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Silva DSD, de Sousa RPC, Vallinoto M, Costa Lima MRD, Costa RAD, Furo IDO, Gomes AJB, Oliveira EHCD. Comparative molecular and conventional cytogenetic analyses of three species of Rhinella (Anura; Bufonidae). PLoS One 2024; 19:e0308785. [PMID: 39146271 PMCID: PMC11326569 DOI: 10.1371/journal.pone.0308785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024] Open
Abstract
The genus Rhinella corresponds to a group of anurans characterized by numerous taxonomic and systemic challenges, leading to their organization into species complexes. Cytogenetic data for this genus thus far are limited to the diploid number and chromosome morphology, which remain highly conserved among the species. In this study, we analyse the karyotypes of three species of the genus Rhinella (Rhinella granulosa, Rhinella margaritifera, and Rhinella marina) using both classical (conventional staining and C-banding) and molecular (FISH-fluorescence in situ hybridization with 18S rDNA, telomeric sequences, and microsatellite probes) cytogenetic approaches. The aim of this study is to provide data that can reveal variations in the distribution of repetitive sequences that can contribute to understanding karyotypic diversification in these species. The results revealed a conserved karyotype across the species, with 2n = 22 and FN = 44, with metacentric and submetacentric chromosomes. C-banding revealed heterochromatic blocks in the pericentromeric region for all species, with a proximal block on the long arms of pairs 3 and 6 in R. marina and on the short arms of pairs 4 and 6 in R. margaritifera. Additionally, 18S rDNA probes hybridized to pair 5 in R. granulosa, to pair 7 in R. marina, and to pair 10 in R. margaritifera. Telomeric sequence probes displayed signals exclusively in the distal region of the chromosomes, while microsatellite DNA probes showed species-specific patterns. These findings indicate that despite a conserved karyotypical macrostructure, chromosomal differences exist among the species due to the accumulation of repetitive sequences. This variation may be attributed to chromosome rearrangements or differential accumulation of these sequences, highlighting the dynamic role of repetitive sequences in the chromosomal evolution of Rhinella species. Ultimately, this study emphasizes the importance of the role of repetitive DNAs in chromosomal rearrangements to elucidate the evolutionary mechanisms leading to independent diversification in the distinct phylogenetic groups of Rhinella.
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Affiliation(s)
- David Santos da Silva
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | - Marcelo Vallinoto
- Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Marlon Ramires da Costa Lima
- Laboratório de Biologia Molecular, Evolução e Microbiologia, Instituto Federal do Pará, Abaetetuba, Pará, Brazil
| | - Renato Araújo da Costa
- Laboratório de Biologia Molecular, Evolução e Microbiologia, Instituto Federal do Pará, Abaetetuba, Pará, Brazil
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, Universidade Federal Rural da Amazônia, Parauapebas, Pará, Brazil
| | - Anderson José Baia Gomes
- Laboratório de Biologia Molecular, Evolução e Microbiologia, Instituto Federal do Pará, Abaetetuba, Pará, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas Naturais e Exatas, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
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2
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Hu C, Zhu XT, He MH, Shao Y, Qin Z, Wu ZJ, Zhou JQ. Elimination of subtelomeric repeat sequences exerts little effect on telomere essential functions in Saccharomyces cerevisiae. eLife 2024; 12:RP91223. [PMID: 38656297 DOI: 10.7554/elife.91223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Telomeres, which are chromosomal end structures, play a crucial role in maintaining genome stability and integrity in eukaryotes. In the baker's yeast Saccharomyces cerevisiae, the X- and Y'-elements are subtelomeric repetitive sequences found in all 32 and 17 telomeres, respectively. While the Y'-elements serve as a backup for telomere functions in cells lacking telomerase, the function of the X-elements remains unclear. This study utilized the S. cerevisiae strain SY12, which has three chromosomes and six telomeres, to investigate the role of X-elements (as well as Y'-elements) in telomere maintenance. Deletion of Y'-elements (SY12YΔ), X-elements (SY12XYΔ+Y), or both X- and Y'-elements (SY12XYΔ) did not impact the length of the terminal TG1-3 tracks or telomere silencing. However, inactivation of telomerase in SY12YΔ, SY12XYΔ+Y, and SY12XYΔ cells resulted in cellular senescence and the generation of survivors. These survivors either maintained their telomeres through homologous recombination-dependent TG1-3 track elongation or underwent microhomology-mediated intra-chromosomal end-to-end joining. Our findings indicate the non-essential role of subtelomeric X- and Y'-elements in telomere regulation in both telomerase-proficient and telomerase-null cells and suggest that these elements may represent remnants of S. cerevisiae genome evolution. Furthermore, strains with fewer or no subtelomeric elements exhibit more concise telomere structures and offer potential models for future studies in telomere biology.
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Affiliation(s)
- Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xue-Ting Zhu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Ming-Hong He
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yangyang Shao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhongjun Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhi-Jing Wu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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3
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Brann T, Beltramini A, Chaparro C, Berriman M, Doyle SR, Protasio AV. Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni. BMC Genomics 2024; 25:217. [PMID: 38413905 PMCID: PMC10900676 DOI: 10.1186/s12864-024-10032-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The genomic region that lies between the telomere and chromosome body, termed the subtelomere, is heterochromatic, repeat-rich, and frequently undergoes rearrangement. Within this region, large-scale structural changes enable gene diversification, and, as such, large multicopy gene families are often found at the subtelomere. In some parasites, genes associated with proliferation, invasion, and survival are often found in these regions, where they benefit from the subtelomere's highly plastic, rapidly changing nature. The increasing availability of complete (or near complete) parasite genomes provides an opportunity to investigate these typically poorly defined and overlooked genomic regions and potentially reveal relevant gene families necessary for the parasite's lifestyle. RESULTS Using the latest chromosome-scale genome assembly and hallmark repeat richness observed at chromosome termini, we have identified and characterised the subtelomeres of Schistosoma mansoni, a metazoan parasitic flatworm that infects over 250 million people worldwide. Approximately 12% of the S. mansoni genome is classified as subtelomeric, and, in line with other organisms, we find these regions to be gene-poor but rich in transposable elements. We find that S. mansoni subtelomeres have undergone extensive interchromosomal recombination and that these sites disproportionately contribute to the 2.3% of the genome derived from segmental duplications. This recombination has led to the expansion of subtelomeric gene clusters containing 103 genes, including the immunomodulatory annexins and other gene families with unknown roles. The largest of these is a 49-copy plexin domain-containing protein cluster, exclusively expressed in the tegument-the tissue located at the host-parasite physical interface-of intramolluscan life stages. CONCLUSIONS We propose that subtelomeric regions act as a genomic playground for trial-and-error of gene duplication and subsequent divergence. Owing to the importance of subtelomeric genes in other parasites, gene families implicated in this subtelomeric expansion within S. mansoni warrant further characterisation for a potential role in parasitism.
