1
|
Udroiu I, Marinaccio J, Sgura A. Many Functions of Telomerase Components: Certainties, Doubts, and Inconsistencies. Int J Mol Sci 2022; 23:ijms232315189. [PMID: 36499514 PMCID: PMC9736166 DOI: 10.3390/ijms232315189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
A growing number of studies have evidenced non-telomeric functions of "telomerase". Almost all of them, however, investigated the non-canonical effects of the catalytic subunit TERT, and not the telomerase ribonucleoprotein holoenzyme. These functions mainly comprise signal transduction, gene regulation and the increase of anti-oxidative systems. Although less studied, TERC (the RNA component of telomerase) has also been shown to be involved in gene regulation, as well as other functions. All this has led to the publication of many reviews on the subject, which, however, are often disseminating personal interpretations of experimental studies of other researchers as original proofs. Indeed, while some functions such as gene regulation seem ascertained, especially because mechanistic findings have been provided, other ones remain dubious and/or are contradicted by other direct or indirect evidence (e.g., telomerase activity at double-strand break site, RNA polymerase activity of TERT, translation of TERC, mitochondrion-processed TERC). In a critical study of the primary evidence so far obtained, we show those functions for which there is consensus, those showing contradictory results and those needing confirmation. The resulting picture, together with some usually neglected aspects, seems to indicate a link between TERT and TERC functions and cellular stemness and gives possible directions for future research.
Collapse
|
2
|
Guzmán-Markevich K, Roco ÁS, Ruiz-García A, Bullejos M. Cytogenetic Analysis in the Toad Species Bufo spinosus, Bufotes viridis and Epidalea calamita (Anura, Bufonidae) from the Mediterranean Area. Genes (Basel) 2022; 13:genes13081475. [PMID: 36011385 PMCID: PMC9408106 DOI: 10.3390/genes13081475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/13/2022] [Accepted: 08/14/2022] [Indexed: 11/06/2022] Open
Abstract
Taxonomy in Bufonidae witnessed notable transformations. Bufotes viridis and Epidalea calamita, previously included in genus Bufo, were relocated in other genera, while the genus Bufo was restricted to members of the earlier Bufo bufo group. On the other hand, Bufo bufo sensu lato now includes four species: Bufo bufo, Bufo spinosus, Bufo verrucosissimus and Bufo eichwaldi. In this study, we examined three species of three Bufonidae genera (B. spinosus, B. viridis and E. calamita) by conventional (C-banding and Ag-NOR staining) and molecular (in situ hybridization with probes for telomeric repeats and rDNA loci, and genomic in situ hybridization (GISH)) cytogenetic methods. C-banding patterns are reported for the first time for B. spinosus and E. calamita populations from Iberian Peninsula and for B. viridis from Greece, and reveal several differences with the reported C-banded karyotypes described for other European populations of these species. Silver staining shows size heteromorphisms of the signals at the Nucleolar Organizing Region (NOR). By contrast, FISH with ribosomal probes only reveal size heteromorphism of rDNA sequences in E. calamita, suggesting that the differences observed after silver staining in B. spinosus and B. viridis should be attributed to differences in chromosomal condensation and/or gene activity rather than to differences in the copy number for ribosomal genes. Regarding telomeric repeats, E. calamita is the only species with interstitial telomeric sequences (ITS) located on centromeric regions, probably originated by accumulation of telomeric sequences in the centromeric heterochromatin. Finally, we analyzed the composition and distribution of repetitive sequences by genome in situ hybridization. These experiments reveal the accumulation of repetitive sequences in centromeric regions of the three species, although these sequences are not conserved when species from different genera are compared.
Collapse
|
3
|
Molecular Dynamics and Evolution of Centromeres in the Genus Equus. Int J Mol Sci 2022; 23:ijms23084183. [PMID: 35457002 PMCID: PMC9024551 DOI: 10.3390/ijms23084183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
The centromere is the chromosomal locus essential for proper chromosome segregation. While the centromeric function is well conserved and epigenetically specified, centromeric DNA sequences are typically composed of satellite DNA and represent the most rapidly evolving sequences in eukaryotic genomes. The presence of satellite sequences at centromeres hampered the comprehensive molecular analysis of these enigmatic loci. The discovery of functional centromeres completely devoid of satellite repetitions and fixed in some animal and plant species represented a turning point in centromere biology, definitively proving the epigenetic nature of the centromere. The first satellite-free centromere, fixed in a vertebrate species, was discovered in the horse. Later, an extraordinary number of satellite-free neocentromeres had been discovered in other species of the genus Equus, which remains the only mammalian genus with numerous satellite-free centromeres described thus far. These neocentromeres arose recently during evolution and are caught in a stage of incomplete maturation. Their presence made the equids a unique model for investigating, at molecular level, the minimal requirements for centromere seeding and evolution. This model system provided new insights on how centromeres are established and transmitted to the progeny and on the role of satellite DNA in different aspects of centromere biology.
Collapse
|
4
|
Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
Collapse
Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
5
|
Telomeric-Like Repeats Flanked by Sequences Retrotranscribed from the Telomerase RNA Inserted at DNA Double-Strand Break Sites during Vertebrate Genome Evolution. Int J Mol Sci 2021; 22:ijms222011048. [PMID: 34681704 PMCID: PMC8537989 DOI: 10.3390/ijms222011048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 01/28/2023] Open
Abstract
Interstitial telomeric sequences (ITSs) are stretches of telomeric-like repeats located at internal chromosomal sites. We previously demonstrated that ITSs have been inserted during the repair of DNA double-strand breaks in the course of evolution and that some rodent ITSs, called TERC-ITSs, are flanked by fragments retrotranscribed from the telomerase RNA component (TERC). In this work, we carried out an extensive search of TERC-ITSs in 30 vertebrate genomes and identified 41 such loci in 22 species, including in humans and other primates. The fragment retrotranscribed from the TERC RNA varies in different lineages and its sequence seems to be related to the organization of TERC. Through comparative analysis of TERC-ITSs with orthologous empty loci, we demonstrated that, at each locus, the TERC-like sequence and the ITS have been inserted in one step in the course of evolution. Our findings suggest that telomerase participated in a peculiar pathway of DNA double-strand break repair involving retrotranscription of its RNA component and that this mechanism may be active in all vertebrate species. These results add new evidence to the hypothesis that RNA-templated DNA repair mechanisms are active in vertebrate cells.
Collapse
|
6
|
Souza J, Guimarães E, Pinheiro-Figliuolo V, Cioffi MB, Bertollo LAC, Feldberg E. Chromosomal Analysis of Ctenolucius hujeta Valenciennes, 1850 (Characiformes): A New Piece in the Chromosomal Evolution of the Ctenoluciidae. Cytogenet Genome Res 2021; 161:195-202. [PMID: 34126615 DOI: 10.1159/000515456] [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: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 11/19/2022] Open
Abstract
Ctenoluciidae (Characiformes), a family of freshwater fishes, comprises 2 genera, Ctenolucius and Boulengerella, with 7 recognized species. Up to now, only species of the genus Boulengerella have been subjected to cytogenetic studies. Here, we investigated the karyotype and other cytogenetic features of pike characin, Ctenolucius hujeta, using conventional (Giemsa staining, C-banding, Ag-NOR staining) and molecular (rDNA, telomeric sequences, and fiber-FISH mapping) procedures. This species has a diploid chromosome number of 2n = 36, and a karyotype composed of 12m + 20sm + 4a and FN = 68, similar to that found in Boulengerella species. However, differences regarding the number and distribution of several chromosomal markers support a distinct generic status. Colocalization of the 18S and 5S rDNA genes is an exclusive characteristic of the C. hujeta genome, with an interspersed distribution in the chromosomal fiber, an unusual phenomenon among eukaryotes. Additionally, our results support the view that Ctenoluciidae and Lebiasinidae families are closely related.
Collapse
Affiliation(s)
- José Souza
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Erika Guimarães
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | | | - Marcelo B Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Luiz A C Bertollo
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Eliana Feldberg
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| |
Collapse
|
7
|
Oliveira VCS, Viana PF, Gross MC, Feldberg E, Da Silveira R, de Bello Cioffi M, Bertollo LAC, Schneider CH. Looking for genetic effects of polluted anthropized environments on Caiman crocodilus crocodilus (Reptilia, Crocodylia): A comparative genotoxic and chromosomal analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111835. [PMID: 33383344 DOI: 10.1016/j.ecoenv.2020.111835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
The Amazon aquatic ecosystems have been modified by the human population growth, going through changes in their water bodies and aquatic biota. The spectacled alligator (Caiman crocodilus crocodilus) has a wide distribution and adaptability to several environments, even those polluted ones. This study aimed to investigate if a Caiman species living in urban streams of Manaus city (Amazonas State, Brazil) is affected by environmental pollution. For that, it was used classical and molecular cytogenetic procedures, in addition to micronucleus and comet assays. Although the karyotype macrostructure remains unaltered (2 n = 42 chromosomes; 24 t + 18 m/sm; NF = 60), the genotoxic analysis and the cytogenetic mapping of repetitive DNA sequences demonstrated that polluted environments alter the genome of the specimens, affecting both the chromosomal organization and the genetic material.
Collapse
Affiliation(s)
- Vanessa Cristina Sales Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil; Laboratório de Citogenômica Animal, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Patrik Ferreira Viana
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Maria Claudia Gross
- Parque Tecnológico Itaipu, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu, Paraná, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Ronis Da Silveira
- Laboratório de Zoologia Aplicada à Conservação, Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Carlos Henrique Schneider
- Centro Universitário Dinâmica das Cataratas, Faculdade Anglo Americano, Foz do Iguaçu, Paraná, Brazil
| |
Collapse
|
8
|
The Amazonian Red Side-Necked Turtle Rhinemys rufipes (Spix, 1824) (Testudines, Chelidae) Has a GSD Sex-Determining Mechanism with an Ancient XY Sex Microchromosome System. Cells 2020; 9:cells9092088. [PMID: 32932633 PMCID: PMC7563702 DOI: 10.3390/cells9092088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023] Open
Abstract
The Amazonian red side-necked turtle Rhynemis rufipes is an endemic Amazonian Chelidae species that occurs in small streams throughout Colombia and Brazil river basins. Little is known about various biological aspects of this species, including its sex determination strategies. Among chelids, the greatest karyotype diversity is found in the Neotropical species, with several 2n configurations, including cases of triploidy. Here, we investigate the karyotype of Rhinemys rufipes by applying combined conventional and molecular cytogenetic procedures. This allowed us to discover a genetic sex-determining mechanism that shares an ancestral micro XY sex chromosome system. This ancient micro XY system recruited distinct repeat motifs before it diverged from several South America and Australasian species. We propose that such a system dates back to the earliest lineages of the chelid species before the split of South America and Australasian lineages.
