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Maclay T, Whalen J, Johnson M, Freudenreich CH. The DNA Replication Checkpoint Targets the Kinetochore for Relocation of Collapsed Forks to the Nuclear Periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599319. [PMID: 38948692 PMCID: PMC11212917 DOI: 10.1101/2024.06.17.599319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Hairpin forming expanded CAG/CTG repeats pose significant challenges to DNA replication which can lead to replication fork collapse. Long CAG/CTG repeat tracts relocate to the nuclear pore complex to maintain their integrity. Forks impeded by DNA structures are known to activate the DNA damage checkpoint, thus we asked whether checkpoint proteins play a role in relocation of collapsed forks to the nuclear periphery in S. cerevisiae . We show that relocation of a (CAG/CTG) 130 tract is dependent on activation of the Mrc1/Rad53 replication checkpoint. Further, checkpoint-mediated phosphorylation of the kinetochore protein Cep3 is required for relocation, implicating detachment of the centromere from the spindle pole body. Activation of this pathway leads to DNA damage-induced microtubule recruitment to the repeat. These data suggest a role for the DNA replication checkpoint in facilitating movement of collapsed replication forks to the nuclear periphery by centromere release and microtubule-directed motion. Highlights The DNA replication checkpoint initiates relocation of a structure-forming CAG repeat tract to the nuclear pore complex (NPC)The importance of Mrc1 (hClaspin) implicates fork uncoupling as the initial checkpoint signalPhosphorylation of the Cep3 kinetochore protein by Dun1 kinase allows for centromere release, which is critical for collapsed fork repositioningDamage-inducible nuclear microtubules (DIMs) colocalize with the repeat locus and are required for relocation to the NPCEstablishes a new role for the DNA replication and DNA damage checkpoint response to trigger repositioning of collapsed forks within the nucleus.
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2
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da Roza PA, Muller H, Sullivan GJ, Walker RSK, Goold HD, Willows RD, Palenik B, Paulsen IT. Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C 4 photosynthesis. Microb Genom 2024; 10. [PMID: 38625719 DOI: 10.1099/mgen.0.001223] [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: 04/17/2024] Open
Abstract
Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.
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Affiliation(s)
- Patrick A da Roza
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Héloïse Muller
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Roy S K Walker
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Hugh D Goold
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia
| | - Robert D Willows
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
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3
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Al-Zain AM, Nester MR, Ahmed I, Symington LS. Double-strand breaks induce inverted duplication chromosome rearrangements by a DNA polymerase δ-dependent mechanism. Nat Commun 2023; 14:7020. [PMID: 37919272 PMCID: PMC10622511 DOI: 10.1038/s41467-023-42640-5] [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: 01/24/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Inverted duplications, also known as foldback inversions, are commonly observed in cancers and are the major class of chromosome rearrangement recovered from yeast cells lacking Mre11 nuclease activity. Foldback priming at DNA double-strand breaks (DSBs) is one mechanism proposed for the generation of inverted duplications. However, the other pathway steps have not been fully elucidated. Here, we show that a DSB induced near natural inverted repeats drives high frequency inverted duplication in Sae2 and Mre11-deficient cells. We find that DNA polymerase δ proof-reading activity, but not Rad1 nuclease, trims the heterologous flaps formed after foldback annealing. Additionally, Pol32 is required for the generation of inverted duplications, suggesting that Pol δ catalyzes fill-in synthesis primed from the foldback to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric inversion chromosome. Finally, we show that stabilization of the dicentric chromosome after breakage involves telomere capture by non-reciprocal translocation mediated by repeat sequences or by deletion of one centromere.
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Affiliation(s)
- Amr M Al-Zain
- Program in Biological Sciences, Columbia University, New York, NY, 10027, USA
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Mattie R Nester
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Iffat Ahmed
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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4
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Chaux F, Agier N, Garrido C, Fischer G, Eberhard S, Xu Z. Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii. Genome Res 2023; 33:1582-1598. [PMID: 37580131 PMCID: PMC10620057 DOI: 10.1101/gr.278043.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/09/2023] [Indexed: 08/16/2023]
Abstract
Telomeres and subtelomeres, the genomic regions located at chromosome extremities, are essential for genome stability in eukaryotes. In the absence of the canonical maintenance mechanism provided by telomerase, telomere shortening induces genome instability. The landscape of the ensuing genome rearrangements is not accessible by short-read sequencing. Here, we leverage Oxford Nanopore Technologies long-read sequencing to survey the extensive repertoire of genome rearrangements in telomerase mutants of the model green microalga Chlamydomonas reinhardtii In telomerase-mutant strains grown for hundreds of generations, most chromosome extremities were capped by short telomere sequences that were either recruited de novo from other loci or maintained in a telomerase-independent manner. Other extremities did not end with telomeres but only with repeated subtelomeric sequences. The subtelomeric elements, including rDNA, were massively rearranged and involved in breakage-fusion-bridge cycles, translocations, recombinations, and chromosome circularization. These events were established progressively over time and displayed heterogeneity at the subpopulation level. New telomere-capped extremities composed of sequences originating from more internal genomic regions were associated with high DNA methylation, suggesting that de novo heterochromatin formation contributes to the restoration of chromosome end stability in C. reinhardtii The diversity of alternative strategies present in the same organism to maintain chromosome integrity and the variety of rearrangements found in telomerase mutants are remarkable, and illustrate genome plasticity at short timescales.