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Affiliation(s)
- T Brann
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK
| | - A Beltramini
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK
| | - C Chaparro
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, F-66860, France
| | - M Berriman
- School of Infection and Immunity, University of Glasgow, Glasgow, G12 8TA, UK
| | - S R Doyle
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - A V Protasio
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK.
- Christ's College, Cambridge, CB2 3BU, UK.
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4
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Collier JL, Rest JS, Gallot-Lavallée L, Lavington E, Kuo A, Jenkins J, Plott C, Pangilinan J, Daum C, Grigoriev IV, Filloramo GV, Novák Vanclová AMG, Archibald JM. The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Curr Biol 2023; 33:5199-5207.e4. [PMID: 37913769 DOI: 10.1016/j.cub.2023.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/08/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.1 50 years ago, "herpes-type" viral particles2 were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes,3,4 but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ∼300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions.
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Affiliation(s)
- Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA.
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA.
| | - Lucie Gallot-Lavallée
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
| | - Erik Lavington
- Department of Ecology and Evolution, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Jerry Jenkins
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; HudsonAlpha Institute for Biotechnology, Genome Way Northwest, Huntsville, AL 35806, USA
| | - Chris Plott
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; HudsonAlpha Institute for Biotechnology, Genome Way Northwest, Huntsville, AL 35806, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, University Avenue, Berkeley, CA 94720, USA
| | - Gina V Filloramo
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
| | | | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
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5
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Kanoh J. Subtelomeres: hotspots of genome variation. Genes Genet Syst 2023; 98:155-160. [PMID: 37648502 DOI: 10.1266/ggs.23-00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Eukaryotic cells contain multiple types of duplicated sequences. Typical examples are tandem repeat sequences including telomeres, centromeres, rDNA genes and transposable elements. Most of these sequences are unstable; thus, their copy numbers or sequences change rapidly in the course of evolution. In this review, I will describe roles of subtelomere regions, which are located adjacent to telomeres at chromosome ends, and recent discoveries about their sequence variation.
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Affiliation(s)
- Junko Kanoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
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6
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Kanoh J. Roles of Specialized Chromatin and DNA Structures at Subtelomeres in Schizosaccharomyces pombe. Biomolecules 2023; 13:biom13050810. [PMID: 37238680 DOI: 10.3390/biom13050810] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Eukaryotes have linear chromosomes with domains called telomeres at both ends. The telomere DNA consists of a simple tandem repeat sequence, and multiple telomere-binding proteins including the shelterin complex maintain chromosome-end structures and regulate various biological reactions, such as protection of chromosome ends and control of telomere DNA length. On the other hand, subtelomeres, which are located adjacent to telomeres, contain a complex mosaic of multiple common segmental sequences and a variety of gene sequences. This review focused on roles of the subtelomeric chromatin and DNA structures in the fission yeast Schizosaccharomyces pombe. The fission yeast subtelomeres form three distinct chromatin structures; one is the shelterin complex, which is localized not only at the telomeres but also at the telomere-proximal regions of subtelomeres to form transcriptionally repressive chromatin structures. The others are heterochromatin and knob, which have repressive effects in gene expression, but the subtelomeres are equipped with a mechanism that prevents these condensed chromatin structures from invading adjacent euchromatin regions. On the other hand, recombination reactions within or near subtelomeric sequences allow chromosomes to be circularized, enabling cells to survive in telomere shortening. Furthermore, DNA structures of the subtelomeres are more variable than other chromosomal regions, which may have contributed to biological diversity and evolution while changing gene expression and chromatin structures.
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Affiliation(s)
- Junko Kanoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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7
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Contreras SM, Zambrano Siri RT, Rivera EM, Cristaldi C, Kamenetzky L, Kim K, Clemente M, Ocampo J, Vanagas L, Angel SO. Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres. EPIGENOMES 2022; 6:29. [PMID: 36135316 PMCID: PMC9498087 DOI: 10.3390/epigenomes6030029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Subtelomeres (ST) are chromosome regions that separate telomeres from euchromatin and play relevant roles in various biological processes of the cell. While their functions are conserved, ST structure and genetic compositions are unique to each species. This study aims to identify and characterize the subtelomeric regions of the 13 Toxoplasma gondii chromosomes of the Me49 strain. Here, STs were defined at chromosome ends based on poor gene density. The length of STs ranges from 8.1 to 232.4 kbp, with a gene density of 0.049 genes/kbp, lower than the Me49 genome (0.15 kbp). Chromatin organization showed that H3K9me3, H2A.X, and H3.3 are highly enriched near telomeres and the 5' end of silenced genes, decaying in intensity towards euchromatin. H3K4me3 and H2A.Z/H2B.Z are shown to be enriched in the 5' end of the ST genes. Satellite DNA was detected in almost all STs, mainly the sat350 family and a novel satellite named sat240. Beyond the STs, only short dispersed fragments of sat240 and sat350 were found. Within STs, there were 12 functional annotated genes, 59 with unknown functions (Hypothetical proteins), 15 from multigene FamB, and 13 from multigene family FamC. Some genes presented low interstrain synteny associated with the presence of satellite DNA. Orthologues of FamB and FamC were also detected in Neospora caninum and Hammondia hammondi. A re-analysis of previous transcriptomic data indicated that ST gene expression is strongly linked to the adaptation to different situations such as extracellular passage (evolve and resequencing study) and changes in metabolism (lack of acetyl-CoA cofactor). In conclusion, the ST region of the T. gondii chromosomes was defined, the STs genes were determined, and it was possible to associate them with high interstrain plasticity and a role in the adaptability of T. gondii to environmental changes.
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Affiliation(s)
- Susana M. Contreras
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Romina T. Zambrano Siri
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires C1428ADN, Argentina
| | - Elías M. Rivera
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Constanza Cristaldi
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Laura Kamenetzky
- Laboratorio de Genómica y Bioinformática de Patógenos, iB3|Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Marina Clemente
- Laboratorio de Molecular Farming y Vacunas, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires C1428ADN, Argentina
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
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8
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Gu X, Ye T, Zhang XR, Nie L, Wang H, Li W, Lu R, Fu C, Du LL, Zhou JQ. Single-chromosome fission yeast models reveal the configuration robustness of a functional genome. Cell Rep 2022; 40:111237. [PMID: 36001961 DOI: 10.1016/j.celrep.2022.111237] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022] Open
Abstract
In eukaryotic organisms, genetic information is usually carried on multiple chromosomes. Whether and how the number and configuration of chromosomes affect organismal fitness and speciation remain unclear. Here, we have successfully established several single-chromosome fission yeast Schizosaccharomyces pombe strains, in which the three natural chromosomes have been fused into one giant chromosome in different orders. Chromosome fusions accompanied by the deletions of telomeres and centromeres result in the loss of chromosomal interactions and a drastic change of global chromosome organization, but alter gene expression marginally. The single-chromosome strains display little defects in cell morphology, mitosis, genotoxin sensitivity, and meiosis. Crosses between a wild-type strain and a single-chromosome strain or between two single-chromosome strains with different fusion orders suffer defective meiosis and poor spore viability. We conclude that eukaryotic genomes are robust against dramatic chromosomal reconfiguration, and stochastic changes in chromosome number and genome organization during evolution underlie reproductive isolation and speciation.