Collapse
|
9
|
Hidaka D, Onozawa M, Miyashita N, Yokoyama S, Nakagawa M, Hashimoto D, Teshima T. Short-term treatment with imetelstat sensitizes hematopoietic malignant cells to a genotoxic agent via suppression of the telomerase-mediated DNA repair process. Leuk Lymphoma 2020; 61:2722-2732. [PMID: 32571117 DOI: 10.1080/10428194.2020.1779256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Imetelstat is a specific and competitive inhibitor of telomerase enzymatic activity. We demonstrated that imetelstat could interfere with the DNA repair process and enhance the effect of DNA damaging agents using hematological tumor cell lines. Short-term administration of imetelstat enhanced growth suppression by anticancer agents and radiation. It also upregulated γH2AX expression induced by irradiation. Immunofluorescence staining showed that both human telomerase reverse transcriptase (hTERT) and γH2AX were upregulated and co-localized in the nucleus of peripheral blood mononuclear cells after irradiation, suggesting that hTERT was involved in the DNA-DSB repair process. Imetelstat enhanced growth inhibitory effect of cytotoxic agents in short-term culture without shortening of telomeres, indicating that this effect was attributed by telomere length independent mechanism. Our results suggest that the combination of short-term treatment with imetelstat and cytotoxic agent is a promising strategy to treat a wide variety of hematopoietic malignancies.
Collapse
Affiliation(s)
- Daisuke Hidaka
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Sapporo, Japan
| | - Masahiro Onozawa
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Sapporo, Japan
| | - Naohiro Miyashita
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Sapporo, Japan
| | - Shota Yokoyama
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Sapporo, Japan
| | - Masao Nakagawa
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Sapporo, Japan
| | - Daigo Hashimoto
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Sapporo, Japan
| |
Collapse
|
10
|
Clemente L, Mazzoleni S, Pensabene Bellavia E, Augstenová B, Auer M, Praschag P, Protiva T, Velenský P, Wagner P, Fritz U, Kratochvíl L, Rovatsos M. Interstitial Telomeric Repeats Are Rare in Turtles. Genes (Basel) 2020; 11:genes11060657. [PMID: 32560114 PMCID: PMC7348932 DOI: 10.3390/genes11060657] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/18/2023] Open
Abstract
Telomeres are nucleoprotein complexes protecting chromosome ends in most eukaryotic organisms. In addition to chromosome ends, telomeric-like motifs can be accumulated in centromeric, pericentromeric and intermediate (i.e., between centromeres and telomeres) positions as so-called interstitial telomeric repeats (ITRs). We mapped the distribution of (TTAGGG)n repeats in the karyotypes of 30 species from nine families of turtles using fluorescence in situ hybridization. All examined species showed the expected terminal topology of telomeric motifs at the edges of chromosomes. We detected ITRs in only five species from three families. Combining our and literature data, we inferred seven independent origins of ITRs among turtles. ITRs occurred in turtles in centromeric positions, often in several chromosomal pairs, in a given species. Their distribution does not correspond directly to interchromosomal rearrangements. Our findings support that centromeres and non-recombining parts of sex chromosomes are very dynamic genomic regions, even in turtles, a group generally thought to be slowly evolving. However, in contrast to squamate reptiles (lizards and snakes), where ITRs were found in more than half of the examined species, and birds, the presence of ITRs is generally rare in turtles, which agrees with the expected low rates of chromosomal rearrangements and rather slow karyotype evolution in this group.
Collapse
Affiliation(s)
- Lorenzo Clemente
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Eleonora Pensabene Bellavia
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Markus Auer
- Museum of Zoology, Senckenberg Dresden, 01109 Dresden, Germany; (M.A.); (U.F.)
| | | | | | - Petr Velenský
- Prague Zoological Garden, 17100 Prague, Czech Republic;
| | | | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, 01109 Dresden, Germany; (M.A.); (U.F.)
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
- Correspondence:
| |
Collapse
|
11
|
Santagostino M, Piras FM, Cappelletti E, Del Giudice S, Semino O, Nergadze SG, Giulotto E. Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective. Int J Mol Sci 2020; 21:ijms21082838. [PMID: 32325780 PMCID: PMC7215372 DOI: 10.3390/ijms21082838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Interstitial telomeric sequences (ITSs) are short stretches of telomeric-like repeats (TTAGGG)n at nonterminal chromosomal sites. We previously demonstrated that, in the genomes of primates and rodents, ITSs were inserted during the repair of DNA double-strand breaks. These conclusions were derived from sequence comparisons of ITS-containing loci and ITS-less orthologous loci in different species. To our knowledge, insertion polymorphism of ITSs, i.e., the presence of an ITS-containing allele and an ITS-less allele in the same species, has not been described. In this work, we carried out a genome-wide analysis of 2504 human genomic sequences retrieved from the 1000 Genomes Project and a PCR-based analysis of 209 human DNA samples. In spite of the large number of individual genomes analyzed we did not find any evidence of insertion polymorphism in the human population. On the contrary, the analysis of ITS loci in the genome of a single horse individual, the reference genome, allowed us to identify five heterozygous ITS loci, suggesting that insertion polymorphism of ITSs is an important source of genetic variability in this species. Finally, following a comparative sequence analysis of horse ITSs and of their orthologous empty loci in other Perissodactyla, we propose models for the mechanism of ITS insertion during the evolution of this order.
Collapse
|
12
|
Campos AS, Favarato RM, Feldberg E. Interspecific cytogenetic relationships in three Acestrohynchus species (Acestrohynchinae, Characiformes) reveal the existence of possible cryptic species. COMPARATIVE CYTOGENETICS 2020; 14:27-42. [PMID: 31998448 PMCID: PMC6976687 DOI: 10.3897/compcytogen.v14i1.33483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
The karyotypes and chromosomal characteristics of three Acestrorhynchus Eigenmann et Kennedy, 1903 species were examined using conventional and molecular protocols. These species had invariably a diploid chromosome number 2n = 50. Acestrorhynchus falcatus (Block, 1794) and Acestrorhynchus falcirostris (Cuvier, 1819) had the karyotype composed of 16 metacentric (m) + 28 submetacentric (sm) + 6 subtelocentric (st) chromosomes while Acestrorhynchus microlepis (Schomburgk, 1841) had the karyotype composed of 14m+30sm+6st elements. In this species, differences of the conventional and molecular markers between the populations of Catalão Lake (AM) and of Apeu Stream (PA) were found. Thus the individuals of Pará (Apeu) were named Acestrorhynchus prope microlepis. The distribution of the constitutive heterochromatin blocks was species-specific, with C-positive bands in the centromeric and telomeric regions of a number of different chromosomes, as well as in interstitial sites and completely heterochromatic arms. The phenotypes of nucleolus organizer region (NOR) were simple, i. e. in a terminal position on the p arm of pair No. 23 except in A. microlepis, in which it was located on the q arm. Fluorescence in situ hybridization (FISH) revealed 18S rDNA sites on one chromosome pair in karyotype of A. falcirostris and A. prope microlepis (pair No. 23) and three pairs (Nos. 12, 23, 24) in A. falcatus and (Nos. 8, 23, 24) in A. microlepis; 5S rDNA sites were detected in one chromosome pair in all three species. The mapping of the telomeric sequences revealed terminal sequences in all the chromosomes, as well as the presence of interstitial telomeric sequences (ITSs) in a number of chromosome pairs. The cytogenetic data recorded in the present study indicate that A. prope microlepis may be an unnamed species.
Collapse
Affiliation(s)
- Alber Sousa Campos
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG GCBEv). Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, , Av. André Araújo, 2936, Petrópolis, Manaus, Amazonas, BrazilInstituto Nacional de Pesquisas da AmazôniaManausBrazil
| | - Ramon Marin Favarato
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG GCBEv). Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, , Av. André Araújo, 2936, Petrópolis, Manaus, Amazonas, BrazilInstituto Nacional de Pesquisas da AmazôniaManausBrazil
| | - Eliana Feldberg
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG GCBEv). Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, , Av. André Araújo, 2936, Petrópolis, Manaus, Amazonas, BrazilInstituto Nacional de Pesquisas da AmazôniaManausBrazil
| |
Collapse
|
13
|
Silva CEFE, Souza ÉMSD, Eler ES, Silva MNFD, Feldberg E. Comparison of the heterochromatin and telomeric sequences distribuition in chromosomes of 11 species of Amazonian marsupials (Didelphimorphia; Didelphidae). Genet Mol Biol 2020; 43:e20190357. [PMID: 32396598 PMCID: PMC7216969 DOI: 10.1590/1678-4685-gmb-2019-0357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/18/2020] [Indexed: 12/02/2022] Open
Abstract
In recent decades the diploid numbers recorded in the New World marsupials have
been widely discussed in the context of the processes of karyotype evolution in
these mammals. While Interstitial Telomeric Sequences (ITS) have long been
interpreted as remnants of chromosomal fusion, the biological role of these
features, together with their intraspecific variation, has raised a number of
questions. In the present study, we analyzed the karyotype of 11 species of
Amazonian didelphids, comparing the distribution of the heterochromatin with
that of the telomeric signals, and found that, in six species, the ITS coincided
with the blocks of heterochromatin. While ITS were found in the X chromosomes of
all Marmosa murina individuals, they were variable in all the
other species, representing a specific character of each lineage. Our results
support the conclusion that ITS may not always be a consequence of chromosomal
rearrangements, and that the mechanisms that produce them are still unclear.
