrated to one region and attributed to gene conversion. Cell-biological and molecular evidence is consistent with the absence of key features of meiosis I, including synapsis and recombination. We propose that D. pachys preserves heterozygosity and produces diploid embryos without fertilization through a truncated meiosis. As a prelude to functional studies, we demonstrate that D. pachys is amenable to experimental manipulation by RNA interference.
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Affiliation(s)
- Hélène Fradin
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Kiontke
- Department of Biology, New York University, New York, NY 10003, USA
| | - Charles Zegar
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michelle Gutwein
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Jessica Lucas
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Mikhail Kovtun
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - David L Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - David H A Fitch
- Department of Biology, New York University, New York, NY 10003, USA.
| | - Fabio Piano
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Kristin C Gunsalus
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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27
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Lai AG, Pouchkina-Stantcheva N, Di Donfrancesco A, Kildisiute G, Sahu S, Aboobaker AA. The protein subunit of telomerase displays patterns of dynamic evolution and conservation across different metazoan taxa. BMC Evol Biol 2017; 17:107. [PMID: 28441946 PMCID: PMC5405514 DOI: 10.1186/s12862-017-0949-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Most animals employ telomerase, which consists of a catalytic subunit known as the telomerase reverse transcriptase (TERT) and an RNA template, to maintain telomere ends. Given the importance of TERT and telomere biology in core metazoan life history traits, like ageing and the control of somatic cell proliferation, we hypothesised that TERT would have patterns of sequence and regulatory evolution reflecting the diverse life histories across the Animal Kingdom. RESULTS We performed a complete investigation of the evolutionary history of TERT across animals. We show that although TERT is almost ubiquitous across Metazoa, it has undergone substantial sequence evolution within canonical motifs. Beyond the known canonical motifs, we also identify and compare regions that are highly variable between lineages, but show conservation within phyla. Recent data have highlighted the importance of alternative splice forms of TERT in non-canonical functions and although animals may share some conserved introns, we find that the selection of exons for alternative splicing appears to be highly variable, and regulation by alternative splicing appears to be a very dynamic feature of TERT evolution. We show that even within a closely related group of triclad flatworms, where alternative splicing of TERT was previously correlated with reproductive strategy, we observe highly diverse splicing patterns. CONCLUSIONS Our work establishes that the evolutionary history and structural evolution of TERT involves previously unappreciated levels of change and the emergence of lineage specific motifs. The sequence conservation we describe within phyla suggests that these new motifs likely serve essential biological functions of TERT, which along with changes in splicing, underpin diverse functions of TERT important for animal life histories.
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Affiliation(s)
- Alvina G Lai
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
| | | | | | - Gerda Kildisiute
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Sounak Sahu
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - A Aziz Aboobaker
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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28
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Kwon M, Min J, Jeon H, Hwang K, Kim C, Lee J, Joung J, Park W, Lee H. Paradoxical delay of senescence upon depletion of BRCA2 in telomerase-deficient worms. FEBS Open Bio 2016; 6:1016-1024. [PMID: 27761361 PMCID: PMC5055038 DOI: 10.1002/2211-5463.12109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/03/2016] [Accepted: 08/22/2016] [Indexed: 11/07/2022] Open
Abstract
BRCA2 is a multifunctional tumor suppressor involved in homologous recombination (HR), mitotic checkpoint regulation, and telomere homeostasis. Absence of Brca2 in mice results in progressive shortening of telomeres and senescence, yet cells are prone to neoplastic transformation with elongated telomeres, suggesting that BRCA2 has positive and negative effects on telomere length regulation along the path to tumorigenesis. Using Caenorhabditis elegans as a model, we show here that depletion of BRC‐2, an ortholog of BRCA2, paradoxically delays senescence in telomerase‐deficient mutant worms. Telomerase‐deficient worms (trt‐1) exhibit early replication senescence due to short telomeres. It should be noted that worms mutated in brc‐2 are not viable as well due to massive genotoxic insults. However, when BRC‐2 is depleted by RNA interference in trt‐1 mutant worms, the number of generations is unexpectedly increased with telomere length maintained, compared to telomerase mutants. Interestingly, depletion of other HR genes such as rad‐51 and rad‐54 exhibited similar effects. In worms doubly deficient of telomerase and brc‐2, rad‐51, or rad‐54, extra telomeric C‐circles were generated, suggesting that abrogation of HR induces an alteration in telomere environment favorable to illegitimate telomere maintenance when telomerase is absent. Collectively, absence of BRC‐2 in telomerase‐deficient background first leads to telomere shortening, followed by an induction of an as‐yet‐unknown telomere maintenance pathway, resulting in delay of senescence. The results have implications in the understanding of dysfunctional BRCA2‐associated tumorigenesis.