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Affiliation(s)
- Frédéric Chaux
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Nicolas Agier
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Clotilde Garrido
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Gilles Fischer
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Stephan Eberhard
- 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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5
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Kuse R, Ishii K. Flexible Attachment and Detachment of Centromeres and Telomeres to and from Chromosomes. Biomolecules 2023; 13:1016. [PMID: 37371596 DOI: 10.3390/biom13061016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Accurate transmission of genomic information across multiple cell divisions and generations, without any losses or errors, is fundamental to all living organisms. To achieve this goal, eukaryotes devised chromosomes. Eukaryotic genomes are represented by multiple linear chromosomes in the nucleus, each carrying a centromere in the middle, a telomere at both ends, and multiple origins of replication along the chromosome arms. Although all three of these DNA elements are indispensable for chromosome function, centromeres and telomeres possess the potential to detach from the original chromosome and attach to new chromosomal positions, as evident from the events of telomere fusion, centromere inactivation, telomere healing, and neocentromere formation. These events seem to occur spontaneously in nature but have not yet been elucidated clearly, because they are relatively infrequent and sometimes detrimental. To address this issue, experimental setups have been developed using model organisms such as yeast. In this article, we review some of the key experiments that provide clues as to the extent to which these paradoxical and elusive features of chromosomally indispensable elements may become valuable in the natural context.
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Affiliation(s)
- Riku Kuse
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
| | - Kojiro Ishii
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
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6
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Hill HJ, Bonser D, Golic KG. Dicentric chromosome breakage in Drosophila melanogaster is influenced by pericentric heterochromatin and occurs in nonconserved hotspots. Genetics 2023; 224:iyad052. [PMID: 37010100 PMCID: PMC10213500 DOI: 10.1093/genetics/iyad052] [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: 10/18/2022] [Revised: 10/18/2022] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Chromosome breakage plays an important role in the evolution of karyotypes and can produce deleterious effects within a single individual, such as aneuploidy or cancer. Forces that influence how and where chromosomes break are not fully understood. In humans, breakage tends to occur in conserved hotspots called common fragile sites (CFS), especially during replication stress. By following the fate of dicentric chromosomes in Drosophila melanogaster, we find that breakage under tension also tends to occur in specific hotspots. Our experimental approach was to induce sister chromatid exchange in a ring chromosome to generate a dicentric chromosome with a double chromatid bridge. In the following cell division, the dicentric bridges may break. We analyzed the breakage patterns of 3 different ring-X chromosomes. These chromosomes differ by the amount and quality of heterochromatin they carry as well as their genealogical history. For all 3 chromosomes, breakage occurs preferentially in several hotspots. Surprisingly, we found that the hotspot locations are not conserved between the 3 chromosomes: each displays a unique array of breakage hotspots. The lack of hotspot conservation, along with a lack of response to aphidicolin, suggests that these breakage sites are not entirely analogous to CFS and may reveal new mechanisms of chromosome fragility. Additionally, the frequency of dicentric breakage and the durability of each chromosome's spindle attachment vary significantly between the 3 chromosomes and are correlated with the origin of the centromere and the amount of pericentric heterochromatin. We suggest that different centromere strengths could account for this.
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Affiliation(s)
- Hunter J Hill
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Danielle Bonser
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kent G Golic
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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7
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Al-Zain A, Nester MR, Symington LS. Double-strand breaks induce inverted duplication chromosome rearrangements by a DNA polymerase δ and Rad51-dependent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525421. [PMID: 36747747 PMCID: PMC9900772 DOI: 10.1101/2023.01.24.525421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Inverted duplications, also known as foldback inversions, are commonly observed in cancers and are the major class of chromosome rearrangement recovered from yeast cells lacking Mre11 nuclease. Foldback priming at naturally occurring inverted repeats is one mechanism proposed for the generation of inverted duplications. However, the initiating lesion for these events and the mechanism by which they form has not been fully elucidated. Here, we show that a DNA double-strand break (DSB) induced near natural short, inverted repeats drives high frequency inverted duplication in Sae2 and Mre11-deficient cells. We find that DNA polymerase δ proof-reading activity acts non-redundantly with Rad1 nuclease to remove heterologous tails formed during foldback annealing. Additionally, Pol32 is required for the generation of inverted duplications, suggesting that Pol δ catalyzes fill-in synthesis primed from the foldback to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric isochromosome. Stabilization of the dicentric chromosome after breakage involves telomere capture by non-reciprocal translocation mediated by repeat sequences and requires Rad51.
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8
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Lysak MA. Celebrating Mendel, McClintock, and Darlington: On end-to-end chromosome fusions and nested chromosome fusions. THE PLANT CELL 2022; 34:2475-2491. [PMID: 35441689 PMCID: PMC9252491 DOI: 10.1093/plcell/koac116] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/13/2022] [Indexed: 05/04/2023]
Abstract
The evolution of eukaryotic genomes is accompanied by fluctuations in chromosome number, reflecting cycles of chromosome number increase (polyploidy and centric fissions) and decrease (chromosome fusions). Although all chromosome fusions result from DNA recombination between two or more nonhomologous chromosomes, several mechanisms of descending dysploidy are exploited by eukaryotes to reduce their chromosome number. Genome sequencing and comparative genomics have accelerated the identification of inter-genome chromosome collinearity and gross chromosomal rearrangements and have shown that end-to-end chromosome fusions (EEFs) and nested chromosome fusions (NCFs) may have played a more important role in the evolution of eukaryotic karyotypes than previously thought. The present review aims to summarize the limited knowledge on the origin, frequency, and evolutionary implications of EEF and NCF events in eukaryotes and especially in land plants. The interactions between nonhomologous chromosomes in interphase nuclei and chromosome (mis)pairing during meiosis are examined for their potential importance in the origin of EEFs and NCFs. The remaining open questions that need to be addressed are discussed.