Collapse
Affiliation(s)
| | | | - Eduardo Schmidt Eler
- Instituto Nacional de Pesquisas da Amazônia, Brazil; Universidade Anhembi Morumbi, Brazil
| | | | | |
Collapse
|
14
|
Aksenova AY, Mirkin SM. At the Beginning of the End and in the Middle of the Beginning: Structure and Maintenance of Telomeric DNA Repeats and Interstitial Telomeric Sequences. Genes (Basel) 2019; 10:genes10020118. [PMID: 30764567 PMCID: PMC6410037 DOI: 10.3390/genes10020118] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Tandem DNA repeats derived from the ancestral (TTAGGG)n run were first detected at chromosome ends of the majority of living organisms, hence the name telomeric DNA repeats. Subsequently, it has become clear that telomeric motifs are also present within chromosomes, and they were suitably called interstitial telomeric sequences (ITSs). It is well known that telomeric DNA repeats play a key role in chromosome stability, preventing end-to-end fusions and precluding the recurrent DNA loss during replication. Recent data suggest that ITSs are also important genomic elements as they confer its karyotype plasticity. In fact, ITSs appeared to be among the most unstable microsatellite sequences as they are highly length polymorphic and can trigger chromosomal fragility and gross chromosomal rearrangements. Importantly, mechanisms responsible for their instability appear to be similar to the mechanisms that maintain the length of genuine telomeres. This review compares the mechanisms of maintenance and dynamic properties of telomeric repeats and ITSs and discusses the implications of these dynamics on genome stability.
Collapse
Affiliation(s)
- Anna Y Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
| |
Collapse
|
15
|
Mlinarec J, Skuhala A, Jurković A, Malenica N, McCann J, Weiss-Schneeweiss H, Bohanec B, Besendorfer V. The Repetitive DNA Composition in the Natural Pesticide Producer Tanacetum cinerariifolium: Interindividual Variation of Subtelomeric Tandem Repeats. FRONTIERS IN PLANT SCIENCE 2019; 10:613. [PMID: 31156676 PMCID: PMC6532368 DOI: 10.3389/fpls.2019.00613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/25/2019] [Indexed: 05/02/2023]
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.), a plant species endemic to the east Adriatic coast, is used worldwide for production of the organic insecticide, pyrethrin. Most studies concerning Dalmatian pyrethrum have focused on its morphological and biochemical traits relevant for breeding. However, little is known about the chromosomal evolution and genome organization of this species. Our study aims are to identify, classify, and characterize repetitive DNA in the T. cinerariifolium genome using clustering analysis of a low coverage genomic dataset. Repetitive DNA represents about 71.63% of the genome. T. cinerariifolium exhibits linked 5S and 35S rDNA configuration (L-type). FISH reveals amplification of interstitial telomeric repeats (ITRs) in T. cinerariifolium. Of the three newly identified satellite DNA families, TcSAT1 and TcSAT2 are located subterminally on most of T. cinerariifolium chromosomes, while TcSAT3 family is located intercalary within the longer arm of two chromosome pairs. FISH reveals high levels of polymorphism of the TcSAT1 and TcSAT2 sites by comparative screening of 28 individuals. TcSAT2 is more variable than TcSAT1 regarding the number and position of FISH signals. Altogether, our data highlights the dynamic nature of DNA sequences associated with subtelomeres in T. cinerariifolium and suggests that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.
Collapse
Affiliation(s)
- Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | - Ana Skuhala
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Jamie McCann
- Institute of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | | | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| |
Collapse
|
16
|
Dumont BL, Williams CL, Ng BL, Horncastle V, Chambers CL, McGraw LA, Adams D, Mackay TFC, Breen M. Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American Voles. Genetics 2018; 210:83-97. [PMID: 30002081 PMCID: PMC6116968 DOI: 10.1534/genetics.118.301182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/07/2018] [Indexed: 11/18/2022] Open
Abstract
In most mammals, the X and Y chromosomes synapse and recombine along a conserved region of homology known as the pseudoautosomal region (PAR). These homology-driven interactions are required for meiotic progression and are essential for male fertility. Although the PAR fulfills key meiotic functions in most mammals, several exceptional species lack PAR-mediated sex chromosome associations at meiosis. Here, we leveraged the natural variation in meiotic sex chromosome programs present in North American voles (Microtus) to investigate the relationship between meiotic sex chromosome dynamics and X/Y sequence homology. To this end, we developed a novel, reference-blind computational method to analyze sparse sequencing data from flow-sorted X and Y chromosomes isolated from vole species with sex chromosomes that always (Microtus montanus), never (Microtus mogollonensis), and occasionally synapse (Microtus ochrogaster) at meiosis. Unexpectedly, we find more shared X/Y homology in the two vole species with no and sporadic X/Y synapsis compared to the species with obligate synapsis. Sex chromosome homology in the asynaptic and occasionally synaptic species is interspersed along chromosomes and largely restricted to low-complexity sequences, including a striking enrichment for the telomeric repeat sequence, TTAGGG. In contrast, homology is concentrated in high complexity, and presumably euchromatic, sequence on the X and Y chromosomes of the synaptic vole species, M. montanus Taken together, our findings suggest key conditions required to sustain the standard program of X/Y synapsis at meiosis and reveal an intriguing connection between heterochromatic repeat architecture and noncanonical, asynaptic mechanisms of sex chromosome segregation in voles.
Collapse
Affiliation(s)
- Beth L Dumont
- Initiative in Biological Complexity, North Carolina State University, Raleigh, North Carolina 04609
| | - Christina L Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 04609
| | - Bee Ling Ng
- Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, United Kingdom, CB10 1SA
| | - Valerie Horncastle
- School of Forestry, Northern Arizona University, Flagstaff, Arizona 86011
| | - Carol L Chambers
- School of Forestry, Northern Arizona University, Flagstaff, Arizona 86011
| | - Lisa A McGraw
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 04609
| | - David Adams
- Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, United Kingdom, CB10 1SA
| | - Trudy F C Mackay
- Initiative in Biological Complexity, North Carolina State University, Raleigh, North Carolina 04609
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 04609
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 04609
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 04609
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 04609
| |
Collapse
|
17
|
Expression of functional alternative telomerase RNA component gene in mouse brain and in motor neurons cells protects from oxidative stress. Oncotarget 2018; 7:78297-78309. [PMID: 27823970 PMCID: PMC5346639 DOI: 10.18632/oncotarget.13049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/28/2016] [Indexed: 11/30/2022] Open
Abstract
Telomerase, a ribonucleoprotein, is highly expressed and active in many tumor cells and types, therefore it is considered to be a target for anti-cancer agents. On the other hand, recent studies demonstrated that activation of telomerase is a potential therapeutic target for age related diseases. Telomerase mainly consists of a catalytic protein subunit with a reverse transcription activity (TERT) and an RNA component (TERC), a long non-coding RNA, which serves as a template for the re-elongation of telomeres by TERT. We previously showed that TERT is highly expressed in distinct neuronal cells of the mouse brain and its expression declined with age. To understand the role of telomerase in non-mitotic, fully differentiated cells such neurons we here examined the expression of the other component, TERC, in mouse brain. Surprisingly, by first using bioinformatics analysis, we identified an alternative TERC gene (alTERC) in the mouse genome. Using further experimental approaches we described the presence of a functional alTERC in the mouse brain and spleen, in cultures of motor neurons- like cells and neuroblastoma tumor cells. The alTERC is similar (87%) to mouse TERC (mTERC) with a deletion of 18 bp in the TERC conserved region 4 (CR4). This alTERC gene is expressed and its product interacts with the endogenous mTERT protein and with an exogenous human TERT protein (hTERT) to form an active enzyme. Overexpression of the alTERC and the mTERC genes, in mouse motor neurons like cells, increased the activity of TERT without affecting its protein level. Under oxidative stress conditions, alTERC significantly increased the survival of motor neurons cells without altering the level of TERT protein or its activity. The results suggest that the expression of the alTERC gene in the mouse brain provides an additional way for regulating telomerase activity under normal and stress conditions and confers protection to neuronal cells from oxidative stress.
Collapse
|
18
|
Chirino MG, Dalíková M, Marec FR, Bressa MJ. Chromosomal distribution of interstitial telomeric sequences as signs of evolution through chromosome fusion in six species of the giant water bugs (Hemiptera, Belostoma). Ecol Evol 2017. [PMID: 28770061 DOI: 10.1002/ece3.3098/pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Tandem arrays of TTAGG repeats show a highly conserved location at the telomeres across the phylogenetic tree of arthropods. In giant water bugs Belostoma, the chromosome number changed during speciation by fragmentation of the single ancestral X chromosome, resulting in a multiple sex chromosome system. Several autosome-autosome fusions and a fusion between the sex chromosome pair and an autosome pair resulted in the reduced number in several species. We mapped the distribution of telomeric sequences and interstitial telomeric sequences (ITSs) in Belostoma candidulum (2n = 12 + XY/XX; male/female), B. dentatum (2n = 26 + X1X2Y/X1X1X2X2), B. elegans (2n = 26 + X1X2Y/X1X1X2X2), B. elongatum (2n = 26 + X1X2Y/X1X1X2X2), B. micantulum (2n = 14 + XY/XX), and B. oxyurum (2n = 6 + XY/XX) by FISH with the (TTAGG) n probes. Hybridization signals confirmed the presence of TTAGG repeats in the telomeres of all species examined. The three species with reduced chromosome numbers showed additional hybridization signals in interstitial positions, indicating the occurrence of ITS. From the comparison of all species here analyzed, we observed inverse relationships between chromosome number and chromosome size, and between presence/absence of ITS and chromosome number. The ITS distribution between these closely related species supports the hypothesis that several telomere-telomere fusions of the chromosomes from an ancestral diploid chromosome number 2n = 26 + XY/XX played a major role in the karyotype evolution of Belostoma. Consequently, our study provide valuable features that can be used to understand the karyotype evolution, may contribute to a better understanding of taxonomic relationships, and also elucidate the high plasticity of nuclear genomes at the chromosomal level during the speciation processes.