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Affiliation(s)
- Mi‐Sun Kwon
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG)Seoul National UniversityGwanak‐GuSeoulKorea
| | - Jaewon Min
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG)Seoul National UniversityGwanak‐GuSeoulKorea
| | - Hee‐Yeon Jeon
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG)Seoul National UniversityGwanak‐GuSeoulKorea
| | - Kwangwoo Hwang
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG)Seoul National UniversityGwanak‐GuSeoulKorea
| | - Chuna Kim
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG)Seoul National UniversityGwanak‐GuSeoulKorea
| | - Junho Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG)Seoul National UniversityGwanak‐GuSeoulKorea
| | - Je‐Gun Joung
- Samsung Genome InstituteSamsung Medical CenterSeoulKorea
| | | | - Hyunsook Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG)Seoul National UniversityGwanak‐GuSeoulKorea
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29
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Ijomone OM, Miah MR, Peres TV, Nwoha PU, Aschner M. Null allele mutants of trt-1, the catalytic subunit of telomerase in Caenorhabditis elegans, are less sensitive to Mn-induced toxicity and DAergic degeneration. Neurotoxicology 2016; 57:54-60. [PMID: 27593554 DOI: 10.1016/j.neuro.2016.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/31/2016] [Accepted: 08/31/2016] [Indexed: 02/06/2023]
Abstract
Exposure to manganese (Mn) represents an environmental risk factor for Parkinson's disease (PD). Recent evidence suggests that telomerase reverse transcriptase (TERT), the catalytic subunit of mammalian telomerase participates in non-telomeric functions and may play a role in cellular protection from oxidative stress and DNA damage. trt-1 is the catalytic subunit of telomerase in Caenorhabditis elegans (C. elegans). The present study investigated the relationship between trt-1 mutation and Mn-induced neurotoxicity. Wild-type (wt) and trt-1 worms were subjected to an acute Mn treatment of 1h at the first larval (L1) stage. Survival assay and behavior (Basal slowing response, chemotaxis) were assessed. Dopaminergic (DAergic) neurodegeneration was evaluated in successful crosses of trt-1 worms expressing green fluorescent protein (GFP) (dat-1:GFP worms). trt-1 worms were less sensitive to Mn-induced lethality compared to wt worms. Mn induced DAergic degeneration in wt worms, but not in trt-1 worms. Basal slowing was altered in both wt and trt-1 worms; however trt-1 worms were significantly less affected in their basal slowing behavior compared to wt worms. Mn treatment did not affect chemotaxis by NaCl in either wt or trt-1 mutants worms. Combined, the results establish that null mutation in trt-1 improves survival and attenuates damage to the DAergic system.
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Affiliation(s)
- Omamuyovwi M Ijomone
- Department of Anatomy, Faculty of Basic Medical Sciences, Cross River University of Technology, Okuku Campus, Cross River, Nigeria; Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, USA; Department of Anatomy and Cell Biology, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Mahfuzur R Miah
- Department of Neuroscience, Albert Einstein College of Medicine, New York, USA
| | - Tanara V Peres
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, USA
| | - Polycarp U Nwoha
- Department of Anatomy and Cell Biology, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, USA; Department of Neuroscience, Albert Einstein College of Medicine, New York, USA.
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30
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Seo B, Lee J. Observation and Quantification of Telomere and Repetitive Sequences Using Fluorescence In Situ Hybridization (FISH) with PNA Probes in Caenorhabditis elegans. J Vis Exp 2016:54224. [PMID: 27583462 PMCID: PMC5091719 DOI: 10.3791/54224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Telomere is a ribonucleoprotein structure that protects chromosomal ends from aberrant fusion and degradation. Telomere length is maintained by telomerase or an alternative pathway, known as alternative lengthening of telomeres (ALT)(1). Recently, C. elegans has emerged as a multicellular model organism for the study of telomere and ALT(2). Visualization of repetitive sequences in the genome is critical in understanding the biology of telomeres. While telomere length can be measured by telomere restriction fragment assay or quantitative PCR, these methods only provide the averaged telomere length. On the contrary, fluorescence in situ hybridization (FISH) can provide the information of the individual telomeres in cells. Here, we provide protocols and representative results of the method to determine telomere length of C. elegans by fluorescent in situ hybridization. This method provides a simple, but powerful, in situ procedure that does not cause noticeable damage to morphology. By using fluorescently labeled peptide nucleic acid (PNA) and digoxigenin-dUTP-labeled probe, we were able to visualize two different repetitive sequences: telomere repeats and template of ALT (TALT) in C. elegans embryos and gonads.
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Affiliation(s)
- Beomseok Seo
- Institute of Molecular Biology and Genetics (IMBG), Seoul National University
| | - Junho Lee
- Institute of Molecular Biology and Genetics (IMBG), Seoul National University; Department of Biological Sciences, Seoul National University; Department of Biophysics and Chemical Biology, Seoul National University;
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31
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The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length. Genetics 2016; 204:371-83. [PMID: 27449056 PMCID: PMC5012401 DOI: 10.1534/genetics.116.191148] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/14/2016] [Indexed: 01/03/2023] Open
Abstract
Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans.