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Affiliation(s)
- Martin A Lysak
- CEITEC—Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
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9
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Breakage in breakage–fusion–bridge cycle: an 80-year-old mystery. Trends Genet 2022; 38:641-645. [DOI: 10.1016/j.tig.2022.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/20/2022]
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10
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Pobiega S, Alibert O, Marcand S. A new assay capturing chromosome fusions shows a protection trade-off at telomeres and NHEJ vulnerability to low-density ionizing radiation. Nucleic Acids Res 2021; 49:6817-6831. [PMID: 34125900 PMCID: PMC8266670 DOI: 10.1093/nar/gkab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 11/14/2022] Open
Abstract
Chromosome fusions threaten genome integrity and promote cancer by engaging catastrophic mutational processes, namely chromosome breakage-fusion-bridge cycles and chromothripsis. Chromosome fusions are frequent in cells incurring telomere dysfunctions or those exposed to DNA breakage. Their occurrence and therefore their contribution to genome instability in unchallenged cells is unknown. To address this issue, we constructed a genetic assay able to capture and quantify rare chromosome fusions in budding yeast. This chromosome fusion capture (CFC) assay relies on the controlled inactivation of one centromere to rescue unstable dicentric chromosome fusions. It is sensitive enough to quantify the basal rate of end-to-end chromosome fusions occurring in wild-type cells. These fusions depend on canonical nonhomologous end joining (NHEJ). Our results show that chromosome end protection results from a trade-off at telomeres between positive effectors (Rif2, Sir4, telomerase) and a negative effector partially antagonizing them (Rif1). The CFC assay also captures NHEJ-dependent chromosome fusions induced by ionizing radiation. It provides evidence for chromosomal rearrangements stemming from a single photon-matter interaction.
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Affiliation(s)
- Sabrina Pobiega
- Université de Paris and Université Paris-Saclay, Inserm, CEA IBFJ/iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, 92265 Fontenay-au-Roses, France
| | | | - Stéphane Marcand
- To whom correspondence should be addressed. Tel: +33 1 46 54 82 33;
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11
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Telomere Shortening and Fusions: A Link to Aneuploidy in Early Human Embryo Development. Obstet Gynecol Surv 2021; 76:429-436. [PMID: 34324695 DOI: 10.1097/ogx.0000000000000907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Importance It is known that oocytes undergo aging that is caused by exposure to an aged ovarian microenvironment. Telomere length in mouse and bovine oocytes declines with age, and age-associated telomere shortening in oocytes is considered a sign of poor development competency. Women with advanced age undergoing assisted reproductive technologies have poor outcomes because of increasing aneuploidy rates with age. Research has shown that aneuploidy is associated with DNA damage, reactive oxygen species, and telomere dysfunction. Objective In this review, we focus on the possible relationship between telomere dysfunction and aneuploidy in human early embryo development and several reproductive and perinatal outcomes, discussing the mechanism of aneuploidy caused by telomere shortening and fusion in human embryos. Evidence Acquisition We reviewed the current literature evidence concerning telomere dysfunction and aneuploidy in early human embryo development. Results Shorter telomeres in oocytes, leukocytes, and granulosa cells, related to aging in women, were associated with recurrent miscarriage, trisomy 21, ovarian insufficiency, and decreasing chance of in vitro fertilization success. Telomere length and telomerase activity in embryos have been related to the common genomic instability at the cleavage stage of human development. Complications of assisted reproductive technology pregnancies, such as miscarriage, birth defects, preterm births, and intrauterine growth restriction, also might result from telomere shortening as observed in oocytes, polar body, granulosa cells, and embryos. Conclusions and Relevance Telomere length clearly plays an important role in the development of the embryo and fetus, and the abnormal shortening of telomeres is likely involved in embryo loss during early human development. However, telomere fusion studies have yet to be performed in early human development.
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12
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Kim E, Kim J, Kim C, Lee J. Long-read sequencing and de novo genome assemblies reveal complex chromosome end structures caused by telomere dysfunction at the single nucleotide level. Nucleic Acids Res 2021; 49:3338-3353. [PMID: 33693840 PMCID: PMC8034613 DOI: 10.1093/nar/gkab141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/28/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Karyotype change and subsequent evolution is triggered by chromosome fusion and rearrangement events, which often occur when telomeres become dysfunctional. Telomeres protect linear chromosome ends from DNA damage responses (DDRs), and telomere dysfunction may result in genome instability. However, the complex chromosome end structures and the other possible consequences of telomere dysfunction have rarely been resolved at the nucleotide level due to the lack of the high-throughput methods needed to analyse these highly repetitive regions. Here we applied long-read sequencing technology to Caenorhabditis elegans survivor lines that emerged after telomere dysfunction. The survivors have preserved traces of DDRs in their genomes and our data revealed that variants generated by telomere dysfunction are accumulated along all chromosomes. The reconstruction of the chromosome end structures through de novo genome assemblies revealed diverse types of telomere damage processing at the nucleotide level. When telomeric repeats were totally eroded by telomere dysfunction, DDRs were mostly terminated by chromosome fusion events. We also partially reconstructed the most complex end structure and its DDR signatures, which would have been accumulated via multiple cell divisions. These finely resolved chromosome end structures suggest possible mechanisms regarding the repair processes after telomere dysfunction, providing insights into chromosome evolution in nature.