Collapse
Affiliation(s)
- Mónica G Chirino
- Grupo de Citogenética de Insectos Instituto de Ecología, Genética y Evolución de Buenos Aires Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Autónoma de Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas Ciudad Autónoma de Buenos Aires Argentina
| | - Martina Dalíková
- Laboratory of Molecular Cytogenetics Institute of Entomology Biology Centre ASCR České Budějovice Czech Republic
| | - František R Marec
- Laboratory of Molecular Cytogenetics Institute of Entomology Biology Centre ASCR České Budějovice Czech Republic
| | - María J Bressa
- Grupo de Citogenética de Insectos Instituto de Ecología, Genética y Evolución de Buenos Aires Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Autónoma de Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas Ciudad Autónoma de Buenos Aires Argentina
| |
Collapse
|
19
|
Chirino MG, Dalíková M, Marec FR, Bressa MJ. Chromosomal distribution of interstitial telomeric sequences as signs of evolution through chromosome fusion in six species of the giant water bugs (Hemiptera, Belostoma). Ecol Evol 2017; 7:5227-5235. [PMID: 28770061 PMCID: PMC5528210 DOI: 10.1002/ece3.3098] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 11/11/2022] Open
Abstract
Tandem arrays of TTAGG repeats show a highly conserved location at the telomeres across the phylogenetic tree of arthropods. In giant water bugs Belostoma, the chromosome number changed during speciation by fragmentation of the single ancestral X chromosome, resulting in a multiple sex chromosome system. Several autosome–autosome fusions and a fusion between the sex chromosome pair and an autosome pair resulted in the reduced number in several species. We mapped the distribution of telomeric sequences and interstitial telomeric sequences (ITSs) in Belostoma candidulum (2n = 12 + XY/XX; male/female), B. dentatum (2n = 26 + X1X2Y/X1X1X2X2), B. elegans (2n = 26 + X1X2Y/X1X1X2X2), B. elongatum (2n = 26 + X1X2Y/X1X1X2X2), B. micantulum (2n = 14 + XY/XX), and B. oxyurum (2n = 6 + XY/XX) by FISH with the (TTAGG)n probes. Hybridization signals confirmed the presence of TTAGG repeats in the telomeres of all species examined. The three species with reduced chromosome numbers showed additional hybridization signals in interstitial positions, indicating the occurrence of ITS. From the comparison of all species here analyzed, we observed inverse relationships between chromosome number and chromosome size, and between presence/absence of ITS and chromosome number. The ITS distribution between these closely related species supports the hypothesis that several telomere–telomere fusions of the chromosomes from an ancestral diploid chromosome number 2n = 26 + XY/XX played a major role in the karyotype evolution of Belostoma. Consequently, our study provide valuable features that can be used to understand the karyotype evolution, may contribute to a better understanding of taxonomic relationships, and also elucidate the high plasticity of nuclear genomes at the chromosomal level during the speciation processes.
Collapse
Affiliation(s)
- Mónica G Chirino
- Grupo de Citogenética de Insectos Instituto de Ecología, Genética y Evolución de Buenos Aires Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Autónoma de Buenos Aires Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas Ciudad Autónoma de Buenos Aires Argentina
| | - Martina Dalíková
- Laboratory of Molecular Cytogenetics Institute of Entomology Biology Centre ASCR České Budějovice Czech Republic
| | - František R Marec
- Laboratory of Molecular Cytogenetics Institute of Entomology Biology Centre ASCR České Budějovice Czech Republic
| | - María J Bressa
- Grupo de Citogenética de Insectos Instituto de Ecología, Genética y Evolución de Buenos Aires Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Autónoma de Buenos Aires Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas Ciudad Autónoma de Buenos Aires Argentina
| |
Collapse
|
20
|
Bolzán AD. Interstitial telomeric sequences in vertebrate chromosomes: Origin, function, instability and evolution. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:51-65. [PMID: 28927537 DOI: 10.1016/j.mrrev.2017.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/13/2017] [Accepted: 04/17/2017] [Indexed: 12/21/2022]
Abstract
By definition, telomeric sequences are located at the very ends or terminal regions of chromosomes. However, several vertebrate species show blocks of (TTAGGG)n repeats present in non-terminal regions of chromosomes, the so-called interstitial telomeric sequences (ITSs), interstitial telomeric repeats or interstitial telomeric bands, which include those intrachromosomal telomeric-like repeats located near (pericentromeric ITSs) or within the centromere (centromeric ITSs) and those telomeric repeats located between the centromere and the telomere (i.e., truly interstitial telomeric sequences) of eukaryotic chromosomes. According with their sequence organization, localization and flanking sequences, ITSs can be classified into four types: 1) short ITSs, 2) subtelomeric ITSs, 3) fusion ITSs, and 4) heterochromatic ITSs. The first three types have been described mainly in the human genome, whereas heterochromatic ITSs have been found in several vertebrate species but not in humans. Several lines of evidence suggest that ITSs play a significant role in genome instability and evolution. This review aims to summarize our current knowledge about the origin, function, instability and evolution of these telomeric-like repeats in vertebrate chromosomes.
Collapse
Affiliation(s)
- Alejandro D Bolzán
- Laboratorio de Citogenética y Mutagénesis, Instituto Multidisciplinario de Biología Celular (IMBICE, CICPBA-UNLP-CONICET La Plata), C.C. 403, 1900 La Plata, Argentina; Facultad de Ciencias Naturales y Museo, UNLP, Calle 60 y 122, 1900 La Plata, Argentina.
| |
Collapse
|
21
|
Teixeira LSR, Seger KR, Targueta CP, Orrico VGD, Lourenço LB. Comparative cytogenetics of tree frogs of the Dendropsophus marmoratus (Laurenti, 1768) group: conserved karyotypes and interstitial telomeric sequences. COMPARATIVE CYTOGENETICS 2016; 10:753-767. [PMID: 28123692 PMCID: PMC5240522 DOI: 10.3897/compcytogen.v10i4.9972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
The diploid number 2n = 30 is a presumed synapomorphy of Dendropsophus Fitzinger, 1843, although a noticeable variation in the number of biarmed/telocentric chromosomes is observed in this genus. Such a variation suggests that several chromosomal rearrangements took place after the evolutionary origin of the hypothetical ancestral 30-chromosome karyotype; however, the inferred rearrangements remain unknown. Distinct numbers of telocentric chromosomes are found in the two most cytogenetically studied species groups of Dendropsophus. In contrast, all three species of the Dendropsophus marmoratus (Laurenti, 1768) group that are already karyotyped presented five pairs of telocentric chromosomes. In this study, we analyzed cytogenetically three additional species of this group to investigate if the number of telocentric chromosomes in this group is not as variable as in other Dendropsophus groups. We described the karyotypes of Dendropsophus seniculus (Cope, 1868), Dendropsophus soaresi (Caramaschi & Jim, 1983) and Dendropsophus novaisi (Bokermann, 1968) based on Giemsa staining, C-banding, silver impregnation and in situ hybridization with telomeric probes. Dendropsophus seniculus, Dendropsophus soaresi and Dendropsophus novaisi presented five pairs of telocentric chromosomes, as did the remaining species of the group previously karyotyped. Though the species of this group show a high degree of karyotypic similarity, Dendropsophus soaresi was unique in presenting large blocks of het-ITSs (heterochromatic internal telomeric sequences) in the majority of the centromeres. Although the ITSs have been interpreted as evidence of ancestral chromosomal fusions and inversions, the het-ITSs detected in the karyotype of Dendropsophus soaresi could not be explained as direct remnants of ancestral chromosomal rearrangements because no evidence of chromosomal changes emerged from the comparison of the karyotypes of all of the species of the Dendropsophus marmoratus group.
Collapse
Affiliation(s)
- Lívia S. R. Teixeira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brasil
| | - Karin Regina Seger
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brasil
| | - Cíntia Pelegrineti Targueta
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brasil
| | - Victor G. Dill Orrico
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, 45662-900 Ilhéus, Bahia, Brasil
| | - Luciana Bolsoni Lourenço
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brasil
| |
Collapse
|
22
|
Onozawa M, Aplan PD. Templated Sequence Insertion Polymorphisms in the Human Genome. Front Chem 2016; 4:43. [PMID: 27900318 PMCID: PMC5110952 DOI: 10.3389/fchem.2016.00043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/27/2016] [Indexed: 12/26/2022] Open
Abstract
Templated Sequence Insertion Polymorphism (TSIP) is a recently described form of polymorphism recognized in the human genome, in which a sequence that is templated from a distant genomic region is inserted into the genome, seemingly at random. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; Class 1 TSIPs show features of insertions that are mediated via the LINE-1 ORF2 protein, including (1) target-site duplication (TSD), (2) polyadenylation 10–30 nucleotides downstream of a “cryptic” polyadenylation signal, and (3) preference for insertion at a 5′-TTTT/A-3′ sequence. In contrast, class 2 TSIPs show features consistent with repair of a DNA double-strand break (DSB) via insertion of a DNA “patch” that is derived from a distant genomic region. Survey of a large number of normal human volunteers demonstrates that most individuals have 25–30 TSIPs, and that these TSIPs track with specific geographic regions. Similar to other forms of human polymorphism, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases.
Collapse
Affiliation(s)
- Masahiro Onozawa
- Genetics Branch, National Cancer Institute, National Institutes of HealthBethesda, MD, USA; Department of Hematology, Hokkaido University Graduate School of MedicineSapporo, Japan
| | - Peter D Aplan
- Genetics Branch, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| |
Collapse
|
23
|
Gomes Júnior RG, Schneider CH, de Lira T, Carvalho NDM, Feldberg E, da Silva MNF, Gross MC. Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae): comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon. COMPARATIVE CYTOGENETICS 2016; 10:401-426. [PMID: 27830049 PMCID: PMC5088352 DOI: 10.3897/compcytogen.v10i3.8306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/29/2016] [Indexed: 05/31/2023]
Abstract
Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939), Oecomys bicolor (Tomes, 1860) and Oecomys rutilus (Anthony, 1921). COI sequence analysis grouped Oecomys auyantepui, Oecomys bicolor and Oecomys rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for Oecomys auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while Oecomys bicolor exhibited 2n=80/NFa=142 and Oecomys rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in Oecomys auyantepui. The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas.