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32
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Blackburn EH, Epel ES, Lin J. Human telomere biology: A contributory and interactive factor in aging, disease risks, and protection. Science 2016; 350:1193-8. [PMID: 26785477 DOI: 10.1126/science.aab3389] [Citation(s) in RCA: 1002] [Impact Index Per Article: 125.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Telomeres are the protective end-complexes at the termini of eukaryotic chromosomes. Telomere attrition can lead to potentially maladaptive cellular changes, block cell division, and interfere with tissue replenishment. Recent advances in the understanding of human disease processes have clarified the roles of telomere biology, especially in diseases of human aging and in some aging-related processes. Greater overall telomere attrition predicts mortality and aging-related diseases in inherited telomere syndrome patients, and also in general human cohorts. However, genetically caused variations in telomere maintenance either raise or lower risks and progression of cancers, in a highly cancer type-specific fashion. Telomere maintenance is determined by genetic factors and is also cumulatively shaped by nongenetic influences throughout human life; both can interact. These and other recent findings highlight both causal and potentiating roles for telomere attrition in human diseases.
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Affiliation(s)
- Elizabeth H Blackburn
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.
| | - Elissa S Epel
- Department of Psychiatry, University of California, San Francisco, CA 94143, USA
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
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33
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Pech MF, Garbuzov A, Hasegawa K, Sukhwani M, Zhang RJ, Benayoun BA, Brockman SA, Lin S, Brunet A, Orwig KE, Artandi SE. High telomerase is a hallmark of undifferentiated spermatogonia and is required for maintenance of male germline stem cells. Genes Dev 2015; 29:2420-34. [PMID: 26584619 PMCID: PMC4691947 DOI: 10.1101/gad.271783.115] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/27/2015] [Indexed: 01/15/2023]
Abstract
Telomerase inactivation causes loss of the male germline in worms, fish, and mice, indicating a conserved dependence on telomere maintenance in this cell lineage. Here, using telomerase reverse transcriptase (Tert) reporter mice, we found that very high telomerase expression is a hallmark of undifferentiated spermatogonia, the mitotic population where germline stem cells reside. We exploited these high telomerase levels as a basis for purifying undifferentiated spermatogonia using fluorescence-activated cell sorting. Telomerase levels in undifferentiated spermatogonia and embryonic stem cells are comparable and much greater than in somatic progenitor compartments. Within the germline, we uncovered an unanticipated gradient of telomerase activity that also enables isolation of more mature populations. Transcriptomic comparisons of Tert(High) undifferentiated spermatogonia and Tert(Low) differentiated spermatogonia by RNA sequencing reveals marked differences in cell cycle and key molecular features of each compartment. Transplantation studies show that germline stem cell activity is confined to the Tert(High) cKit(-) population. Telomere shortening in telomerase knockout strains causes depletion of undifferentiated spermatogonia and eventual loss of all germ cells after undifferentiated spermatogonia drop below a critical threshold. These data reveal that high telomerase expression is a fundamental characteristic of germline stem cells, thus explaining the broad dependence on telomerase for germline immortality in metazoans.
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Affiliation(s)
- Matthew F Pech
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alina Garbuzov
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University, California 94305, USA
| | - Kazuteru Hasegawa
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Meena Sukhwani
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh Pennsylvania 15213, USA; Magee-Womens Research Institute, Pittsburgh, Pennsylvania 15213, USA
| | - Ruixuan J Zhang
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Stephanie A Brockman
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Shengda Lin
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, California 94305, USA
| | - Kyle E Orwig
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh Pennsylvania 15213, USA; Magee-Womens Research Institute, Pittsburgh, Pennsylvania 15213, USA
| | - Steven E Artandi
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
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34
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Simons MJP. Questioning causal involvement of telomeres in aging. Ageing Res Rev 2015; 24:191-6. [PMID: 26304838 DOI: 10.1016/j.arr.2015.08.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/03/2015] [Accepted: 08/17/2015] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated that telomere length predicts mortality and that telomeres shorten with age. Although rarely acknowledged these associations do not dictate causality. I review telomerase knockout and overexpression studies and find little support that telomeres cause aging. In addition, the causality hypothesis assumes that there is a critical telomere length at which senescence is induced. This generates the prediction that variance in telomere length decreases with age. In contrast, using meta-analysis of human data, I find no such decline. Inferring the causal involvement of telomeres in aging from current knowledge is therefore speculative and could hinder scientific progress.
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Affiliation(s)
- Mirre J P Simons
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, Sheffield, United Kingdom.