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Affiliation(s)
- Eunkyeong Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Chuna Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro 125, Daejeon 34141, Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea.,Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
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13
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Abid HZ, McCaffrey J, Raseley K, Young E, Lassahn K, Varapula D, Riethman H, Xiao M. Single-molecule analysis of subtelomeres and telomeres in Alternative Lengthening of Telomeres (ALT) cells. BMC Genomics 2020; 21:485. [PMID: 32669102 PMCID: PMC7364475 DOI: 10.1186/s12864-020-06901-7] [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: 05/12/2020] [Accepted: 07/08/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Telomeric DNA is typically comprised of G-rich tandem repeat motifs and maintained by telomerase (Greider CW, Blackburn EH; Cell 51:887-898; 1987). In eukaryotes lacking telomerase, a variety of DNA repair and DNA recombination based pathways for telomere maintenance have evolved in organisms normally dependent upon telomerase for telomere elongation (Webb CJ, Wu Y, Zakian VA; Cold Spring Harb Perspect Biol 5:a012666; 2013); collectively called Alternative Lengthening of Telomeres (ALT) pathways. By measuring (TTAGGG) n tract lengths from the same large DNA molecules that were optically mapped, we simultaneously analyzed telomere length dynamics and subtelomere-linked structural changes at a large number of specific subtelomeric loci in the ALT-positive cell lines U2OS, SK-MEL-2 and Saos-2. RESULTS Our results revealed loci-specific ALT telomere features. For example, while each subtelomere included examples of single molecules with terminal (TTAGGG) n tracts as well as examples of recombinant telomeric single molecules, the ratio of these molecules was subtelomere-specific, ranging from 33:1 (19p) to 1:25 (19q) in U2OS. The Saos-2 cell line shows a similar percentage of recombinant telomeres. The frequency of recombinant subtelomeres of SK-MEL-2 (11%) is about half that of U2OS and Saos-2 (24 and 19% respectively). Terminal (TTAGGG) n tract lengths and heterogeneity levels, the frequencies of telomere signal-free ends, and the frequency and size of retained internal telomere-like sequences (ITSs) at recombinant telomere fusion junctions all varied according to the specific subtelomere involved in a particular cell line. Very large linear extrachromosomal telomere repeat (ECTR) DNA molecules were found in all three cell lines; these are in principle capable of templating synthesis of new long telomere tracts via break-induced repair (BIR) long-tract DNA synthesis mechanisms and contributing to the very long telomere tract length and heterogeneity characteristic of ALT cells. Many of longest telomere tracts (both end-telomeres and linear ECTRs) displayed punctate CRISPR/Cas9-dependent (TTAGGG) n labeling patterns indicative of interspersion of stretches of non-canonical telomere repeats. CONCLUSION Identifying individual subtelomeres and characterizing linked telomere (TTAGGG) n tract lengths and structural changes using our new single-molecule methodologies reveals the structural consequences of telomere damage, repair and recombination mechanisms in human ALT cells in unprecedented molecular detail and significant differences in different ALT-positive cell lines.
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Affiliation(s)
- Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Katy Lassahn
- School of Medical Diagnostic and Transnational Sciences, Old Dominion University, Norfolk, VA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Harold Riethman
- School of Medical Diagnostic and Transnational Sciences, Old Dominion University, Norfolk, VA, USA.
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA. .,Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, USA.
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14
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Shao Y, Lu N, Xue X, Qin Z. Creating functional chromosome fusions in yeast with CRISPR-Cas9. Nat Protoc 2019; 14:2521-2545. [PMID: 31300803 DOI: 10.1038/s41596-019-0192-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/14/2019] [Indexed: 11/09/2022]
Abstract
CRISPR-Cas9-facilitated functional chromosome fusion allows the generation of a series of yeast strains with progressively reduced chromosome numbers that are valuable resources for the study of fundamental concepts in chromosome biology, including replication, recombination and segregation. We created a new yeast strain with a single chromosome by using the protocol for chromosome fusion described herein. To ensure the accuracy of chromosome fusions in yeast, the long redundant repetitive sequences near linear chromosomal ends are deleted, and the fusion orders are correspondingly determined. Possible influence on gene expression is minimized to retain gene functionality. This protocol provides experimentally derived guidelines for the generation of functional chromosome fusions in yeast, especially for the deletion of repetitive sequences, the determination of the fusion order and cleavage sites, and primary evaluation of the functionality of chromosome fusions. Beginning with design, one round of typical chromosome fusion and functional verifications can be accomplished within 18 d.
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Affiliation(s)
- 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, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, 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, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, 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, 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, Shanghai, China.
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15
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Guérin TM, Béneut C, Barinova N, López V, Lazar-Stefanita L, Deshayes A, Thierry A, Koszul R, Dubrana K, Marcand S. Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis. Mol Cell 2019; 75:131-144.e3. [PMID: 31204167 DOI: 10.1016/j.molcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/12/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins.
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Affiliation(s)
- Thomas M Guérin
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Claire Béneut
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Natalja Barinova
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Virginia López
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Alice Deshayes
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Karine Dubrana
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Stéphane Marcand
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France.