Collapse
Affiliation(s)
- Renan Gabriel Gomes Júnior
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Carlos Henrique Schneider
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Thatianna de Lira
- Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936 Zip Code 69077-000, Manaus, AM, Brazil
| | - Natália Dayane Moura Carvalho
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936 Zip Code 69077-000, Manaus, AM, Brazil
| | | | - Maria Claudia Gross
- Universidade Federal da Integração Latino Americana, Laboratório de Genética, Av. Tarquínio Joslin dos Santos, 1000, Jardim Universitário, Zip code 85857-190, Foz do Iguaçu, PR, Brazil
| |
Collapse
|
24
|
Viana PF, Ribeiro LB, Souza GM, Chalkidis HDM, Gross MC, Feldberg E. Is the Karyotype of Neotropical Boid Snakes Really Conserved? Cytotaxonomy, Chromosomal Rearrangements and Karyotype Organization in the Boidae Family. PLoS One 2016; 11:e0160274. [PMID: 27494409 PMCID: PMC4975421 DOI: 10.1371/journal.pone.0160274] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/15/2016] [Indexed: 11/19/2022] Open
Abstract
Boids are primitive snakes from a basal lineage that is widely distributed in Neotropical region. Many of these species are both morphologically and biogeographically divergent, and the relationship among some species remains uncertain even with evolutionary and phylogenetic studies being proposed for the group. For a better understanding of the evolutionary relationship between these snakes, we cytogenetically analysed 7 species and 3 subspecies of Neotropical snakes from the Boidae family using different chromosomal markers. The karyotypes of Boa constrictor occidentalis, Corallus hortulanus, Eunectes notaeus, Epicrates cenchria and Epicrates assisi are presented here for the first time with the redescriptions of the karyotypes of Boa constrictor constrictor, B. c. amarali, Eunectes murinus and Epicrates crassus. The three subspecies of Boa, two species of Eunectes and three species of Epicrates exhibit 2n = 36 chromosomes. In contrast, C. hortulanus presented a totally different karyotype composition for the Boidae family, showing 2n = 40 chromosomes with a greater number of macrochromosomes. Furthermore, chromosomal mapping of telomeric sequences revealed the presence of interstitial telomeric sites (ITSs) on many chromosomes in addition to the terminal markings on all chromosomes of all taxa analysed, with the exception of E. notaeus. Thus, we demonstrate that the karyotypes of these snakes are not as highly conserved as previously thought. Moreover, we provide an overview of the current cytotaxonomy of the group.
Collapse
Affiliation(s)
- Patrik F. Viana
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araujo 2936, Petrópolis, CEP: 69067-375 Manaus, AM, Brazil
- * E-mail:
| | - Leila B. Ribeiro
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araujo 2936, Petrópolis, CEP: 69067-375 Manaus, AM, Brazil
| | | | | | - Maria Claudia Gross
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Rua General Rodrigo Otávio Num. 3000, Mini-Campus Coroado, CEP: 66077070 Manaus, AM, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araujo 2936, Petrópolis, CEP: 69067-375 Manaus, AM, Brazil
| |
Collapse
|
25
|
Schmid M, Steinlein C. Chromosome Banding in Amphibia. XXXIV. Intrachromosomal Telomeric DNA Sequences in Anura. Cytogenet Genome Res 2016; 148:211-26. [PMID: 27233250 DOI: 10.1159/000446298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 11/19/2022] Open
Abstract
The mitotic chromosomes of 4 anuran species were examined by various classical banding techniques and by fluorescence in situ hybridization using a (TTAGGG)n repeat. Large intrachromosomal telomeric sequences (ITSs) were demonstrated in differing numbers and chromosome locations. A detailed comparison of the present results with numerous published and unpublished data allowed a consistent classification of the various categories of large ITSs present in the genomes of anurans and other vertebrates. The classification takes into consideration the total numbers of large ITSs in the karyotypes, their chromosomal locations and their specific distribution patterns. A new category of large ITSs was recognized to exist in anuran species. It consists of large clusters of ITSs located in euchromatic chromosome segments, which is in clear contrast to the large ITSs in heterochromatic chromosome regions known in vertebrates. The origin of the different categories of large ITSs in heterochromatic and euchromatic chromosome regions, their mode of distribution in the karyotypes and evolutionary fixation in the genomes, as well as their cytological detection are discussed.
Collapse
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Wx00FC;rzburg, Wx00FC;rzburg, Germany
| | | |
Collapse
|
26
|
Dumas F, Cuttaia H, Sineo L. Chromosomal distribution of interstitial telomeric sequences in nine neotropical primates (Platyrrhini): possible implications in evolution and phylogeny. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Dumas
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche; Università degli Studi Palermo; Palermo Italy
| | - Helenia Cuttaia
- Azienda ospedaliera Ospedali Riuniti Villa Sofia - Cervello; Laboratorio di Citogenetica Medica; Palermo Italy
| | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche; Università degli Studi Palermo; Palermo Italy
| |
Collapse
|
27
|
Kour S, Rath PC. Long noncoding RNAs in aging and age-related diseases. Ageing Res Rev 2016; 26:1-21. [PMID: 26655093 DOI: 10.1016/j.arr.2015.12.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/08/2015] [Accepted: 12/01/2015] [Indexed: 12/14/2022]
Abstract
Aging is the universal, intrinsic, genetically-controlled, evolutionarily-conserved and time-dependent intricate biological process characterised by the cumulative decline in the physiological functions and their coordination in an organism after the attainment of adulthood resulting in the imbalance of neurological, immunological and metabolic functions of the body. Various biological processes and mechanisms along with altered levels of mRNAs and proteins have been reported to be involved in the progression of aging. It is one of the major risk factors in the patho-physiology of various diseases and disorders. Recently, the discovery of pervasive transcription of a vast pool of heterogeneous regulatory noncoding RNAs (ncRNAs), including small ncRNAs (sncRNAs) and long ncRNAs (lncRNAs), in the mammalian genome have provided an alternative way to study and explore the missing links in the aging process, its mechanism(s) and related diseases in a whole new dimension. The involvement of small noncoding RNAs in aging and age-related diseases have been extensively studied and recently reviewed. However, lncRNAs, whose function is far less explored in relation to aging, have emerged as a class of major regulators of genomic functions. Here, we have described some examples of known as well as novel lncRNAs that have been implicated in the progression of the aging process and age-related diseases. This may further stimulate research on noncoding RNAs and the aging process.
Collapse
Affiliation(s)
- Sukhleen Kour
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| |
Collapse
|
28
|
Early-Life Telomere Dynamics Differ between the Sexes and Predict Growth in the Barn Swallow (Hirundo rustica). PLoS One 2015; 10:e0142530. [PMID: 26565632 PMCID: PMC4643985 DOI: 10.1371/journal.pone.0142530] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022] Open
Abstract
Telomeres are conserved DNA-protein structures at the termini of eukaryotic chromosomes which contribute to maintenance of genome integrity, and their shortening leads to cell senescence, with negative consequences for organismal functions. Because telomere erosion is influenced by extrinsic and endogenous factors, telomere dynamics may provide a mechanistic basis for evolutionary and physiological trade-offs. Yet, knowledge of fundamental aspects of telomere biology under natural selection regimes, including sex- and context-dependent variation in early-life, and the covariation between telomere dynamics and growth, is scant. In this study of barn swallows (Hirundo rustica) we investigated the sex-dependent telomere erosion during nestling period, and the covariation between relative telomere length and body and plumage growth. Finally, we tested whether any covariation between growth traits and relative telomere length depends on the social environment, as influenced by sibling sex ratio. Relative telomere length declined on average over the period of nestling maximal growth rate (between 7 and 16 days of age) and differently covaried with initial relative telomere length in either sex. The frequency distribution of changes in relative telomere length was bimodal, with most nestlings decreasing and some increasing relative telomere length, but none of the offspring traits predicted the a posteriori identified group to which individual nestlings belonged. Tail and wing length increased with relative telomere length, but more steeply in males than females, and this relationship held both at the within- and among-broods levels. Moreover, the increase in plumage phenotypic values was steeper when the sex ratio of an individual’s siblings was female-biased. Our study provides evidence for telomere shortening during early life according to subtly different dynamics in either sex. Furthermore, it shows that the positive covariation between growth and relative telomere length depends on sex as well as social environment, in terms of sibling sex ratio.
Collapse
|
29
|
Aksenova AY, Han G, Shishkin AA, Volkov KV, Mirkin SM. Expansion of Interstitial Telomeric Sequences in Yeast. Cell Rep 2015; 13:1545-51. [PMID: 26586439 DOI: 10.1016/j.celrep.2015.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 08/07/2015] [Accepted: 10/08/2015] [Indexed: 11/18/2022] Open
Abstract
Telomeric repeats located within chromosomes are called interstitial telomeric sequences (ITSs). They are polymorphic in length and are likely hotspots for initiation of chromosomal rearrangements that have been linked to human disease. Using our S. cerevisiae system to study repeat-mediated genome instability, we have previously shown that yeast telomeric (Ytel) repeats induce various gross chromosomal rearrangements (GCR) when their G-rich strands serve as the lagging strand template for replication (G orientation). Here, we show that interstitial Ytel repeats in the opposite C orientation prefer to expand rather than cause GCR. A tract of eight Ytel repeats expands at a rate of 4 × 10(-4) per replication, ranking them among the most expansion-prone DNA microsatellites. A candidate-based genetic analysis implicates both post-replication repair and homologous recombination pathways in the expansion process. We propose a model for Ytel repeat expansions and discuss its applications for genome instability and alternative telomere lengthening (ALT).