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35
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Telomere maintenance through recruitment of internal genomic regions. Nat Commun 2015; 6:8189. [PMID: 26382656 PMCID: PMC4595603 DOI: 10.1038/ncomms9189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 07/28/2015] [Indexed: 01/21/2023] Open
Abstract
Cells surviving crisis are often tumorigenic and their telomeres are commonly maintained through the reactivation of telomerase. However, surviving cells occasionally activate a recombination-based mechanism called alternative lengthening of telomeres (ALT). Here we establish stably maintained survivors in telomerase-deleted Caenorhabditis elegans that escape from sterility by activating ALT. ALT survivors trans-duplicate an internal genomic region, which is already cis-duplicated to chromosome ends, across the telomeres of all chromosomes. These ‘Template for ALT' (TALT) regions consist of a block of genomic DNA flanked by telomere-like sequences, and are different between two genetic background. We establish a model that an ancestral duplication of a donor TALT region to a proximal telomere region forms a genomic reservoir ready to be incorporated into telomeres on ALT activation. Telomeres in post-crisis cells are maintained by re-activated telomerase or by alternative lengthening of telomeres (ALT). Here, Seo et al. report a stable mode of ALT in worm where internal genomic regions generate a genomic reservoir ready to be incorporated into telomeres upon ALT activation.
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36
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Caenorhabditis elegans RSD-2 and RSD-6 promote germ cell immortality by maintaining small interfering RNA populations. Proc Natl Acad Sci U S A 2014; 111:E4323-31. [PMID: 25258416 DOI: 10.1073/pnas.1406131111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Germ cells are maintained in a pristine non-aging state as they proliferate over generations. Here, we show that a novel function of the Caenorhabditis elegans RNA interference proteins RNAi spreading defective (RSD)-2 and RSD-6 is to promote germ cell immortality at high temperature. rsd mutants cultured at high temperatures became progressively sterile and displayed loss of small interfering RNAs (siRNAs) that target spermatogenesis genes, simple repeats, and transposons. Desilencing of spermatogenesis genes occurred in late-generation rsd mutants, although defective spermatogenesis was insufficient to explain the majority of sterility. Increased expression of repetitive loci occurred in both germ and somatic cells of late-generation rsd mutant adults, suggesting that desilencing of many heterochromatic segments of the genome contributes to sterility. Nuclear RNAi defective (NRDE)-2 promotes nuclear silencing in response to exogenous double-stranded RNA, and our data imply that RSD-2, RSD-6, and NRDE-2 function in a common transgenerational nuclear silencing pathway that responds to endogenous siRNAs. We propose that RSD-2 and RSD-6 promote germ cell immortality at stressful temperatures by maintaining transgenerational epigenetic inheritance of endogenous siRNA populations that promote genome silencing.
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37
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Meier B, Cooke SL, Weiss J, Bailly AP, Alexandrov LB, Marshall J, Raine K, Maddison M, Anderson E, Stratton MR, Gartner A, Campbell PJ. C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency. Genome Res 2014; 24:1624-36. [PMID: 25030888 PMCID: PMC4199376 DOI: 10.1101/gr.175547.114] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mutation is associated with developmental and hereditary disorders, aging, and cancer. While we understand some mutational processes operative in human disease, most remain mysterious. We used Caenorhabditis elegans whole-genome sequencing to model mutational signatures, analyzing 183 worm populations across 17 DNA repair-deficient backgrounds propagated for 20 generations or exposed to carcinogens. The baseline mutation rate in C. elegans was approximately one per genome per generation, not overtly altered across several DNA repair deficiencies over 20 generations. Telomere erosion led to complex chromosomal rearrangements initiated by breakage–fusion–bridge cycles and completed by simultaneously acquired, localized clusters of breakpoints. Aflatoxin B1 induced substitutions of guanines in a GpC context, as observed in aflatoxin-induced liver cancers. Mutational burden increased with impaired nucleotide excision repair. Cisplatin and mechlorethamine, DNA crosslinking agents, caused dose- and genotype-dependent signatures among indels, substitutions, and rearrangements. Strikingly, both agents induced clustered rearrangements resembling “chromoanasynthesis,” a replication-based mutational signature seen in constitutional genomic disorders, suggesting that interstrand crosslinks may play a pathogenic role in such events. Cisplatin mutagenicity was most pronounced in xpf-1 mutants, suggesting that this gene critically protects cells against platinum chemotherapy. Thus, experimental model systems combined with genome sequencing can recapture and mechanistically explain mutational signatures associated with human disease.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Susanna L Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Joerg Weiss
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Aymeric P Bailly
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom; CRBM/CNRS UMR5237, University of Montpellier, Montpellier 34293, France
| | - Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - John Marshall
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Mark Maddison
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Elizabeth Anderson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom;
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom; Department of Haematology, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
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38
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Reduced insulin/IGF-1 signaling restores germ cell immortality to Caenorhabditis elegans Piwi mutants. Cell Rep 2014; 7:762-73. [PMID: 24767993 DOI: 10.1016/j.celrep.2014.03.056] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 01/24/2014] [Accepted: 03/22/2014] [Indexed: 02/05/2023] Open
Abstract
Defects in the Piwi/piRNA pathway lead to transposon desilencing and immediate sterility in many organisms. We found that the C. elegans Piwi mutant prg-1 became sterile after growth for many generations. This phenotype did not occur for RNAi mutants with strong transposon-silencing defects and was separable from the role of PRG-1 in transgene silencing. Brief periods of starvation extended the transgenerational lifespan of prg-1 mutants by stimulating the DAF-16/FOXO longevity transcription factor. Constitutive activation of DAF-16 via reduced daf-2 insulin/IGF-1 signaling immortalized prg-1 strains via RNAi proteins and histone H3 lysine 4 demethylases. In late-generation prg-1 mutants, desilencing of repetitive segments of the genome occurred, and silencing of repetitive loci was restored in prg-1; daf-2 mutants. This study reveals an unexpected interface between aging and transgenerational maintenance of germ cells, where somatic longevity is coupled to a genome-silencing pathway that promotes germ cell immortality in parallel to the Piwi/piRNA system.