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16
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Adaptation to DNA damage checkpoint in senescent telomerase-negative cells promotes genome instability. Genes Dev 2018; 32:1499-1513. [PMID: 30463903 PMCID: PMC6295172 DOI: 10.1101/gad.318485.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/03/2018] [Indexed: 01/04/2023]
Abstract
Here, Coutelier et al. used a microfluidic-based approach and live-cell imaging in yeast to capture early mutation events during replicative senescence and observed that prolonged checkpoint arrests occurred frequently in telomerase-negative lineages. Their results demonstrate that the adaptation pathway is a major contributor to the genome instability induced during replicative senescence. In cells lacking telomerase, telomeres gradually shorten during each cell division to reach a critically short length, permanently activate the DNA damage checkpoint, and trigger replicative senescence. The increase in genome instability that occurs as a consequence may contribute to the early steps of tumorigenesis. However, because of the low frequency of mutations and the heterogeneity of telomere-induced senescence, the timing and mechanisms of genome instability increase remain elusive. Here, to capture early mutation events during replicative senescence, we used a combined microfluidic-based approach and live-cell imaging in yeast. We analyzed DNA damage checkpoint activation in consecutive cell divisions of individual cell lineages in telomerase-negative yeast cells and observed that prolonged checkpoint arrests occurred frequently in telomerase-negative lineages. Cells relied on the adaptation to the DNA damage pathway to bypass the prolonged checkpoint arrests, allowing further cell divisions despite the presence of unrepaired DNA damage. We demonstrate that the adaptation pathway is a major contributor to the genome instability induced during replicative senescence. Therefore, adaptation plays a critical role in shaping the dynamics of genome instability during replicative senescence.
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17
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Fission Yeast CENP-C (Cnp3) Plays a Role in Restricting the Site of CENP-A Accumulation. G3-GENES GENOMES GENETICS 2018; 8:2723-2733. [PMID: 29925533 PMCID: PMC6071599 DOI: 10.1534/g3.118.200486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The centromere is a chromosomal locus where a microtubule attachment site, termed kinetochore, is assembled in mitosis. In most eukaryotes, with the exception of holocentric species, each chromosome contains a single distinct centromere. A chromosome with an additional centromere undergoes successive rounds of anaphase bridge formation and breakage, or triggers a cell cycle arrest imposed by DNA damage and replication checkpoints. We report here a study in Schizosaccharomyces pombe to characterize a mutant (cnp3-1) in a gene encoding a homolog of mammalian centromere-specific protein, CENP-C. At the restrictive temperature 36°, the Cnp3-1 mutant protein loses its localization at the centromere. In the cnp3-1 mutant, the level of the Cnp1 (a homolog of a centromere-specific histone CENP-A) also decreases at the centromere. Interestingly, the cnp3-1 mutant is prone to promiscuous accumulation of Cnp1 at non-centromeric regions, when Cnp1 is present in excess. Unlike the wild type protein, Cnp3-1 mutant protein is found at the sites of promiscuous accumulation of Cnp1, suggesting that Cnp3-1 may stabilize or promote accumulation of Cnp1 at non-centromeric regions. From these results, we infer the role of Cnp3 in restricting the site of accumulation of Cnp1 and thus to prevent formation of de novo centromeres.
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18
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Hou H, Cooper JP. Stretching, scrambling, piercing and entangling: Challenges for telomeres in mitotic and meiotic chromosome segregation. Differentiation 2018; 100:12-20. [PMID: 29413748 DOI: 10.1016/j.diff.2018.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/21/2018] [Accepted: 01/23/2018] [Indexed: 12/24/2022]
Abstract
The consequences of telomere loss or dysfunction become most prominent when cells enter the nuclear division stage of the cell cycle. At this climactic stage when chromosome segregation occurs, telomere fusions or entanglements can lead to chromosome breakage, wreaking havoc on genome stability. Here we review recent progress in understanding the mechanisms of detangling and breaking telomere associations at mitosis, as well as the unique ways in which telomeres are processed to allow regulated sister telomere separation. Moreover, we discuss unexpected roles for telomeres in orchestrating nuclear envelope breakdown and spindle formation, crucial processes for nuclear division. Finally, we discuss the discovery that telomeres create microdomains in the nucleus that are conducive to centromere assembly, cementing the unexpectedly influential role of telomeres in mitosis.
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Affiliation(s)
- Haitong Hou
- Telomere Biology Section, LBMB, NCI, NIH, Building 37, Room 6050, Bethesda MD 20892, USA
| | - Julia Promisel Cooper
- Telomere Biology Section, LBMB, NCI, NIH, Building 37, Room 6050, Bethesda MD 20892, USA.
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19
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Beyer T, Weinert T. Ontogeny of Unstable Chromosomes Generated by Telomere Error in Budding Yeast. PLoS Genet 2016; 12:e1006345. [PMID: 27716774 PMCID: PMC5065131 DOI: 10.1371/journal.pgen.1006345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022] Open
Abstract
DNA replication errors at certain sites in the genome initiate chromosome instability that ultimately leads to stable genomic rearrangements. Where instability begins is often unclear. And, early instability may form unstable chromosome intermediates whose transient nature also hinders mechanistic understanding. We report here a budding yeast model that reveals the genetic ontogeny of genome rearrangements, from initial replication error to unstable chromosome formation to their resolution. Remarkably, the initial error often arises in or near the telomere, and frequently forms unstable chromosomes. Early unstable chromosomes may then resolve to an internal "collection site" where a dicentric forms and resolves to an isochromosome (other outcomes are possible at each step). The initial telomere-proximal unstable chromosome is increased in mutants in telomerase subunits, Tel1, and even Rad9, with no known telomere-specific function. Defects in Tel1 and in Rrm3, a checkpoint protein kinase with a role in telomere maintenance and a DNA helicase, respectively, synergize dramatically to generate unstable chromosomes, further illustrating the consequence of replication error in the telomere. Collectively, our results suggest telomeric replication errors may be a common cause of seemingly unrelated genomic rearrangements located hundreds of kilobases away.