Collapse
Affiliation(s)
- Anna Y Aksenova
- Department of Biology, Tufts University, Medford, MA 02155, USA; Department of Genetics, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Gil Han
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | - Kirill V Volkov
- Department of Genetics, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
| |
Collapse
|
30
|
Santagostino M, Khoriauli L, Gamba R, Bonuglia M, Klipstein O, Piras FM, Vella F, Russo A, Badiale C, Mazzagatti A, Raimondi E, Nergadze SG, Giulotto E. Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression. BMC Genet 2015; 16:126. [PMID: 26503543 PMCID: PMC4623272 DOI: 10.1186/s12863-015-0281-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In mammals, an important source of genomic variation is insertion polymorphism of retrotransposons. These may acquire a functional role when inserted inside genes or in their proximity. The aim of this work was to carry out a genome wide analysis of ERE1 retrotransposons in the horse and to analyze insertion polymorphism in relation to evolution and function. The effect of an ERE1 insertion in the promoter of the myostatin gene, which is involved in muscle development, was also investigated. RESULTS In the horse population, the fraction of ERE1 polymorphic loci is related to the degree of similarity to their consensus sequence. Through the analysis of ERE1 conservation in seven equid species, we established that the level of identity to their consensus is indicative of evolutionary age of insertion. The position of ERE1s relative to genes suggests that some elements have acquired a functional role. Reporter gene assays showed that the ERE1 insertion within the horse myostatin promoter affects gene expression. The frequency of this variant promoter correlates with sport aptitude and racing performance. CONCLUSIONS Sequence conservation and insertion polymorphism of ERE1 elements are related to the time of their appearance in the horse lineage, therefore, ERE1s are a useful tool for evolutionary and population studies. Our results suggest that the ERE1 insertion at the myostatin locus has been unwittingly selected by breeders to obtain horses with specific racing abilities. Although a complex combination of environmental and genetic factors contributes to athletic performance, breeding schemes may take into account ERE1 insertion polymorphism at the myostatin promoter.
Collapse
Affiliation(s)
- Marco Santagostino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Lela Khoriauli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Riccardo Gamba
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Margherita Bonuglia
- Laboratorio di Genetica Forense Veterinaria, UNIRELAB srl, Via A. Gramsci 70, 20019, Settimo Milanese (MI), Italy.
| | - Ori Klipstein
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Francesca M Piras
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Francesco Vella
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Alessandra Russo
- Laboratorio di Genetica Forense Veterinaria, UNIRELAB srl, Via A. Gramsci 70, 20019, Settimo Milanese (MI), Italy.
| | - Claudia Badiale
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Alice Mazzagatti
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Elena Raimondi
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Solomon G Nergadze
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Elena Giulotto
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| |
Collapse
|
31
|
Garrobo I, Marión RM, Domínguez O, Pisano DG, Blasco MA. Genome-wide analysis of in vivo TRF1 binding to chromatin restricts its location exclusively to telomeric repeats. Cell Cycle 2015; 13:3742-9. [PMID: 25483083 DOI: 10.4161/15384101.2014.965044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Telomeres are nucleoprotein structures at the ends of eukaryotic chromosomes that protect them from degradation, end-to-end fusions, and fragility. In mammals, telomeres are composed of TTAGGG tandem repeats bound by a protein complex called shelterin, which has fundamental roles in the regulation of telomere protection and length. The telomeric repeat binding factor 1 (TERF1 or TRF1) is one of the components of shelterin and has been shown to be essential for telomere protection. Telomeric repeats can also be found throughout the genome, as Internal or Interstitial Telomeric Sequences (ITSs). Some of the components of shelterin have been described to bind to ITSs as well as other extra-telomeric regions, which in the case of RAP1 exert a key role in transcriptional regulation. Here, we set to address whether TRF1 can be found at extra-telomeric sites both under normal conditions and upon induction of telomere shortening. In particular, we performed a ChIP-sequencing technique to map TRF1 binding sites in MEFs wild-type and deficient for the telomerase RNA component (Terc(-/-)), with increasingly short telomeres. Our findings indicate that TRF1 is exclusively located at telomeres both under normal conditions, as well as under extreme telomere shortening. These results indicate that in mice not all members of shelterin have extra-telomeric roles as it was described for RAP1.
Collapse
Affiliation(s)
- Ianire Garrobo
- a Telomeres and Telomerase Group; Molecular Oncology Program; Spanish National Cancer Research Center (CNIO) ; Madrid , Spain
| | | | | | | | | |
Collapse
|
32
|
Venkatesan S, Natarajan AT, Hande MP. Chromosomal instability--mechanisms and consequences. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 793:176-84. [PMID: 26520388 DOI: 10.1016/j.mrgentox.2015.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 01/08/2023]
Abstract
Chromosomal instability is defined as a state of numerical and/or structural chromosomal anomalies in cells. Numerous studies have documented the incidence of chromosomal instability, which acutely or chronically may lead to accelerated ageing (tissue-wide or even organismal), cancer or other genetic disorders. Potential mechanisms leading to the generation of chromosome-genome instability include erroneous/inefficient DNA repair, chromosome segregation defects, spindle assembly defects, DNA replication stress, telomere shortening/dysfunction - to name a few. Understanding the cellular and molecular mechanisms for chromosomal instability in various human cells and tissues will be useful in elucidating the cause for many age associated diseases including cancer. This approach holds a great promise for the cytogenetic assays not only for prognosis but also for diagnostic purposes in clinical settings. In this review, a multi-dimensional approach has been attempted to portray the complexity behind the incidence of chromosome-genome instability including evolutionary implications at the species level for some of the mechanisms of chromosomal instability.
Collapse
Affiliation(s)
- Shriram Venkatesan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597
| | - Adayapalam T Natarajan
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
| | - M Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597; Tembusu College, National University of Singapore, Singapore, 138597.
| |
Collapse
|
33
|
Interstitial Telomeric Motifs in Squamate Reptiles: When the Exceptions Outnumber the Rule. PLoS One 2015; 10:e0134985. [PMID: 26252002 PMCID: PMC4529230 DOI: 10.1371/journal.pone.0134985] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/15/2015] [Indexed: 12/19/2022] Open
Abstract
Telomeres are nucleoprotein complexes protecting the physical ends of linear eukaryotic chromosomes and therefore helping to ensure their stability and integrity. Additionally, telomeric sequences can be localized in non-terminal regions of chromosomes, forming so-called interstitial telomeric sequences (ITSs). ITSs are traditionally considered to be relics of chromosomal rearrangements and thus very informative in the reconstruction of the evolutionary history of karyotype formation. We examined the distribution of the telomeric motifs (TTAGGG)n using fluorescence in situ hybridization (FISH) in 30 species, representing 17 families of squamate reptiles, and compared them with the collected data from another 38 species from literature. Out of the 68 squamate species analyzed, 35 possess ITSs in pericentromeric regions, centromeric regions and/or within chromosome arms. We conclude that the occurrence of ITSs is rather common in squamates, despite their generally conserved karyotypes, suggesting frequent and independent cryptic chromosomal rearrangements in this vertebrate group.
Collapse
|
34
|
Nergadze SG, Lupotto M, Pellanda P, Santagostino M, Vitelli V, Giulotto E. Mitochondrial DNA insertions in the nuclear horse genome. Anim Genet 2015; 41 Suppl 2:176-85. [PMID: 21070293 DOI: 10.1111/j.1365-2052.2010.02130.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The insertion of mitochondrial DNA in the nuclear genome generates numts, nuclear sequences of mitochondrial origin. In the horse reference genome, we identified 82 numts and showed that the entire horse mitochondrial DNA is represented as numts without gross bias. Numts were inserted in the horse nuclear genome at random sites and were probably generated during the repair of DNA double-strand breaks. We then analysed 12 numt loci in 20 unrelated horses and found that null alleles, lacking the mitochondrial DNA insertion, were present at six of these loci. At some loci, the null allele is prevalent in the sample analysed, suggesting that, in the horse population, the number of numt loci may be higher than 82 present in the reference genome. Contrary to humans, the insertion polymorphism of numts is extremely frequent in the horse population, supporting the hypothesis that the genome of this species is in a rapidly evolving state.
Collapse
Affiliation(s)
- S G Nergadze
- Dipartimento di Genetica e Microbiologia Adriano Buzzati-Traverso, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | | | | | | | | | | |
Collapse
|
35
|
Ziemniczak K, Traldi JB, Nogaroto V, Almeida MC, Artoni RF, Moreira-Filho O, Vicari MR. In situ Localization of (GATA)n and (TTAGGG)n Repeated DNAs and W Sex Chromosome Differentiation in Parodontidae (Actinopterygii: Characiformes). Cytogenet Genome Res 2015; 144:325-32. [DOI: 10.1159/000370297] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2014] [Indexed: 11/19/2022] Open
|
36
|
Extensive spreading of interstitial telomeric sites on the chromosomes of Characidium (Teleostei, Characiformes). Genetica 2014; 143:263-70. [PMID: 25547849 DOI: 10.1007/s10709-014-9812-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022]
Abstract
Characidium comprises several species of small freshwater fish that display conserved diploid chromosome numbers and karyotypic formulae. In this study, a comparative cytogenetic analysis using telomeric DNA probes was carried out in nine species of Characidium; a molecular phylogenetic analysis with mitochondrial DNA was also performed in order to investigate the direction of the evolutionary chromosome changes observed here. Our results showed the existence of species with several and variable interstitial telomeric sites (ITSs), with other species showing only terminal signals in their chromosomes. Molecular phylogenetic data suggested that these ITSs emerged once in the evolutionary history of Characidium and were later differentially spread in distinct species/populations of this clade. Additionally, the origin of an exclusive acrocentric pair found in C. pterostictum, C. serrano and C. timbuiense was also investigated, revealing that this pair possibly had a common origin to these species. These results evidence the occurrence of intense and continuous genomic changes among species of Characidium.