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Affiliation(s)
- Xin Gu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiantian Ye
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ran Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lingyun Nie
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, CAS Center for Excellence in Molecular Cell Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Huan Wang
- Frasergen Bioinformatics, Wuhan, China
| | - Wei Li
- Frasergen Bioinformatics, Wuhan, China
| | - Rui Lu
- Frasergen Bioinformatics, Wuhan, China
| | - Chuanhai Fu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, CAS Center for Excellence in Molecular Cell Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China.
| | - Jin-Qiu Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou 310024, China.
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9
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Yamamoto I, Nakaoka H, Takikawa M, Tashiro S, Kanoh J, Miyoshi T, Ishikawa F. Fission yeast Stn1 maintains stability of repetitive DNA at subtelomere and ribosomal DNA regions. Nucleic Acids Res 2021; 49:10465-10476. [PMID: 34520548 PMCID: PMC8501966 DOI: 10.1093/nar/gkab767] [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: 10/09/2020] [Revised: 08/03/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022] Open
Abstract
Telomere binding protein Stn1 forms the CST (Cdc13/CTC1-STN1-TEN1) complex in budding yeast and mammals. Likewise, fission yeast Stn1 and Ten1 form a complex indispensable for telomere protection. We have previously reported that stn1-1, a high-temperature sensitive mutant, rapidly loses telomere DNA at the restrictive temperature due to frequent failure of replication fork progression at telomeres and subtelomeres, both containing repetitive sequences. It is unclear, however, whether Stn1 is required for maintaining other repetitive DNAs such as ribosomal DNA. In this study, we have demonstrated that stn1-1 cells, even when grown at the permissive temperature, exhibited dynamic rearrangements in the telomere-proximal regions of subtelomere and ribosomal DNA repeats. Furthermore, Rad52 and γH2A accumulation was observed at ribosomal DNA repeats in the stn1-1 mutant. The phenotypes exhibited by the stn1-1 allele were largely suppressed in the absence of Reb1, a replication fork barrier-forming protein, suggesting that Stn1 is involved in the maintenance of the arrested replication forks. Collectively, we propose that Stn1 maintains the stability of repetitive DNAs at subtelomeres and rDNA regions.
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Affiliation(s)
- Io Yamamoto
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan.,Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Hidenori Nakaoka
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan.,Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Masahiro Takikawa
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Sanki Tashiro
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan.,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Junko Kanoh
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, the University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Tomoichiro Miyoshi
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan.,Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Fuyuki Ishikawa
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan.,Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8501, Japan
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10
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Subtelomeric Chromatin in the Fission Yeast S. pombe. Microorganisms 2021; 9:microorganisms9091977. [PMID: 34576871 PMCID: PMC8466458 DOI: 10.3390/microorganisms9091977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 01/15/2023] Open
Abstract
Telomeres play important roles in safeguarding the genome. The specialized repressive chromatin that assembles at telomeres and subtelomeric domains is key to this protective role. However, in many organisms, the repetitive nature of telomeric and subtelomeric sequences has hindered research efforts. The fission yeast S. pombe has provided an important model system for dissection of chromatin biology due to the relative ease of genetic manipulation and strong conservation of important regulatory proteins with higher eukaryotes. Telomeres and the telomere-binding shelterin complex are highly conserved with mammals, as is the assembly of constitutive heterochromatin at subtelomeres. In this review, we seek to summarize recent work detailing the assembly of distinct chromatin structures within subtelomeric domains in fission yeast. These include the heterochromatic SH subtelomeric domains, the telomere-associated sequences (TAS), and ST chromatin domains that assemble highly condensed chromatin clusters called knobs. Specifically, we review new insights into the sequence of subtelomeric domains, the distinct types of chromatin that assemble on these sequences and how histone H3 K36 modifications influence these chromatin structures. We address the interplay between the subdomains of chromatin structure and how subtelomeric chromatin is influenced by both the telomere-bound shelterin complexes and by euchromatic chromatin regulators internal to the subtelomeric domain. Finally, we demonstrate that telomere clustering, which is mediated via the condensed ST chromatin knob domains, does not depend on knob assembly within these domains but on Set2, which mediates H3K36 methylation.
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11
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Chaux-Jukic F, O'Donnell S, Craig RJ, Eberhard S, Vallon O, Xu Z. Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Nucleic Acids Res 2021; 49:7571-7587. [PMID: 34165564 PMCID: PMC8287924 DOI: 10.1093/nar/gkab534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.
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Affiliation(s)
- Frédéric Chaux-Jukic
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Samuel O'Donnell
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, Edinburgh, UK
| | - Stephan Eberhard
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Olivier Vallon
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Zhou Xu
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
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12
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Chaux-Jukic F, O'Donnell S, Craig RJ, Eberhard S, Vallon O, Xu Z. Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Nucleic Acids Res 2021. [PMID: 34165564 DOI: 10.1101/2021.01.29.428817)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.
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Affiliation(s)
- Frédéric Chaux-Jukic
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Samuel O'Donnell
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, Edinburgh, UK
| | - Stephan Eberhard
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Olivier Vallon
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Zhou Xu
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
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13
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Apte MS, Masuda H, Wheeler DL, Cooper JP. RNAi and Ino80 complex control rate limiting translocation step that moves rDNA to eroding telomeres. Nucleic Acids Res 2021; 49:8161-8176. [PMID: 34244792 PMCID: PMC8373062 DOI: 10.1093/nar/gkab586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/18/2021] [Accepted: 07/01/2021] [Indexed: 01/21/2023] Open
Abstract
The discovery of HAATIrDNA, a telomerase-negative survival mode in which canonical telomeres are replaced with ribosomal DNA (rDNA) repeats that acquire chromosome end-protection capability, raised crucial questions as to how rDNA tracts 'jump' to eroding chromosome ends. Here, we show that HAATIrDNA formation is initiated and limited by a single translocation that juxtaposes rDNA from Chromosome (Chr) III onto subtelomeric elements (STE) on Chr I or II; this rare reaction requires RNAi and the Ino80 nucleosome remodeling complex (Ino80C), thus defining an unforeseen relationship between these two machineries. The unique STE-rDNA junction created by this initial translocation is efficiently copied to the remaining STE chromosome ends, independently of RNAi or Ino80C. Intriguingly, both RNAi and Ino80C machineries contain a component that plays dual roles in HAATI subtype choice. Dcr1 of the RNAi pathway and Iec1 of Ino80C both promote HAATIrDNA formation as part of their respective canonical machineries, but both also inhibit formation of the exceedingly rare HAATISTE (where STE sequences mobilize throughout the genome and assume chromosome end protection capacity) in non-canonical, pathway-independent manners. This work provides a glimpse into a previously unrecognized crosstalk between RNAi and Ino80C in controlling unusual translocation reactions that establish telomere-free linear chromosome ends.