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Affiliation(s)
- Tracey Beyer
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Ted Weinert
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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20
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Cech JN, Peichel CL. Centromere inactivation on a neo-Y fusion chromosome in threespine stickleback fish. Chromosome Res 2016; 24:437-450. [PMID: 27553478 DOI: 10.1007/s10577-016-9535-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/14/2016] [Accepted: 08/16/2016] [Indexed: 02/07/2023]
Abstract
Having one and only one centromere per chromosome is essential for proper chromosome segregation during both mitosis and meiosis. Chromosomes containing two centromeres are known as dicentric and often mis-segregate during cell division, resulting in aneuploidy or chromosome breakage. Dicentric chromosome can be stabilized by centromere inactivation, a process which reestablishes monocentric chromosomes. However, little is known about this process in naturally occurring dicentric chromosomes. Using a combination of fluorescence in situ hybridization (FISH) and immunofluorescence combined with FISH (IF-FISH) on metaphase chromosome spreads, we demonstrate that centromere inactivation has evolved on a neo-Y chromosome fusion in the Japan Sea threespine stickleback fish (Gasterosteus nipponicus). We found that the centromere derived from the ancestral Y chromosome has been inactivated. Our data further suggest that there have been genetic changes to this centromere in the two million years since the formation of the neo-Y chromosome, but it remains unclear whether these genetic changes are a cause or consequence of centromere inactivation.
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Affiliation(s)
- Jennifer N Cech
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, Mailstop C2-023, Seattle, WA, 98109, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, 98195, USA
| | - Catherine L Peichel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland.
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21
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Preferential Breakpoints in the Recovery of Broken Dicentric Chromosomes in Drosophila melanogaster. Genetics 2015; 201:563-72. [PMID: 26294667 DOI: 10.1534/genetics.115.181156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/19/2015] [Indexed: 12/27/2022] Open
Abstract
We designed a system to determine whether dicentric chromosomes in Drosophila melanogaster break at random or at preferred sites. Sister chromatid exchange in a Ring-X chromosome produced dicentric chromosomes with two bridging arms connecting segregating centromeres as cells divide. This double bridge can break in mitosis. A genetic screen recovered chromosomes that were linearized by breakage in the male germline. Because the screen required viability of males with this X chromosome, the breakpoints in each arm of the double bridge must be closely matched to produce a nearly euploid chromosome. We expected that most linear chromosomes would be broken in heterochromatin because there are no vital genes in heterochromatin, and breakpoint distribution would be relatively unconstrained. Surprisingly, approximately half the breakpoints are found in euchromatin, and the breakpoints are clustered in just a few regions of the chromosome that closely match regions identified as intercalary heterochromatin. The results support the Laird hypothesis that intercalary heterochromatin can explain fragile sites in mitotic chromosomes, including fragile X. Opened rings also were recovered after male larvae were exposed to X-rays. This method was much less efficient and produced chromosomes with a strikingly different array of breakpoints, with almost all located in heterochromatin. A series of circularly permuted linear X chromosomes was generated that may be useful for investigating aspects of chromosome behavior, such as crossover distribution and interference in meiosis, or questions of nuclear organization and function.
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22
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Lopez V, Barinova N, Onishi M, Pobiega S, Pringle JR, Dubrana K, Marcand S. Cytokinesis breaks dicentric chromosomes preferentially at pericentromeric regions and telomere fusions. Genes Dev 2015; 29:322-36. [PMID: 25644606 PMCID: PMC4318148 DOI: 10.1101/gad.254664.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. Lopez et al. find that dicentrics without internal telomere sequences preferentially break at pericentromeric regions. In all cases, cleavage does not occur in anaphase but instead requires cytokinesis. Dicentrics cause the spindle pole bodies and centromeres to relocate to the bud neck during cytokinesis, explaining how cytokinesis can sever dicentrics near centromeres. Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. During mitosis, they form anaphase bridges, resulting in chromosome breakage by an unknown mechanism. In budding yeast, dicentrics generated by telomere fusion break at the fusion, a process that restores the parental karyotype and protects cells from rare accidental telomere fusion. Here, we observed that dicentrics lacking telomere fusion preferentially break within a 25- to 30-kb-long region next to the centromeres. In all cases, dicentric breakage requires anaphase exit, ruling out stretching by the elongated mitotic spindle as the cause of breakage. Instead, breakage requires cytokinesis. In the presence of dicentrics, the cytokinetic septa pinch the nucleus, suggesting that dicentrics are severed after actomyosin ring contraction. At this time, centromeres and spindle pole bodies relocate to the bud neck, explaining how cytokinesis can sever dicentrics near centromeres.
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Affiliation(s)
- Virginia Lopez
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - Natalja Barinova
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - Masayuki Onishi
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sabrina Pobiega
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - John R Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karine Dubrana
- UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France; Laboratoire Instabilité Génétique et Organisation Nucléaire, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France
| | - Stéphane Marcand
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France;
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23
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Marcand S. How do telomeres and NHEJ coexist? Mol Cell Oncol 2014; 1:e963438. [PMID: 27308342 PMCID: PMC4904885 DOI: 10.4161/23723548.2014.963438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/01/2014] [Accepted: 08/07/2014] [Indexed: 12/21/2022]
Abstract
The telomeres of eukaryotes are stable open double-strand ends that coexist with nonhomologous end joining (NHEJ), the repair pathway that directly ligates DNA ends generated by double-strand breaks. Since a single end-joining event between 2 telomeres generates a circular chromosome or an unstable dicentric chromosome, NHEJ must be prevented from acting on telomeres. Multiple mechanisms mediated by telomere factors act in synergy to achieve this inhibition.