Collapse
|
37
|
Emadzade K, Jang TS, Macas J, Kovařík A, Novák P, Parker J, Weiss-Schneeweiss H. Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae). ANNALS OF BOTANY 2014; 114:1597-608. [PMID: 25169019 PMCID: PMC4273535 DOI: 10.1093/aob/mcu178] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Chromosomal evolution, including numerical and structural changes, is a major force in plant diversification and speciation. This study addresses genomic changes associated with the extensive chromosomal variation of the Mediterranean Prospero autumnale complex (Hyacinthaceae), which includes four diploid cytotypes each with a unique combination of chromosome number (x = 5, 6, 7), rDNA loci and genome size. METHODS A new satellite repeat PaB6 has previously been identified, and monomers were reconstructed from next-generation sequencing (NGS) data of P. autumnale cytotype B(6)B(6) (2n = 12). Monomers of all other Prospero cytotypes and species were sequenced to check for lineage-specific mutations. Copy number, restriction patterns and methylation levels of PaB6 were analysed using Southern blotting. PaB6 was localized on chromosomes using fluorescence in situ hybridization (FISH). KEY RESULTS The monomer of PaB6 is 249 bp long, contains several intact and truncated vertebrate-type telomeric repeats and is highly methylated. PaB6 is exceptional because of its high copy number and unprecedented variation among diploid cytotypes, ranging from 10(4) to 10(6) copies per 1C. PaB6 is always located in pericentromeric regions of several to all chromosomes. Additionally, two lineages of cytotype B(7)B(7) (x = 7), possessing either a single or duplicated 5S rDNA locus, differ in PaB6 copy number; the ancestral condition of a single locus is associated with higher PaB6 copy numbers. CONCLUSIONS Although present in all Prospero species, PaB6 has undergone differential amplification only in chromosomally variable P. autumnale, particularly in cytotypes B(6)B(6) and B(5)B(5). These arose via independent chromosomal fusions from x = 7 to x = 6 and 5, respectively, accompanied by genome size increases. The copy numbers of satellite DNA PaB6 are among the highest in angiosperms, and changes of PaB6 are exceptionally dynamic in this group of closely related cytotypes of a single species. The evolution of the PaB6 copy numbers is discussed, and it is suggested that PaB6 represents a recent and highly dynamic system originating from a small pool of ancestral repeats.
Collapse
Affiliation(s)
- Khatere Emadzade
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Jiří Macas
- Czech Academy of Sciences, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
| | - Ales Kovařík
- Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Petr Novák
- Czech Academy of Sciences, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
| | - John Parker
- Cambridge University Botanic Garden, Cambridge CB2 1JF, UK
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| |
Collapse
|
38
|
Shubernetskaya OS, Skvortsov DA, Evfratov SA, Rubtsova MP, Belova EV, Strelkova OS, Cherepaninets VD, Zhironkina OA, Olovnikov AM, Zvereva ME, Kireev II, Dontsova OA. High expression levels and nuclear localization of novel Danio rerio ncRNA transcribed from a genomic region containing repetitive elements. Mol Biol 2014. [DOI: 10.1134/s002689331404013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
39
|
Repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome. Proc Natl Acad Sci U S A 2014; 111:7729-34. [PMID: 24821809 DOI: 10.1073/pnas.1321889111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We used the I-SceI endonuclease to produce DNA double-strand breaks (DSBs) and observed that a fraction of these DSBs were repaired by insertion of sequences, which we termed "templated sequence insertions" (TSIs), derived from distant regions of the genome. These TSIs were derived from genic, retrotransposon, or telomere sequences and were not deleted from the donor site in the genome, leading to the hypothesis that they were derived from reverse-transcribed RNA. Cotransfection of RNA and an I-SceI expression vector demonstrated insertion of RNA-derived sequences at the DNA-DSB site, and TSIs were suppressed by reverse-transcriptase inhibitors. Both observations support the hypothesis that TSIs were derived from RNA templates. In addition, similar insertions were detected at sites of DNA DSBs induced by transcription activator-like effector nuclease proteins. Whole-genome sequencing of myeloma cell lines revealed additional TSIs, demonstrating that repair of DNA DSBs via insertion was not restricted to experimentally produced DNA DSBs. Analysis of publicly available databases revealed that many of these TSIs are polymorphic in the human genome. Taken together, these results indicate that insertional events should be considered as alternatives to gross chromosomal rearrangements in the interpretation of whole-genome sequence data and that this mutagenic form of DNA repair may play a role in genetic disease, exon shuffling, and mammalian evolution.
Collapse
|
40
|
Campos-Sánchez R, Kapusta A, Feschotte C, Chiaromonte F, Makova KD. Genomic landscape of human, bat, and ex vivo DNA transposon integrations. Mol Biol Evol 2014; 31:1816-32. [PMID: 24809961 DOI: 10.1093/molbev/msu138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The integration and fixation preferences of DNA transposons, one of the major classes of eukaryotic transposable elements, have never been evaluated comprehensively on a genome-wide scale. Here, we present a detailed study of the distribution of DNA transposons in the human and bat genomes. We studied three groups of DNA transposons that integrated at different evolutionary times: 1) ancient (>40 My) and currently inactive human elements, 2) younger (<40 My) bat elements, and 3) ex vivo integrations of piggyBat and Sleeping Beauty elements in HeLa cells. Although the distribution of ex vivo elements reflected integration preferences, the distribution of human and (to a lesser extent) bat elements was also affected by selection. We used regression techniques (linear, negative binomial, and logistic regression models with multiple predictors) applied to 20-kb and 1-Mb windows to investigate how the genomic landscape in the vicinity of DNA transposons contributes to their integration and fixation. Our models indicate that genomic landscape explains 16-79% of variability in DNA transposon genome-wide distribution. Importantly, we not only confirmed previously identified predictors (e.g., DNA conformation and recombination hotspots) but also identified several novel predictors (e.g., signatures of double-strand breaks and telomere hexamer). Ex vivo integrations showed a bias toward actively transcribed regions. Older DNA transposons were located in genomic regions scarce in most conserved elements-likely reflecting purifying selection. Our study highlights how DNA transposons are integral to the evolution of bat and human genomes, and has implications for the development of DNA transposon assays for gene therapy and mutagenesis applications.
Collapse
Affiliation(s)
- Rebeca Campos-Sánchez
- Genetics Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, PA
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT
| | - Francesca Chiaromonte
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, PADepartment of Statistics, Penn State University, University Park, PA
| | - Kateryna D Makova
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, PADepartment of Biology, Penn State University, University Park, PA
| |
Collapse
|
41
|
Bruschi DP, Rivera M, Lima AP, Zúñiga AB, Recco-Pimentel SM. Interstitial Telomeric Sequences (ITS) and major rDNA mapping reveal insights into the karyotypical evolution of Neotropical leaf frogs species (Phyllomedusa, Hylidae, Anura). Mol Cytogenet 2014; 7:22. [PMID: 24602295 PMCID: PMC3975639 DOI: 10.1186/1755-8166-7-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 02/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The combination of classical cytogenetics with molecular techniques represents a powerful approach for the comparative analysis of the genome, providing data for the systematic identification of chromosomal homologies among species and insights into patterns of chromosomal evolution within phylogenetically related groups. Here, we present cytogenetic data on four species of Neotropical treefrogs of the genus Phyllomedusa (P. vaillantii, P. tarsius, P. distincta, and P. bahiana), collected in Brazil and Ecuador, with the aim of contributing to the understanding of the chromosomal diversification of this genus. RESULTS With the exception of P. tarsius, which presented three telocentric pairs, all the species analyzed had conservative karyotypic features. Heterochromatic patterns in the genomes of these species revealed by C-banding and fluorochrome staining indicated the presence of a large number of non-centromeric blocks. Using the Ag-NOR method and FISH with an rDNA 28S probe, we detected NOR in the pericentromeric region of the short arm of pair 7 in P. vaillantii, pair 1 in P. tarsius, chromosomes 1 and 9 in P. distincta, and in chromosome 9 in P. bahiana, in addition to the presence of NOR in one homologue of chromosome pair 10 in some individuals of this species. As expected, the telomeric probe detected the terminal regions of the chromosomes of these four species, although it also detected Interstitial Telomeric Sequences (ITS) in some chromosomes of the P. vaillantii, P. distincta and P. bahiana karyotypes. CONCLUSION A number of conservative chromosomal structures permitted the recognition of karyotypic homologies. The data indicate that the presence of a NOR-bearing chromosome in pair 9 is the plesiomorphic condition in the P. burmeisteri group. The interspecific and intraspecific variation in the number and location of rDNA sites reflects the rapid rate of evolution of this character in Phyllomedusa. The ITS detected in this study does not appear to be a remnant of structural chromosome rearrangements. Telomeric repeats were frequently found in association with heterochromatin regions, primarily in the centromeres, which suggests that (TTAGGG)n repeats might be an important component of this heterochromatin. We propose that the ITSs originated independently during the chromosomal evolution of these species and may provide important insights into the role of these repeats in vertebrate karyotype diversification.
Collapse
Affiliation(s)
- Daniel Pacheco Bruschi
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-863 Campinas, São Paulo, Brazil
| | - Miryan Rivera
- Escuela de Ciencias Biológicas, Pontifícia Universidad Católica Del Ecuador, Quito, Ecuador
| | | | - Ailín Blasco Zúñiga
- Escuela de Ciencias Biológicas, Pontifícia Universidad Católica Del Ecuador, Quito, Ecuador
| | - Shirlei Maria Recco-Pimentel
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-863 Campinas, São Paulo, Brazil
| |
Collapse
|
42
|
Shim G, Ricoul M, Hempel WM, Azzam EI, Sabatier L. Crosstalk between telomere maintenance and radiation effects: A key player in the process of radiation-induced carcinogenesis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2014; 760:S1383-5742(14)00002-7. [PMID: 24486376 PMCID: PMC4119099 DOI: 10.1016/j.mrrev.2014.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 01/14/2014] [Accepted: 01/22/2014] [Indexed: 02/06/2023]
Abstract
It is well established that ionizing radiation induces chromosomal damage, both following direct radiation exposure and via non-targeted (bystander) effects, activating DNA damage repair pathways, of which the proteins are closely linked to telomeric proteins and telomere maintenance. Long-term propagation of this radiation-induced chromosomal damage during cell proliferation results in chromosomal instability. Many studies have shown the link between radiation exposure and radiation-induced changes in oxidative stress and DNA damage repair in both targeted and non-targeted cells. However, the effect of these factors on telomeres, long established as guardians of the genome, still remains to be clarified. In this review, we will focus on what is known about how telomeres are affected by exposure to low- and high-LET ionizing radiation and during proliferation, and will discuss how telomeres may be a key player in the process of radiation-induced carcinogenesis.