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Affiliation(s)
- Manasi S Apte
- Laboratory of Biochemistry and Molecular Biology, NCI, NIH, Bethesda, MD 20892, USA
| | - Hirohisa Masuda
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David Lee Wheeler
- Laboratory of Biochemistry and Molecular Biology, NCI, NIH, Bethesda, MD 20892, USA
| | - Julia Promisel Cooper
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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14
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Idiopathic Infertility as a Feature of Genome Instability. Life (Basel) 2021; 11:life11070628. [PMID: 34209597 PMCID: PMC8307193 DOI: 10.3390/life11070628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/18/2022] Open
Abstract
Genome instability may play a role in severe cases of male infertility, with disrupted spermatogenesis being just one manifestation of decreased general health and increased morbidity. Here, we review the data on the association of male infertility with genetic, epigenetic, and environmental alterations, the causes and consequences, and the methods for assessment of genome instability. Male infertility research has provided evidence that spermatogenic defects are often not limited to testicular dysfunction. An increased incidence of urogenital disorders and several types of cancer, as well as overall reduced health (manifested by decreased life expectancy and increased morbidity) have been reported in infertile men. The pathophysiological link between decreased life expectancy and male infertility supports the notion of male infertility being a systemic rather than an isolated condition. It is driven by the accumulation of DNA strand breaks and premature cellular senescence. We have presented extensive data supporting the notion that genome instability can lead to severe male infertility termed “idiopathic oligo-astheno-teratozoospermia.” We have detailed that genome instability in men with oligo-astheno-teratozoospermia (OAT) might depend on several genetic and epigenetic factors such as chromosomal heterogeneity, aneuploidy, micronucleation, dynamic mutations, RT, PIWI/piRNA regulatory pathway, pathogenic allelic variants in repair system genes, DNA methylation, environmental aspects, and lifestyle factors.
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15
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Bertazzoni S, Jones DAB, Phan HT, Tan KC, Hane JK. Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome. BMC Genomics 2021; 22:382. [PMID: 34034667 PMCID: PMC8146201 DOI: 10.1186/s12864-021-07699-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Background The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised – ToxA, Tox1 and Tox3. Results A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions. Conclusions We present an updated series of genomic resources for P. nodorum Sn15 – an important reference isolate and model necrotroph – with a comprehensive survey of its predicted pathogenicity content. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07699-8.
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Affiliation(s)
| | - Darcy A B Jones
- Centre for Crop & Disease Management, Curtin University, Perth, Australia
| | - Huyen T Phan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - James K Hane
- Centre for Crop & Disease Management, Curtin University, Perth, Australia. .,Curtin Institute for Computation, Curtin University, Perth, Australia.
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16
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Roco ÁS, Liehr T, Ruiz-García A, Guzmán K, Bullejos M. Comparative Distribution of Repetitive Sequences in the Karyotypes of Xenopus tropicalis and Xenopus laevis (Anura, Pipidae). Genes (Basel) 2021; 12:617. [PMID: 33919402 PMCID: PMC8143290 DOI: 10.3390/genes12050617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/29/2022] Open
Abstract
Xenopus laevis and its diploid relative, Xenopus tropicalis, are the most used amphibian models. Their genomes have been sequenced, and they are emerging as model organisms for research into disease mechanisms. Despite the growing knowledge on their genomes based on data obtained from massive genome sequencing, basic research on repetitive sequences in these species is lacking. This study conducted a comparative analysis of repetitive sequences in X. laevis and X. tropicalis. Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) with Cot DNA of both species revealed a conserved enrichment of repetitive sequences at the ends of the chromosomes in these Xenopus species. The repeated sequences located on the short arm of chromosome 3 from X. tropicalis were not related to the sequences on the short arm of chromosomes 3L and 3S from X. laevis, although these chromosomes were homoeologous, indicating that these regions evolved independently in these species. Furthermore, all the other repetitive sequences in X. tropicalis and X. laevis may be species-specific, as they were not revealed in cross-species hybridizations. Painting experiments in X. laevis with chromosome 7 from X. tropicalis revealed shared sequences with the short arm of chromosome 3L. These regions could be related by the presence of the nucleolus organizer region (NOR) in both chromosomes, although the region revealed by chromosome painting in the short arm of chromosome 3L in X. laevis did not correspond to 18S + 28S rDNA sequences, as they did not colocalize. The identification of these repeated sequences is of interest as they provide an explanation to some problems already described in the genome assemblies of these species. Furthermore, the distribution of repetitive DNA in the genomes of X. laevis and X. tropicalis might be a valuable marker to assist us in understanding the genome evolution in a group characterized by numerous polyploidization events coupled with hybridizations.
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Affiliation(s)
- Álvaro S. Roco
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany;
| | - Adrián Ruiz-García
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Kateryna Guzmán
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
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17
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Pinheiro Figliuolo VS, Ferreira AMV, Guimarães EMC, de Sousa E Souza JF, Feldberg E, Gross MC. Cryptic Diversity in the Terminal Portion of the Chromosomes of the Dogtooth Characins, Family Cynodontidae (Ostariophysi: Characiformes). Zebrafish 2021; 18:221-230. [PMID: 33847525 DOI: 10.1089/zeb.2020.1973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The chromosomes of the dogtooth characins, fish species of the family Cynodontidae, have only a relatively small amount of heterochromatin, including the terminal portion. Curiously, in the cynodontid Cynodon gibbus, the terminal portion is rich in repetitive DNAs, including transposable retroelements and microsatellite sequences. Given this, this study investigated the composition of the terminal portion of the chromosomes of two cynodontid species (Rhaphiodon vulpinus and Hydrolycus armatus), to compile a database for the evaluation of all three cynodontid genera, and in particular, verify the possible tendency for the accumulation of repetitive DNAs in the terminal portion of the chromosomes of C. gibbus, H. armatus, and R. vulpinus. The Rex1, Rex3, and Rex6 transposable retroelements and the (CA)15, (GA)15, (GATA)8, (GACA)8, (CAT)10, and (CAC)10 microsatellite motifs are found primarily in the terminal portion of the chromosomes of the species analyzed in this study, except R. vulpinus, which has no evidence of the presence of Rex1 or Rex3 through the fluorescent in situ hybridization technique. The mapping of the repetitive sequences, principally the microsatellite motifs, indicates a marked tendency for the accumulation of these sequences in the terminal portions of the chromosomes, which may have played a fundamental role in the differentiation of the three species.