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Alvares SM, Mayberry GA, Joyner EY, Lakowski B, Ahmed S. H3K4 demethylase activities repress proliferative and postmitotic aging. Aging Cell 2014; 13:245-53. [PMID: 24134677 PMCID: PMC4020274 DOI: 10.1111/acel.12166] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2013] [Indexed: 12/16/2022] Open
Abstract
Homeostasis of postmitotic and proliferating cells is maintained by pathways that repress stress. We found that the Caenorhabditis elegans histone 3 lysine 4 (H3K4) demethylases RBR-2 and SPR-5 promoted postmitotic longevity of stress-resistant daf-2 adults, altered pools of methylated H3K4, and promoted silencing of some daf-2 target genes. In addition, RBR-2 and SPR-5 were required for germ cell immortality at a high temperature. Transgenerational proliferative aging was enhanced for spr-5; rbr-2 double mutants, suggesting that these histone demethylases may function sequentially to promote germ cell immortality by targeting distinct H3K4 methyl marks. RBR-2 did not play a comparable role in the maintenance of quiescent germ cells in dauer larvae, implying that it represses stress that occurs as a consequence of germ cell proliferation, rather than stress that accumulates in nondividing cells. We propose that H3K4 demethylase activities promote the maintenance of chromatin states during stressful growth conditions, thereby repressing postmitotic aging of somatic cells as well as proliferative aging of germ cells.
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Affiliation(s)
- Stacy M. Alvares
- Department of Genetics University of North Carolina Chapel Hill NC 27599‐3280USA
- SPIRE Postdoctoral Fellowship Program University of North Carolina Chapel Hill NC 27599‐3280USA
| | - Gaea A. Mayberry
- Department of Biology University of North Carolina Chapel Hill NC 27599‐3280USA
| | - Ebony Y. Joyner
- Department of Natural Sciences Fayetteville State University Fayetteville NC 28301‐4298USA
| | - Bernard Lakowski
- Department of Neuroscience Institut Pasteur 75724 Paris Cedex 15 France
| | - Shawn Ahmed
- Department of Genetics University of North Carolina Chapel Hill NC 27599‐3280USA
- Department of Biology University of North Carolina Chapel Hill NC 27599‐3280USA
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Ferreira HC, Towbin BD, Jegou T, Gasser SM. The shelterin protein POT-1 anchors Caenorhabditis elegans telomeres through SUN-1 at the nuclear periphery. ACTA ACUST UNITED AC 2013; 203:727-35. [PMID: 24297748 PMCID: PMC3857485 DOI: 10.1083/jcb.201307181] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Telomere positioning near the nuclear envelope during Caenorhabditis elegans development requires the nuclear envelope protein SUN-1, the Shelterin component POT-1, and the SUMO ligase GEI-17. Telomeres are specialized protein–DNA structures that protect chromosome ends. In budding yeast, telomeres form clusters at the nuclear periphery. By imaging telomeres in embryos of the metazoan Caenorhabditis elegans, we found that telomeres clustered only in strains that had activated an alternative telomere maintenance pathway (ALT). Moreover, as in yeast, the unclustered telomeres in wild-type embryos were located near the nuclear envelope (NE). This bias for perinuclear localization increased during embryogenesis and persisted in differentiated cells. Telomere position in early embryos required the NE protein SUN-1, the single-strand binding protein POT-1, and the small ubiquitin-like modifier (SUMO) ligase GEI-17. However, in postmitotic larval cells, none of these factors individually were required for telomere anchoring, which suggests that additional mechanisms anchor in late development. Importantly, targeted POT-1 was sufficient to anchor chromatin to the NE in a SUN-1–dependent manner, arguing that its effect at telomeres is direct. This high-resolution description of telomere position within C. elegans extends our understanding of telomere organization in eukaryotes.