Collapse
|
43
|
Rojo V, Giovannotti M, Naveira H, Nisi Cerioni P, González-Tizón AM, Caputo Barucchi V, Galán P, Olmo E, Martínez-Lage A. Karyological characterization of the endemic Iberian rock lizard, Iberolacerta monticola (Squamata, Lacertidae): insights into sex chromosome evolution. Cytogenet Genome Res 2013; 142:28-39. [PMID: 24296524 DOI: 10.1159/000356049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2013] [Indexed: 11/19/2022] Open
Abstract
Rock lizards of the genus Iberolacerta constitute a promising model to examine the process of sex chromosome evolution, as these closely related taxa exhibit remarkable diversity in the degree of sex chromosome differentiation with no clear phylogenetic segregation, ranging from cryptic to highly heteromorphic ZW chromosomes and even multiple chromosome systems (Z1Z1Z2Z2/Z1Z2W). To gain a deeper insight into the patterns of karyotype and sex chromosome evolution, we performed a cytogenetic analysis based on conventional staining, banding techniques and fluorescence in situ hybridization in the species I. monticola, for which previous cytogenetic investigations did not detect differentiated sex chromosomes. The karyotype is composed of 2n = 36 acrocentric chromosomes. NORs and the major ribosomal genes were located in the subtelomeric region of chromosome pair 6. Hybridization signals of the telomeric sequences (TTAGGG)n were visualized at the telomeres of all chromosomes and interstitially in 5 chromosome pairs. C-banding showed constitutive heterochromatin at the centromeres of all chromosomes, as well as clear pericentromeric and light telomeric C-bands in several chromosome pairs. These results highlight some chromosomal markers which can be useful to identify species-specific diagnostic characters, although they may not accurately reflect the phylogenetic relationships among the taxa. In addition, C-banding revealed the presence of a heteromorphic ZW sex chromosome pair, where W is smaller than Z and almost completely heterochromatic. This finding sheds light on sex chromosome evolution in the genus Iberolacerta and suggests that further comparative cytogenetic analyses are needed to understand the processes underlying the origin, differentiation and plasticity of sex chromosome systems in lacertid lizards.
Collapse
Affiliation(s)
- V Rojo
- Departamento de Bioloxía Celular e Molecular, Grupo de Investigación en Bioloxía Evolutiva (GIBE), Universidade da Coruña, A Coruña, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Genome rearrangements caused by interstitial telomeric sequences in yeast. Proc Natl Acad Sci U S A 2013; 110:19866-71. [PMID: 24191060 DOI: 10.1073/pnas.1319313110] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interstitial telomeric sequences (ITSs) are present in many eukaryotic genomes and are linked to genome instabilities and disease in humans. The mechanisms responsible for ITS-mediated genome instability are not understood in molecular detail. Here, we use a model Saccharomyces cerevisiae system to characterize genome instability mediated by yeast telomeric (Ytel) repeats embedded within an intron of a reporter gene inside a yeast chromosome. We observed a very high rate of small insertions and deletions within the repeats. We also found frequent gross chromosome rearrangements, including deletions, duplications, inversions, translocations, and formation of acentric minichromosomes. The inversions are a unique class of chromosome rearrangement involving an interaction between the ITS and the true telomere of the chromosome. Because we previously found that Ytel repeats cause strong replication fork stalling, we suggest that formation of double-stranded DNA breaks within the Ytel sequences might be responsible for these gross chromosome rearrangements.
Collapse
|
45
|
Abstract
Mutations of the breast and ovarian cancer susceptibility gene 1 (BRCA1) account for about 40-45% of hereditary breast cancer cases. Moreover, a significant fraction of sporadic (non-hereditary) breast and ovarian cancers exhibit reduced or absent expression of the BRCA1 protein, suggesting an additional role for BRCA1 in sporadic cancers. BRCA1 follows the classic pattern of a highly penetrant Knudsen-type tumor suppressor gene in which one allele is inactivated through a germ-line mutation and the other is mutated or deleted within the tumor. BRCA1 is a multi-functional protein but it is not fully understood which function(s) is (are) most important for tumor suppression, nor is it clear why BRCA1-mutations confer a high risk for breast and ovarian cancers and not a broad spectrum of tumor types. Here, we will review BRCA1 functions in the DNA damage response (DDR), which are likely to contribute to tumor suppression. In the process, we will highlight some of the controversies and unresolved issues in the field. We will also describe a recently identified and under-investigated role for BRCA1 in the regulation of telomeres and the implications of this role in the DDR and cancer suppression.
Collapse
Affiliation(s)
- Eliot M Rosen
- Department of Oncology, Georgetown University School of Medicine Washington, DC, USA ; Department of Biochemistry, Molecular and Cellular Biology, Georgetown University School of Medicine Washington, DC, USA ; Department of Radiation Medicine, Georgetown University School of Medicine Washington, DC, USA
| |
Collapse
|
46
|
The involvement of repetitive sequences in the remodelling of karyotypes: The Phodopus genomes (Rodentia, Cricetidae). Micron 2013; 46:27-34. [DOI: 10.1016/j.micron.2012.11.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 02/08/2023]
|
47
|
|
48
|
Romanenko SA, Volobouev V. Non-Sciuromorph rodent karyotypes in evolution. Cytogenet Genome Res 2012; 137:233-45. [PMID: 22699115 DOI: 10.1159/000339294] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rodents are, taxonomically, the most species-rich mammalian order. They display a series of special genomic features including the highest karyotypic diversity, frequent occurrence of complex intraspecies chromosome variability, and a variety of unusual chromosomal sex determination mechanisms not encountered in other mammalian taxa. Rodents also have an abundance of cytochemically heterogeneous heterochromatin. There are also instances of extremely rapid karyotype reorganization and speciation not accompanied by significant genetic differentiation. All these peculiarities make it clear that a detailed study of rodent genomic evolution is indispensable to understand the mode and tempo of mammalian evolution. The aim of this review is to update the data obtained by classical and molecular cytogenetics as well as comparative genomics in order to outline the range of old and emerging problems that remain to be resolved.
Collapse
Affiliation(s)
- S A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.
| | | |
Collapse
|
49
|
Zahnreich S, Krunic D, Melnikova L, Szejka A, Drossel B, Sabatier L, Durante M, Ritter S, Fournier C. Duplicated chromosomal fragments stabilize shortened telomeres in normal human IMR-90 cells before transition to senescence. J Cell Physiol 2012; 227:1932-40. [PMID: 21732364 DOI: 10.1002/jcp.22921] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
To assess why during in vitro aging of fibroblasts the maintenance of chromosomal stability is effective or occasionally fails, a detailed cytogenetic analysis was performed in normal human IMR-90 fetal lung fibroblasts. The onset of senescence was inferred from proliferation activity, expression pattern of cell cycle regulating proteins, activity of β-galactosidase, and morphological features. Over the period of proliferation, a moderate increase of non-transmissible structural chromosomal aberrations was observed. In addition, using fluorescence in situ hybridization (mFISH and mBAND) techniques, we detected clonally expanding translocations in up to 70% of the analyzed metaphases, all involving one homolog of chromosome 9 as an acceptor. Notably, chromosomes are randomly involved as donor-chromosomes of the translocated terminal acentric fragments. These fragments result from duplication because the donor chromosomes are apparently unchanged. Interstitial telomeric signals were detectable at fusion sites, most likely belonging to chromosome 9. Quantitative fluorescence in situ hybridization (QFISH) detecting telomere sequences, followed by mFISH technique revealed that already in young cells the respective telomeres of one chromosome 9 were particularly short. For the first time, we have observed dysfunctional telomeres of one specific chromosome in normal human cells that have been stabilized by duplicated terminal sequences.
Collapse
Affiliation(s)
- Sebastian Zahnreich
- Biophysics Department, GSI Helmholtz Center for Heavy Ion Research, Darmstadt, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Eitan E, Tichon A, Gazit A, Gitler D, Slavin S, Priel E. Novel telomerase-increasing compound in mouse brain delays the onset of amyotrophic lateral sclerosis. EMBO Mol Med 2012; 4:313-29. [PMID: 22351600 PMCID: PMC3376858 DOI: 10.1002/emmm.201200212] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Revised: 12/22/2011] [Accepted: 01/03/2012] [Indexed: 01/12/2023] Open
Abstract
Telomerase is expressed in the neonatal brain, in distinct regions of adult brain, and was shown to protect developing neurons from apoptosis. Telomerase reactivation by gene manipulation reverses neurodegeneration in aged telomerase-deficient mice. Hence, we and others hypothesized that increasing telomerase expression by pharmaceutical compounds may protect brain cells from death caused by damaging agents. In this study, we demonstrate for the first time that the novel compound AGS-499 increases telomerase activity and expression in the mouse brain and spinal cord (SC). It exerts neuroprotective effects in NMDA-injected CD-1 mice, delays the onset and progression of the amyotrophic lateral sclerosis (ALS) disease in SOD1 transgenic mice, and, after the onset of ALS, it increases the survival of motor neurons in the SC by 60%. The survival of telomerase-expressing cells (i.e. motor neurons), but not telomerase-deficient cells, exposed to oxidative stress was increased by AGS-499 treatment, suggesting that the AGS-499 effects are telomerase-mediated. Therefore, a controlled and transient increase in telomerase expression and activity in the brain by AGS-499 may exert neuroprotective effects.
Collapse
Affiliation(s)
- Erez Eitan
- The Shraga Segal Department of Immunology and Microbiology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | | | | | | |
Collapse
|