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Affiliation(s)
| | | | | | | | - Eliana Feldberg
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Maria Claudia Gross
- Institute for Natural and Life Sciences, Federal University of Latin American Integration, Foz do Iguaçu, Brazil
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18
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Misova I, Pitelova A, Budis J, Gazdarica J, Sedlackova T, Jordakova A, Benko Z, Smondrkova M, Mayerova N, Pichlerova K, Strieskova L, Prevorovsky M, Gregan J, Cipak L, Szemes T, Polakova SB. Repression of a large number of genes requires interplay between homologous recombination and HIRA. Nucleic Acids Res 2021; 49:1914-1934. [PMID: 33511417 PMCID: PMC7913671 DOI: 10.1093/nar/gkab027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.
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Affiliation(s)
- Ivana Misova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Alexandra Pitelova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Juraj Gazdarica
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Tatiana Sedlackova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Anna Jordakova
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Zsigmond Benko
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, H-4010 Debrecen, Hungary
| | - Maria Smondrkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Nina Mayerova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Karoline Pichlerova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Lucia Strieskova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Martin Prevorovsky
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF and Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Silvia Bagelova Polakova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
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19
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Oizumi Y, Kaji T, Tashiro S, Takeshita Y, Date Y, Kanoh J. Complete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation. Nat Commun 2021; 12:611. [PMID: 33504776 PMCID: PMC7840980 DOI: 10.1038/s41467-020-20595-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022] Open
Abstract
Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1-4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.
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Affiliation(s)
- Yusuke Oizumi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takuto Kaji
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sanki Tashiro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Institute of Molecular Biology, University of Oregon, 1370 Franklin Blvd, Eugene, OR, USA
| | - Yumiko Takeshita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuko Date
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Junko Kanoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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20
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Lei B, Capella M, Montgomery SA, Borg M, Osakabe A, Goiser M, Muhammad A, Braun S, Berger F. A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W. Curr Biol 2021; 31:182-191.e5. [PMID: 33096036 DOI: 10.1016/j.cub.2020.09.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/28/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
Diversification of histone variants is marked by the acquisition of distinct motifs and functional properties through convergent evolution.1-4 H2A variants are distinguished by specific C-terminal motifs and tend to be segregated within defined domains of the genome.5,6 Whether evolution of these motifs pre-dated the evolution of segregation mechanisms or vice versa has remained unclear. A suitable model to address this question is the variant H2A.W, which evolved in plants through acquisition of a KSPK motif7 and is tightly associated with heterochromatin.4 We used fission yeast, where chromatin is naturally devoid of H2A.W, to study the impact of engineered chimeras combining yeast H2A with the KSPK motif. Biochemical assays showed that the KSPK motif conferred nucleosomes with specific properties. Despite uniform incorporation of the engineered H2A chimeras in the yeast genome, the KSPK motif specifically affected heterochromatin composition and function. We conclude that the KSPK motif promotes chromatin properties in yeast that are comparable to the properties and function of H2A.W in plant heterochromatin. We propose that the selection of functional motifs confer histone variants with properties that impact primarily a specific chromatin state. The association between a new histone variant and a preferred chromatin state can thus provide a setting for the evolution of mechanisms that segregate the new variant to this state, thereby enhancing the impact of the selected properties of the variant on genome activity.
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Affiliation(s)
- Bingkun Lei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Matías Capella
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Malgorzata Goiser
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Abubakar Muhammad
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany
| | - Sigurd Braun
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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Grandin N, Gallego ME, White CI, Charbonneau M. Inhibition of the alternative lengthening of telomeres pathway by subtelomeric sequences in Saccharomyces cerevisiae. DNA Repair (Amst) 2020; 96:102996. [PMID: 33126043 DOI: 10.1016/j.dnarep.2020.102996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/24/2020] [Accepted: 10/04/2020] [Indexed: 10/23/2022]
Abstract
In the budding yeast Saccharomyces cerevisiae, telomerase is constitutively active and is essential for chromosome end protection and illimited proliferation of cell populations. However, upon inactivation of telomerase, alternative mechanims of telomere maintenance allow proliferation of only extremely rare survivors. S. cerevisiae type I and type II survivors differ by the nature of the donor sequences used for repair by homologous recombination of the uncapped terminal TG1-3 telomeric sequences. Type I amplifies the subtelomeric Y' sequences and is more efficient than type II, which amplifies the terminal TG1-3 repeats. However, type II survivors grow faster than type I survivors and can easily outgrow them in liquid cultures. The mechanistic interest of studying S. cerevisiae telomeric recombination is reinforced by the fact that type II recombination is the equivalent of the alternative lengthening of telomeres (ALT) pathway that is used by 5-15 % of cancer types as an alternative to telomerase reactivation. In budding yeast, only around half of the 32 telomeres harbor Y' subtelomeric elements. We report here that in strains harboring Y' elements on all telomeres, type II survivors are not observed, most likely due to an increase in the efficiency of type I recombination. However, in a temperature-sensitive cdc13-1 mutant grown at semi-permissive temperature, the increased amount of telomeric TG1-3 repeats could overcome type II inhibition by the subtelomeric Y' sequences. Strikingly, in the 100 % Y' strain the replicative senescence crisis normally provoked by inactivation of telomerase completely disappeared and the severity of the crisis was proportional to the percentage of chromosome-ends lacking Y' subtelomeric sequences. The present study highlights the fact that the nature of subtelomeric elements can influence the selection of the pathway of telomere maintenance by recombination, as well as the response of the cell to telomeric damage caused by telomerase inactivation.
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Affiliation(s)
- Nathalie Grandin
- GReD Institute, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France
| | - Maria Eugenia Gallego
- GReD Institute, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France
| | - Charles I White
- GReD Institute, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France
| | - Michel Charbonneau
- GReD Institute, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France.
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22
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Kalinka A, Achrem M. The distribution pattern of 5-methylcytosine in rye (Secale L.) chromosomes. PLoS One 2020; 15:e0240869. [PMID: 33057421 PMCID: PMC7561101 DOI: 10.1371/journal.pone.0240869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/04/2020] [Indexed: 12/02/2022] Open
Abstract
The rye (Secale L.) genome is large, and it contains many classes of repetitive sequences. Secale species differ in terms of genome size, heterochromatin content, and global methylation level; however, the organization of individual types of sequences in chromosomes is relatively similar. The content of the abundant subtelomeric heterochromatin fraction in rye do not correlate with the global level of cytosine methylation, hence immunofluorescence detection of 5-methylcytosine (5-mC) distribution in metaphase chromosomes was performed. The distribution patterns of 5-methylcytosine in the chromosomes of Secale species/subspecies were generally similar. 5-methylcytosine signals were dispersed along the entire length of the chromosome arms of all chromosomes, indicating high levels of methylation, especially at retrotransposon sequences. 5-mC signals were absent in the centromeric and telomeric regions, as well as in subtelomeric blocks of constitutive heterochromatin, in each of the taxa studied. Pericentromeric domains were methylated, however, there was a certain level of polymorphism in these areas, as was the case with the nucleolus organizer region. Sequence methylation within the region of the heterochromatin intercalary bands were also demonstrated to be heterogenous. Unexpectedly, there was a lack of methylation in rye subtelomeres, indicating that heterochromatin is a very diverse fraction of chromatin, and its epigenetic regulation or potential influence on adjacent regions can be more complex than has conventionally been thought. Like telomeres and centromeres, subtelomeric heterochromatin can has a specific role, and the absence of 5-mC is required to maintain the heterochromatin state.