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Affiliation(s)
- Helder C Ferreira
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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41
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Lackner DH, Karlseder J. C. elegans survivors without telomerase. WORM 2013; 2:e21073. [PMID: 24058854 PMCID: PMC3670455 DOI: 10.4161/worm.21073] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 06/08/2012] [Indexed: 01/21/2023]
Abstract
In most eukaryotic organisms with a linear genome, the telomerase complex is essential for telomere maintenance and, thus, for genomic integrity. Proper telomerase function in stem and germ cell populations counteracts replication-dependent telomere shortening. On the other hand, repression of telomerase expression in most somatic tissues limits the proliferative potential of these cells through the induction of a permanent cell cycle arrest termed senescence upon critical telomere erosion. Thus, senescence, induced by telomere shortening and subsequent DNA damage signaling, is an essential tumor suppressive mechanism, emphasized by the fact that repression of telomerase is lost in about 90% of cancers, endowing them with unlimited proliferative potential. In 10% of cancers telomeres are maintained using the recombination-based alternative mechanism of telomere lengthening (ALT). To date, ALT and ALT-like mechanisms have only been described in the context of individual cells such as cancer cells and yeast. Now, several “survivor” strains of the nematode Caenorhabditis elegans have been generated that can propagate despite mutations of the telomerase gene. These nematode strains represent the first multi-cellular organism with canonical telomerase that can survive in the absence of a functional telomerase pathway.
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Affiliation(s)
- Daniel H Lackner
- Molecular and Cellular Biology Department; The Salk Institute for Biological Studies; La Jolla, CA USA
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42
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A trans-spliced telomerase RNA dictates telomere synthesis in Trypanosoma brucei. Cell Res 2013; 23:537-51. [PMID: 23478302 DOI: 10.1038/cr.2013.35] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Telomerase is a ribonucleoprotein enzyme typically required for sustained cell proliferation. Although both telomerase activity and the telomerase catalytic protein component, TbTERT, have been identified in the eukaryotic pathogen Trypanosoma brucei, the RNA molecule that dictates telomere synthesis remains unknown. Here, we identify the RNA component of Trypanosoma brucei telomerase, TbTR, and provide phylogenetic and in vivo evidence for TbTR's native folding and activity. We show that TbTR is processed through trans-splicing, and is a capped transcript that interacts and copurifies with TbTERT in vivo. Deletion of TbTR caused progressive shortening of telomeres at a rate of 3-5 bp/population doubling (PD), which can be rescued by ectopic expression of a wild-type allele of TbTR in an apparent dose-dependent manner. Remarkably, introduction of mutations in the TbTR template domain resulted in corresponding mutant telomere sequences, demonstrating that telomere synthesis in T. brucei is dependent on TbTR. We also propose a secondary structure model for TbTR based on phylogenetic analysis and chemical probing experiments, thus defining TbTR domains that may have important functional implications in telomere synthesis. Identification and characterization of TbTR not only provide important insights into T. brucei telomere functions, which have been shown to play important roles in T. brucei pathogenesis, but also offer T. brucei as an attractive model system for studying telomerase biology in pathogenic protozoa and for comparative analysis of telomerase function with higher eukaryotes.
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Shtessel L, Lowden MR, Cheng C, Simon M, Wang K, Ahmed S. Caenorhabditis elegans POT-1 and POT-2 repress telomere maintenance pathways. G3 (BETHESDA, MD.) 2013; 3:305-13. [PMID: 23390606 PMCID: PMC3564990 DOI: 10.1534/g3.112.004440] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/11/2012] [Indexed: 12/23/2022]
Abstract
Telomeres are composed of simple tandem DNA repeats that protect the ends of linear chromosomes from replicative erosion or inappropriate DNA damage response mechanisms. The mammalian Protection Of Telomeres (POT1) protein interacts with single-stranded telomeric DNA and can exert positive and negative effects on telomere length. Of four distinct POT1 homologs in the roundworm Caenorhabditis elegans, deficiency for POT-1 or POT-2 resulted in progressive telomere elongation that occurred because both proteins negatively regulate telomerase. We created a POT-1::mCherry fusion protein that forms discrete foci at C. elegans telomeres, independent of POT-2, allowing for live analysis of telomere dynamics. Transgenic pot-1::mCherry repressed telomerase in pot-1 mutants. Animals deficient for pot-1, but not pot-2, displayed mildly enhanced telomere erosion rates in the absence of the telomerase reverse transcriptase, trt-1. However, trt-1; pot-1 double mutants exhibited delayed senescence in comparison to trt-1 animals, and senescence was further delayed in trt-1; pot-2; pot-1 triple mutants, some of which survived robustly in the absence of telomerase. Our results indicate that POT-1 and POT-2 play independent roles in suppressing a telomerase-independent telomere maintenance pathway but may function together to repress telomerase.