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Affiliation(s)
- Stéphane Marcand
- CEA; DSV/IRCM/SIGRR/LTR; Fontenay-aux-roses; France; INSERM UMR 967; Fontenay-aux-roses; France
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24
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Switching the centromeres on and off: epigenetic chromatin alterations provide plasticity in centromere activity stabilizing aberrant dicentric chromosomes. Biochem Soc Trans 2013; 41:1648-53. [DOI: 10.1042/bst20130136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The kinetochore, which forms on a specific chromosomal locus called the centromere, mediates interactions between the chromosome and the spindle during mitosis and meiosis. Abnormal chromosome rearrangements and/or neocentromere formation can cause the presence of multiple centromeres on a single chromosome, which results in chromosome breakage or cell cycle arrest. Analyses of artificial dicentric chromosomes suggested that the activity of the centromere is regulated epigenetically; on some stably maintained dicentric chromosomes, one of the centromeres no longer functions as a platform for kinetochore formation, although the DNA sequence remains intact. Such epigenetic centromere inactivation occurs in cells of various eukaryotes harbouring ‘regional centromeres’, such as those of maize, fission yeast and humans, suggesting that the position of the active centromere is determined by epigenetic markers on a chromosome rather than the nucleotide sequence. Our recent findings in fission yeast revealed that epigenetic centromere inactivation consists of two steps: disassembly of the kinetochore initiates inactivation and subsequent heterochromatinization prevents revival of the inactivated centromere. Kinetochore disassembly followed by heterochromatinization is also observed in normal senescent human cells. Thus epigenetic centromere inactivation may not only stabilize abnormally generated dicentric chromosomes, but also be part of an intrinsic mechanism regulating cell proliferation.
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25
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Sorzano COS, Pascual-Montano A, Sánchez de Diego A, Martínez-A C, van Wely KHM. Chromothripsis: breakage-fusion-bridge over and over again. Cell Cycle 2013; 12:2016-23. [PMID: 23759584 DOI: 10.4161/cc.25266] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The acquisition of massive but localized chromosome translocations, a phenomenon termed chromothripsis, has received widespread attention since its discovery over a year ago. Until recently, chromothripsis was believed to originate from a single catastrophic event, but the molecular mechanisms leading to this event are yet to be uncovered. Because a thorough interpretation of the data are missing, the phenomenon itself has wrongly acquired the status of a mechanism used to justify many kinds of complex rearrangements. Although the assumption that all translocations in chromothripsis originate from a single event has met with criticism, satisfactory explanations for the intense but localized nature of this phenomenon are still missing. Here, we show why the data used to describe massive catastrophic rearrangements are incompatible with a model comprising a single event only and propose a molecular mechanism in which a combination of known cellular pathways accounts for chromothripsis. Instead of a single traumatic event, the protection of undamaged chromosomes by telomeres can limit repetitive breakage-fusion-bridge events to a single chromosome arm. Ultimately, common properties of chromosomal instability, such as aneuploidy and centromere fission, might establish the complex genetic pattern observed in this genomic state.
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26
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Teixeira MT. Saccharomyces cerevisiae as a Model to Study Replicative Senescence Triggered by Telomere Shortening. Front Oncol 2013; 3:101. [PMID: 23638436 PMCID: PMC3636481 DOI: 10.3389/fonc.2013.00101] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/11/2013] [Indexed: 01/22/2023] Open
Abstract
In many somatic human tissues, telomeres shorten progressively because of the DNA-end replication problem. Consequently, cells cease to proliferate and are maintained in a metabolically viable state called replicative senescence. These cells are characterized by an activation of DNA damage checkpoints stemming from eroded telomeres, which are bypassed in many cancer cells. Hence, replicative senescence has been considered one of the most potent tumor suppressor pathways. However, the mechanism through which short telomeres trigger this cellular response is far from being understood. When telomerase is removed experimentally in Saccharomyces cerevisiae, telomere shortening also results in a gradual arrest of population growth, suggesting that replicative senescence also occurs in this unicellular eukaryote. In this review, we present the key steps that have contributed to the understanding of the mechanisms underlying the establishment of replicative senescence in budding yeast. As in mammals, signals stemming from short telomeres activate the DNA damage checkpoints, suggesting that the early cellular response to the shortest telomere(s) is conserved in evolution. Yet closer analysis reveals a complex picture in which the apparent single checkpoint response may result from a variety of telomeric alterations expressed in the absence of telomerase. Accordingly, the DNA replication of eroding telomeres appears as a critical challenge for senescing budding yeast cells and the easy manipulation of S. cerevisiae is providing insights into the way short telomeres are integrated into their chromatin and nuclear environments. Finally, the loss of telomerase in budding yeast triggers a more general metabolic alteration that remains largely unexplored. Thus, telomerase-deficient S. cerevisiae cells may have more common points than anticipated with somatic cells, in which telomerase depletion is naturally programed, thus potentially inspiring investigations in mammalian cells.