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Affiliation(s)
- Anna Kalinka
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
- * E-mail:
| | - Magdalena Achrem
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
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Wu ZJ, Liu JC, Man X, Gu X, Li TY, Cai C, He MH, Shao Y, Lu N, Xue X, Qin Z, Zhou JQ. Cdc13 is predominant over Stn1 and Ten1 in preventing chromosome end fusions. eLife 2020; 9:53144. [PMID: 32755541 PMCID: PMC7406354 DOI: 10.7554/elife.53144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/12/2020] [Indexed: 12/16/2022] Open
Abstract
Telomeres define the natural ends of eukaryotic chromosomes and are crucial for chromosomal stability. The budding yeast Cdc13, Stn1 and Ten1 proteins form a heterotrimeric complex, and the inactivation of any of its subunits leads to a uniformly lethal phenotype due to telomere deprotection. Although Cdc13, Stn1 and Ten1 seem to belong to an epistasis group, it remains unclear whether they function differently in telomere protection. Here, we employed the single-linear-chromosome yeast SY14, and surprisingly found that the deletion of CDC13 leads to telomere erosion and intrachromosome end-to-end fusion, which depends on Rad52 but not Yku. Interestingly, the emergence frequency of survivors in the SY14 cdc13Δ mutant was ~29 fold higher than that in either the stn1Δ or ten1Δ mutant, demonstrating a predominant role of Cdc13 in inhibiting telomere fusion. Chromosomal fusion readily occurred in the telomerase-null SY14 strain, further verifying the default role of intact telomeres in inhibiting chromosome fusion.
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Affiliation(s)
- Zhi-Jing Wu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xin Man
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xin Gu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Ting-Yi Li
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Chen Cai
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ming-Hong He
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yangyang Shao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Ning Lu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaoli Xue
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhongjun Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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24
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Zattera ML, Gazolla CB, Soares ADA, Gazoni T, Pollet N, Recco-Pimentel SM, Bruschi DP. Evolutionary Dynamics of the Repetitive DNA in the Karyotypes of Pipa carvalhoi and Xenopus tropicalis (Anura, Pipidae). Front Genet 2020; 11:637. [PMID: 32793276 PMCID: PMC7385237 DOI: 10.3389/fgene.2020.00637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023] Open
Abstract
The large amphibian genomes contain numerous repetitive DNA components that have played an important role in the karyotypic diversification of this vertebrate group. Hypotheses based on the presumable primitive karyotype (2n = 20) of the anurans of the family Pipidae suggest that they have evolved principally through intrachromosomal rearrangements. Pipa is the only South American pipid, while all the other genera are found in Africa. The divergence of the South American lineages from the African ones occurred at least 136 million years ago and is thought to have had a strong biogeographic component. Here, we tested the potential of the repetitive DNA to enable a better understanding of the differentiation of the karyotype among the family Pipidae and to expand our capacity to interpret the chromosomal evolution in this frog family. Our results indicate a long history of conservation in the chromosome bearing the H3 histone locus, corroborating inferences on the chromosomal homologies between the species in pairs 6, 8, and 9. The chromosomal distribution of the microsatellite motifs also provides useful markers for comparative genomics at the chromosome level between Pipa carvalhoi and Xenopus tropicalis, contributing new insights into the evolution of the karyotypes of these species. We detected similar patterns in the distribution and abundance of the microsatellite arrangements, which reflect the shared organization in the terminal/subterminal region of the chromosomes between these two species. By contrast, the microsatellite probes detected a differential arrangement of the repetitive DNA among the chromosomes of the two species, allowing longitudinal differentiation of pairs that are identical in size and morphology, such as pairs 1, 2, 4, and 5. We also found evidence of the distinctive composition of the repetitive motifs of the centromeric region between the species analyzed in the present study, with a clear enrichment of the (CA) and (GA) microsatellite motifs in P. carvalhoi. Finally, microsatellite enrichment in the pericentromeric region of chromosome pairs 6, 8, and 9 in the P. carvalhoi karyotype, together with interstitial telomeric sequences (ITS), validate the hypothesis that pericentromeric inversions occurred during the chromosomal evolution of P. carvalhoi and reinforce the role of the repetitive DNA in the remodeling of the karyotype architecture of the Pipidae.
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Affiliation(s)
- Michelle Louise Zattera
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Camilla Borges Gazolla
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Amanda de Araújo Soares
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Thiago Gazoni
- Universidade Estadual Paulista (Unesp), Campus Rio Claro, Rio Claro, Brazil
| | - Nicolas Pollet
- Laboratoire Evolution Genomes Comportement Ecologie, CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Daniel Pacheco Bruschi
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
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25
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Hocher A, Taddei A. Subtelomeres as Specialized Chromatin Domains. Bioessays 2020; 42:e1900205. [PMID: 32181520 DOI: 10.1002/bies.201900205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/19/2020] [Indexed: 12/26/2022]
Abstract
Specificities associated with chromosomal linearity are not restricted to telomeres. Here, recent results obtained on fission and budding yeast are summarized and an attempt is made to define subtelomeres using chromatin features extending beyond the heterochromatin emanating from telomeres. Subtelomeres, the chromosome domains adjacent to telomeres, differ from the rest of the genome by their gene content, rapid evolution, and chromatin features that together contribute to organism adaptation. However, current definitions of subtelomeres are generally based on synteny and are largely gene-centered. Taking into consideration both the peculiar gene content and dynamics as well as the chromatin properties of those domains, it is discussed how chromatin features can contribute to subtelomeric properties and functions, and play a pivotal role in the emergence of subtelomeres.
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Affiliation(s)
- Antoine Hocher
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, F-75005, France.,Sorbonne Université, UPMC University Paris 06, CNRS, UMR3664, Paris, F-75005, France
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26
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Srinivas N, Rachakonda S, Kumar R. Telomeres and Telomere Length: A General Overview. Cancers (Basel) 2020; 12:E558. [PMID: 32121056 PMCID: PMC7139734 DOI: 10.3390/cancers12030558] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023] Open
Abstract
Telomeres are highly conserved tandem nucleotide repeats that include proximal double-stranded and distal single-stranded regions that in complex with shelterin proteins afford protection at chromosomal ends to maintain genomic integrity. Due to the inherent limitations of DNA replication and telomerase suppression in most somatic cells, telomeres undergo age-dependent incremental attrition. Short or dysfunctional telomeres are recognized as DNA double-stranded breaks, triggering cells to undergo replicative senescence. Telomere shortening, therefore, acts as a counting mechanism that drives replicative senescence by limiting the mitotic potential of cells. Telomere length, a complex hereditary trait, is associated with aging and age-related diseases. Epidemiological data, in general, support an association with varying magnitudes between constitutive telomere length and several disorders, including cancers. Telomere attrition is also influenced by oxidative damage and replicative stress caused by genetic, epigenetic, and environmental factors. Several single nucleotide polymorphisms at different loci, identified through genome-wide association studies, influence inter-individual variation in telomere length. In addition to genetic factors, environmental factors also influence telomere length during growth and development. Telomeres hold potential as biomarkers that reflect the genetic predisposition together with the impact of environmental conditions and as targets for anti-cancer therapies.