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Affiliation(s)
- Ludmila Shtessel
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-3280
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280
| | - Mia Rochelle Lowden
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-3280
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280
| | - Chen Cheng
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-3280
| | - Matt Simon
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-3280
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280
| | - Kyle Wang
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-3280
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-3280
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280
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Mason PA, Cox LS. The role of DNA exonucleases in protecting genome stability and their impact on ageing. AGE (DORDRECHT, NETHERLANDS) 2012; 34:1317-1340. [PMID: 21948156 PMCID: PMC3528374 DOI: 10.1007/s11357-011-9306-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 08/19/2011] [Indexed: 05/30/2023]
Abstract
Exonucleases are key enzymes involved in many aspects of cellular metabolism and maintenance and are essential to genome stability, acting to cleave DNA from free ends. Exonucleases can act as proof-readers during DNA polymerisation in DNA replication, to remove unusual DNA structures that arise from problems with DNA replication fork progression, and they can be directly involved in repairing damaged DNA. Several exonucleases have been recently discovered, with potentially critical roles in genome stability and ageing. Here we discuss how both intrinsic and extrinsic exonuclease activities contribute to the fidelity of DNA polymerases in DNA replication. The action of exonucleases in processing DNA intermediates during normal and aberrant DNA replication is then assessed, as is the importance of exonucleases in repair of double-strand breaks and interstrand crosslinks. Finally we examine how exonucleases are involved in maintenance of mitochondrial genome stability. Throughout the review, we assess how nuclease mutation or loss predisposes to a range of clinical diseases and particularly ageing.
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Affiliation(s)
- Penelope A. Mason
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Lynne S. Cox
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
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Hrdličková R, Nehyba J, Lim SL, Grützner F, Bose HR. Insights into the evolution of mammalian telomerase: platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes. BMC Genomics 2012; 13:216. [PMID: 22655747 PMCID: PMC3546421 DOI: 10.1186/1471-2164-13-216] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 05/04/2012] [Indexed: 01/05/2023] Open
Abstract
Background The TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT (OanTERT) ortholog, and provide a comparison with genes of other vertebrates. Results The OanTERT encodes a protein with a high sequence similarity to marsupial TERT and avian TERT. Like the TERT of sauropsids and marsupials, as well as that of sharks and echinoderms, OanTERT contains extended variable linkers in the N-terminal region suggesting that they were present already in basal vertebrates and lost independently in ray-finned fish and eutherian mammals. Several alternatively spliced OanTERT variants structurally similar to avian TERT variants were identified. Telomerase activity is expressed in all platypus tissues like that of cold-blooded animals and murine rodents. OanTERT was localized on pseudoautosomal regions of sex chromosomes X3/Y2, expanding the homology between human chromosome 5 and platypus sex chromosomes. Synteny analysis suggests that TERT co-localized with sex-linked genes in the last common mammalian ancestor. Interestingly, female platypuses express higher levels of telomerase in heart and liver tissues than do males. Conclusions OanTERT shares many features with TERT of the reptilian outgroup, suggesting that OanTERT represents the ancestral mammalian TERT. Features specific to TERT of eutherian mammals have, therefore, evolved more recently after the divergence of monotremes.
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Affiliation(s)
- Radmila Hrdličková
- Section of Molecular Genetics and Microbiology, School of Biological Science, University of Texas at Austin, 78712-1095, USA
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46
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Cheng C, Shtessel L, Brady MM, Ahmed S. Caenorhabditis elegans POT-2 telomere protein represses a mode of alternative lengthening of telomeres with normal telomere lengths. Proc Natl Acad Sci U S A 2012. [PMID: 22547822 DOI: 10.1073/pnas.lll9191109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Canonical telomere repeats at chromosome termini can be maintained by a telomerase-independent pathway termed alternative lengthening of telomeres (ALT). Human cancers that survive via ALT can exhibit long and heterogeneous telomeres, although many telomerase-negative tumors possess telomeres of normal length. Here, we report that Caenorhabditis elegans telomerase mutants that survived via ALT possessed either long or normal telomere lengths. Most ALT strains displayed end-to-end chromosome fusions, suggesting that critical telomere shortening occurred before or concomitant with ALT. ALT required the 9-1-1 DNA damage response complex and its clamp loader, HPR-17. Deficiency for the POT-2 telomere binding protein promoted ALT in telomerase mutants, overcame the requirement for the 9-1-1 complex in ALT, and promoted ALT with normal telomere lengths. We propose that telomerase-deficient human tumors with normal telomere lengths could represent a mode of ALT that is facilitated by telomere capping protein dysfunction.
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Affiliation(s)
- Chen Cheng
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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47
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Caenorhabditis elegans POT-2 telomere protein represses a mode of alternative lengthening of telomeres with normal telomere lengths. Proc Natl Acad Sci U S A 2012; 109:7805-10. [PMID: 22547822 DOI: 10.1073/pnas.1119191109] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Canonical telomere repeats at chromosome termini can be maintained by a telomerase-independent pathway termed alternative lengthening of telomeres (ALT). Human cancers that survive via ALT can exhibit long and heterogeneous telomeres, although many telomerase-negative tumors possess telomeres of normal length. Here, we report that Caenorhabditis elegans telomerase mutants that survived via ALT possessed either long or normal telomere lengths. Most ALT strains displayed end-to-end chromosome fusions, suggesting that critical telomere shortening occurred before or concomitant with ALT. ALT required the 9-1-1 DNA damage response complex and its clamp loader, HPR-17. Deficiency for the POT-2 telomere binding protein promoted ALT in telomerase mutants, overcame the requirement for the 9-1-1 complex in ALT, and promoted ALT with normal telomere lengths. We propose that telomerase-deficient human tumors with normal telomere lengths could represent a mode of ALT that is facilitated by telomere capping protein dysfunction.
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48
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Rubtsova M, Vasilkova D, Malyavko A, Naraikina Y, Zvereva M, Dontsova O. Telomere lengthening and other functions of telomerase. Acta Naturae 2012; 4:44-61. [PMID: 22872811 PMCID: PMC3408703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Telomerase is an enzyme that maintains the length of the telomere. The telomere length specifies the number of divisions a cell can undergo before it finally dies (i.e. the proliferative potential of cells). For example, telomerase is activated in embryonic cell lines and the telomere length is maintained at a constant level; therefore, these cells have an unlimited fission potential. Stem cells are characterized by a lower telomerase activity, which enables only partial compensation for the shortening of telomeres. Somatic cells are usually characterized by the absence of telomerase activity. Telomere shortening leads to the attainment of the Hayflick limit, the transition of cells to a state of senescence. The cells subsequently enter a state of crisis, accompanied by massive cell death. The surviving cells become cancer cells, which are capable both of dividing indefinitely and maintaining telomere length (usually with the aid of telomerase). Telomerase is a reverse transcriptase. It consists of two major components: telomerase RNA (TER) and reverse transcriptase (TERT). TER is a non-coding RNA, and it contains the region which serves as a template for telomere synthesis. An increasing number of articles focussing on the alternative functions of telomerase components have recently started appearing. The present review summarizes data on the structure, biogenesis, and functions of telomerase.
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Affiliation(s)
- M.P. Rubtsova
- Lomonosov Moscow State University, Chemistry Department
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State
University
| | | | - A.N. Malyavko
- Lomonosov Moscow State University, Chemistry Department
| | - Yu.V. Naraikina
- Lomonosov Moscow State University, Faculty of Bioengineering and
Bioinformatics
| | - M.I. Zvereva
- Lomonosov Moscow State University, Chemistry Department
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State
University
| | - O.A. Dontsova
- Lomonosov Moscow State University, Chemistry Department
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State
University
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Organismal propagation in the absence of a functional telomerase pathway in Caenorhabditis elegans. EMBO J 2012; 31:2024-33. [PMID: 22425786 PMCID: PMC3343340 DOI: 10.1038/emboj.2012.61] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/14/2012] [Indexed: 11/09/2022] Open
Abstract
To counteract replication-dependent telomere shortening most eukaryotic cells rely on the telomerase pathway, which is crucial for the maintenance of proliferative potential of germ and stem cell populations of multicellular organisms. Likewise, cancer cells usually engage the telomerase pathway for telomere maintenance to gain immortality. However, in ∼10% of human cancers telomeres are maintained through telomerase-independent alternative lengthening of telomeres (ALT) pathways. Here, we describe the generation and characterization of C. elegans survivors in a strain lacking the catalytic subunit of telomerase and the nematode telomere-binding protein CeOB2. These clonal strains, some of which have been propagated for >180 generations, represent the first example of a multicellular organism with canonical telomeres that can survive without a functional telomerase pathway. The animals display the heterogeneous telomere length characteristic for ALT cells, contain single-stranded C-circles, a transcription profile pointing towards an adaptation to chronic stress and are therefore a unique and valuable tool to decipher the ALT mechanism.
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50
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Telomere maintenance and telomerase activity are differentially regulated in asexual and sexual worms. Proc Natl Acad Sci U S A 2012; 109:4209-14. [PMID: 22371573 DOI: 10.1073/pnas.1118885109] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In most sexually reproducing animals, replication and maintenance of telomeres occurs in the germ line and during early development in embryogenesis through the use of telomerase. Somatic cells generally do not maintain telomere sequences, and these cells become senescent in adults as telomeres shorten to a critical length. Some animals reproduce clonally and must therefore require adult somatic mechanisms for maintaining their chromosome ends. Here we study the telomere biology of planarian flatworms with apparently limitless regenerative capacity fueled by a population of highly proliferative adult stem cells. We show that somatic telomere maintenance is different in asexual and sexual animals. Asexual animals maintain telomere length somatically during reproduction by fission or when regeneration is induced by amputation, whereas sexual animals only achieve telomere elongation through sexual reproduction. We demonstrate that this difference is reflected in the expression and alternate splicing of the protein subunit of the telomerase enzyme. Asexual adult planarian stem cells appear to maintain telomere length over evolutionary timescales without passage through a germ-line stage. The adaptations we observe demonstrate indefinite somatic telomerase activity in proliferating stem cells during regeneration or reproduction by fission, and establish planarians as a pertinent model for studying telomere structure, function, and maintenance.
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