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Affiliation(s)
| | | | - Rajiv Kumar
- Division of Functional Genome Analysis, German Cancer Research Center, Im Neunheimer Feld 580, 69120 Heidelberg, Germany; (N.S.); (S.R.)
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27
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Kwapisz M, Morillon A. Subtelomeric Transcription and its Regulation. J Mol Biol 2020; 432:4199-4219. [PMID: 32035903 PMCID: PMC7374410 DOI: 10.1016/j.jmb.2020.01.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 12/13/2022]
Abstract
The subtelomeres, highly heterogeneous repeated sequences neighboring telomeres, are transcribed into coding and noncoding RNAs in a variety of organisms. Telomereproximal subtelomeric regions produce non-coding transcripts i.e., ARRET, αARRET, subTERRA, and TERRA, which function in telomere maintenance. The role and molecular mechanisms of the majority of subtelomeric transcripts remain unknown. This review depicts the current knowledge and puts into perspective the results obtained in different models from yeasts to humans.
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Affiliation(s)
- Marta Kwapisz
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248, Paris, France.
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28
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Henninger E, Teixeira MT. Telomere-driven mutational processes in yeast. Curr Opin Genet Dev 2020; 60:99-106. [DOI: 10.1016/j.gde.2020.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022]
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29
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Ernetti JR, Gazolla CB, Recco-Pimentel SM, Luca EM, Bruschi DP. Non-random distribution of microsatellite motifs and (TTAGGG)n repeats in the monkey frog Pithecopus rusticus (Anura, Phyllomedusidae) karyotype. Genet Mol Biol 2020; 42:e20190151. [PMID: 31968045 PMCID: PMC7198017 DOI: 10.1590/1678-4685-gmb-2019-0151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023] Open
Abstract
The monkey frog, Pithecopus rusticus (Anura, Phyllomedusidae) is endemic to the grasslands of the Araucarias Plateau, southern Brazil. This species is known only from a small population found at the type locality. Here, we analyzed for the first time the chromosomal organization of the repetitive sequences, including seven microsatellite repeats and telomeric sequences (TTAGGG)n in the karyotype of the species by Fluorescence in situ Hybridization. The dinucleotide motifs had a pattern of distribution clearly distinct from those of the tri- and tetranucleotides. The dinucleotide motifs are abundant and widely distributed in the chromosomes, located primarily in the subterminal regions. The tri- and tetranucleotides, by contrast, tend to be clustered, with signals being observed together in the secondary constriction of the homologs of pair 9, which are associated with the nucleolus organizer region. As expected, the (TTAGGG)n probe was hybridized in all the telomeres, with hybridization signals being detected in the interstitial regions of some chromosome pairs. We demonstrated the variation in the abundance and distribution of the different microsatellite motifs and revealed their non-random distribution in the karyotype of P. rusticus. These data contribute to understand the role of repetitive sequences in the karyotype diversification and evolution of this taxon.
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Affiliation(s)
- Julia R Ernetti
- Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil
| | - Camilla B Gazolla
- Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Shirlei M Recco-Pimentel
- Departamento de Biologia Estrutural e Funcional, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Elaine M Luca
- Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil
- Departamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, Campus de Palmeira das Missões, Palmeira das Missões, RS, Brazil
| | - Daniel P Bruschi
- Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
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30
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Dunn MJ, Anderson MZ. To Repeat or Not to Repeat: Repetitive Sequences Regulate Genome Stability in Candida albicans. Genes (Basel) 2019; 10:genes10110866. [PMID: 31671659 PMCID: PMC6896093 DOI: 10.3390/genes10110866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022] Open
Abstract
Genome instability often leads to cell death but can also give rise to innovative genotypic and phenotypic variation through mutation and structural rearrangements. Repetitive sequences and chromatin architecture in particular are critical modulators of recombination and mutability. In Candida albicans, four major classes of repeats exist in the genome: telomeres, subtelomeres, the major repeat sequence (MRS), and the ribosomal DNA (rDNA) locus. Characterization of these loci has revealed how their structure contributes to recombination and either promotes or restricts sequence evolution. The mechanisms of recombination that give rise to genome instability are known for some of these regions, whereas others are generally unexplored. More recent work has revealed additional repetitive elements, including expanded gene families and centromeric repeats that facilitate recombination and genetic innovation. Together, the repeats facilitate C. albicans evolution through construction of novel genotypes that underlie C. albicans adaptive potential and promote persistence across its human host.
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Affiliation(s)
- Matthew J. Dunn
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
- Correspondence: ; Tel.: +614-247-0058
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31
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Telomere DNA length-dependent regulation of DNA replication timing at internal late replication origins. Sci Rep 2019; 9:9946. [PMID: 31289327 PMCID: PMC6617677 DOI: 10.1038/s41598-019-46229-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
DNA replication is initiated at replication origins on chromosomes at their scheduled time during S phase of the cell cycle. Replication timing control is highly conserved among eukaryotes but the underlying mechanisms are not fully understood. Recent studies have revealed that some telomere-binding proteins regulate replication timing at late-replicating origins throughout the genome. To investigate the molecular basis of this process, we analyzed the effects of excessive elongation of telomere DNA on replication timing by deleting telomere-associated shelterin proteins in Schizosaccharomyces pombe. We found that rap1∆ and poz1∆ cells showed abnormally accelerated replication at internal late origins but not at subtelomere regions. These defects were suppressed by removal of telomere DNA and by deletion of the telomere-binding protein Taz1. Furthermore, Sds21—a counter protein phosphatase against Dbf4-dependent kinase (DDK)—accumulated at elongated telomeres in a Taz1-dependent manner but was depleted at internal late origins, indicating that highly elongated telomeres sequester Sds21 at telomeres and perturb replication timing at internal regions. These results demonstrate that telomere DNA length is an important determinant of replication timing at internal regions of chromosomes in eukaryotes.
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32
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TASks for subtelomeres: when nucleosome loss and genome instability are favored. Curr Genet 2019; 65:1153-1160. [DOI: 10.1007/s00294-019-00986-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022]
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van Emden TS, Forn M, Forné I, Sarkadi Z, Capella M, Martín Caballero L, Fischer-Burkart S, Brönner C, Simonetta M, Toczyski D, Halic M, Imhof A, Braun S. Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability. EMBO Rep 2018; 20:embr.201847181. [PMID: 30420521 DOI: 10.15252/embr.201847181] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/03/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Telomeres and the shelterin complex cap and protect the ends of chromosomes. Telomeres are flanked by the subtelomeric sequences that have also been implicated in telomere regulation, although their role is not well defined. Here, we show that, in Schizosaccharomyces pombe, the telomere-associated sequences (TAS) present on most subtelomeres are hyper-recombinogenic, have metastable nucleosomes, and unusual low levels of H3K9 methylation. Ccq1, a subunit of shelterin, protects TAS from nucleosome loss by recruiting the heterochromatic repressor complexes CLRC and SHREC, thereby linking nucleosome stability to gene silencing. Nucleosome instability at TAS is independent of telomeric repeats and can be transmitted to an intrachromosomal locus containing an ectopic TAS fragment, indicating that this is an intrinsic property of the underlying DNA sequence. When telomerase recruitment is compromised in cells lacking Ccq1, DNA sequences present in the TAS promote recombination between chromosomal ends, independent of nucleosome abundance, implying an active function of these sequences in telomere maintenance. We propose that Ccq1 and fragile subtelomeres co-evolved to regulate telomere plasticity by controlling nucleosome occupancy and genome stability.
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Affiliation(s)
- Thomas S van Emden
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, Martinsried, Germany
| | - Marta Forn
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Ignasi Forné
- Protein Analysis Unit (ZfP), BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Zsuzsa Sarkadi
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Matías Capella
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Lucía Martín Caballero
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, Martinsried, Germany
| | - Sabine Fischer-Burkart
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Cornelia Brönner
- Department of Biochemistry, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany
| | - Marco Simonetta
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - David Toczyski
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Mario Halic
- Department of Biochemistry, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany
| | - Axel Imhof
- Protein Analysis Unit (ZfP), BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Sigurd Braun
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany .,International Max Planck Research School for Molecular and Cellular Life Sciences, Martinsried, Germany
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Begnis M, Apte MS, Masuda H, Jain D, Wheeler DL, Cooper JP. RNAi drives nonreciprocal translocations at eroding chromosome ends to establish telomere-free linear chromosomes. Genes Dev 2018; 32:537-554. [PMID: 29654060 PMCID: PMC5959237 DOI: 10.1101/gad.311712.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/29/2018] [Indexed: 12/19/2022]
Abstract
In this study, Begnis et al. show that HAATI, which is a mode of telomerase-minus survival in which canonical telomeres are superseded by blocks of nontelomeric rDNA heterochromatin that have spread to all chromosome ends, is formed and maintained. Their findings demonstrate that HAATI arises when telomere loss triggers a newly recognized illegitimate recombination pathway that requires RNAi factors, uncovering novel roles for ncRNAs in assembling a telomere-free chromosome end protection device. The identification of telomerase-negative HAATI (heterochromatin amplification-mediated and telomerase-independent) cells, in which telomeres are superseded by nontelomeric heterochromatin tracts, challenged the idea that canonical telomeres are essential for chromosome linearity and raised crucial questions as to how such tracts translocate to eroding chromosome ends and confer end protection. Here we show that HAATI arises when telomere loss triggers a newly recognized illegitimate translocation pathway that requires RNAi factors. While RNAi is necessary for the translocation events that mobilize ribosomal DNA (rDNA) tracts to all chromosome ends (forming “HAATIrDNA” chromosomes), it is dispensable for HAATIrDNA maintenance. Surprisingly, Dicer (Dcr1) plays a separate, RNAi-independent role in preventing formation of the rare HAATI subtype in which a different repetitive element (the subtelomeric element) replaces telomeres. Using genetics and fusions between shelterin components and rDNA-binding proteins, we mapped the mechanism by which rDNA loci engage crucial end protection factors—despite the absence of telomere repeats—and secure end protection. Sequence analysis of HAATIrDNA genomes allowed us to propose RNA and DNA polymerase template-switching models for the mechanism of RNAi-triggered rDNA translocations. Collectively, our results reveal unforeseen roles for noncoding RNAs (ncRNAs) in assembling a telomere-free chromosome end protection device.
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Affiliation(s)
- Martina Begnis
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Telomere Biology Laboratory, Cancer Research UK, London Research Institute, London WC2A 3LY, United Kingdom
| | - Manasi S Apte
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hirohisa Masuda
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Devanshi Jain
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - David Lee Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Julia Promisel Cooper
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Telomere Biology Laboratory, Cancer Research UK, London Research Institute, London WC2A 3LY, United Kingdom
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Cohen A, Habib A, Laor D, Yadav S, Kupiec M, Weisman R. TOR complex 2 in fission yeast is required for chromatin-mediated gene silencing and assembly of heterochromatic domains at subtelomeres. J Biol Chem 2018; 293:8138-8150. [PMID: 29632066 DOI: 10.1074/jbc.ra118.002270] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/14/2018] [Indexed: 12/21/2022] Open
Abstract
The conserved serine/threonine protein kinase target of rapamycin (TOR) is a major regulator of eukaryotic cellular and organismal growth and a valuable target for drug therapy. TOR forms the core of two evolutionary conserved complexes, TOR complex 1 (TORC1) and TORC2. In the fission yeast Schizosaccharomyces pombe, TORC2 responds to glucose levels and, by activating the protein kinase Gad8 (an orthologue of human AKT), is required for well-regulated cell cycle progression, starvation responses, and cell survival. Here, we report that TORC2-Gad8 is also required for gene silencing and the formation of heterochromatin at the S. pombe mating-type locus and at subtelomeric regions. Deletion of TORC2-Gad8 resulted in loss of the heterochromatic modification of histone 3 lysine 9 dimethylation (H3K9me2) and an increase in euchromatic modifications, including histone 3 lysine 4 trimethylation (H3K4me3) and histone 4 lysine 16 acetylation (H4K16Ac). Accumulation of RNA polymerase II (Pol II) at subtelomeric genes in TORC2-Gad8 mutant cells indicated a defect in silencing at the transcriptional level. Moreover, a concurrent decrease in histone 4 lysine 20 dimethylation (H4K20me2) suggested elevated histone turnover. Loss of gene silencing in cells lacking TORC2-Gad8 is partially suppressed by loss of the anti-silencer Epe1 and fully suppressed by loss of the Pol II-associated Paf1 complex, two chromatin regulators that have been implicated in heterochromatin stability and spreading. Taken together, our findings suggest that TORC2-Gad8 signaling contributes to epigenetic stability at subtelomeric regions and the mating-type locus in S. pombe.
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Affiliation(s)
- Adiel Cohen
- Department of Natural and Life Sciences, Open University of Israel, University Road 1, 4353701 Ranana, Israel
| | - Aline Habib
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Dana Laor
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Sudhanshu Yadav
- Department of Natural and Life Sciences, Open University of Israel, University Road 1, 4353701 Ranana, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, Open University of Israel, University Road 1, 4353701 Ranana, Israel.
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