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Affiliation(s)
- M Teresa Teixeira
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique Paris, France
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27
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Lescasse R, Pobiega S, Callebaut I, Marcand S. End-joining inhibition at telomeres requires the translocase and polySUMO-dependent ubiquitin ligase Uls1. EMBO J 2013; 32:805-15. [PMID: 23417015 DOI: 10.1038/emboj.2013.24] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 01/21/2013] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, permanent inhibition of the non-homologous end joining (NHEJ) repair pathway at telomeres ensures that chromosome ends do not fuse. In budding yeast, binding of Rap1 to telomere repeats establishes NHEJ inhibition. Here, we show that the Uls1 protein is required for the maintenance of NHEJ inhibition at telomeres. Uls1 protein is a non-essential Swi2/Snf2-related translocase and a Small Ubiquitin-related Modifier (SUMO)-Targeted Ubiquitin Ligase (STUbL) with unknown targets. Loss of Uls1 results in telomere-telomere fusions. Uls1 requirement is alleviated by the absence of poly-SUMO chains and by rap1 alleles lacking SUMOylation sites. Furthermore, Uls1 limits the accumulation of Rap1 poly-SUMO conjugates. We propose that one of Uls1 functions is to clear non-functional poly-SUMOylated Rap1 molecules from telomeres to ensure the continuous efficiency of NHEJ inhibition. Since Uls1 is the only known STUbL with a translocase activity, it can be the general molecular sweeper for the clearance of poly-SUMOylated proteins on DNA in eukaryotes.
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Affiliation(s)
- Rachel Lescasse
- CEA, Direction des sciences du vivant/Institut de radiobiologie cellulaire et moléculaire/Service instabilité génétique réparation recombinaison/Laboratoire télomère et réparation du chromosome, Fontenay-aux-roses, France
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28
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Nonrandom distribution of interhomolog recombination events induced by breakage of a dicentric chromosome in Saccharomyces cerevisiae. Genetics 2013; 194:69-80. [PMID: 23410835 PMCID: PMC3632482 DOI: 10.1534/genetics.113.150144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dicentric chromosomes undergo breakage in mitosis, resulting in chromosome deletions, duplications, and translocations. In this study, we map chromosome break sites of dicentrics in Saccharomyces cerevisiae by a mitotic recombination assay. The assay uses a diploid strain in which one homolog has a conditional centromere in addition to a wild-type centromere, and the other homolog has only the wild-type centromere; the conditional centromere is inactive when cells are grown in galactose and is activated when the cells are switched to glucose. In addition, the two homologs are distinguishable by multiple single-nucleotide polymorphisms (SNPs). Under conditions in which the conditional centromere is activated, the functionally dicentric chromosome undergoes double-stranded DNA breaks (DSBs) that can be repaired by mitotic recombination with the homolog. Such recombination events often lead to loss of heterozygosity (LOH) of SNPs that are centromere distal to the crossover. Using a PCR-based assay, we determined the position of LOH in multiple independent recombination events to a resolution of ∼4 kb. This analysis shows that dicentric chromosomes have recombination breakpoints that are broadly distributed between the two centromeres, although there is a clustering of breakpoints within 10 kb of the conditional centromere.
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29
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Stimpson KM, Matheny JE, Sullivan BA. Dicentric chromosomes: unique models to study centromere function and inactivation. Chromosome Res 2012; 20:595-605. [PMID: 22801777 DOI: 10.1007/s10577-012-9302-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dicentric chromosomes are products of genome rearrangement that place two centromeres on the same chromosome. Depending on the organism, dicentric stability varies after formation. In humans, dicentrics occur naturally in a substantial portion of the population and usually segregate successfully in mitosis and meiosis. Their stability has been attributed to inactivation of one of the two centromeres, creating a functionally monocentric chromosome that can segregate normally during cell division. The molecular basis for centromere inactivation is not well understood, although studies in model organisms and in humans suggest that genomic and epigenetic mechanisms can be involved. Furthermore, constitutional dicentric chromosomes ascertained in patients presumably represent the most stable chromosomes, so the spectrum of dicentric fates, if it exists, is not entirely clear. Studies of engineered or induced dicentrics in budding yeast and plants have provided significant insight into the fate of dicentric chromosomes. And, more recently, studies have shown that dicentrics in humans can also undergo multiple fates after formation. Here, we discuss current experimental evidence from various organisms that has deepened our understanding of dicentric behavior and the intriguingly complex process of centromere inactivation.
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Affiliation(s)
- Kaitlin M Stimpson
- Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
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Luke-Glaser S, Luke B. The Mph1 helicase can promote telomere uncapping and premature senescence in budding yeast. PLoS One 2012; 7:e42028. [PMID: 22848695 PMCID: PMC3407055 DOI: 10.1371/journal.pone.0042028] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 06/29/2012] [Indexed: 11/30/2022] Open
Abstract
Double strand breaks (DSBs) can be repaired via either Non-Homologous End Joining (NHEJ) or Homology directed Repair (HR). Telomeres, which resemble DSBs, are refractory to repair events in order to prevent chromosome end fusions and genomic instability. In some rare instances telomeres engage in Break-Induced Replication (BIR), a type of HR, in order to maintain telomere length in the absence of the enzyme telomerase. Here we have investigated how the yeast helicase, Mph1, affects DNA repair at both DSBs and telomeres. We have found that overexpressed Mph1 strongly inhibits BIR at internal DSBs however allows it to proceed at telomeres. Furthermore, while overexpressed Mph1 potently inhibits NHEJ at telomeres it has no effect on NHEJ at DSBs within the chromosome. At telomeres Mph1 is able to promote telomere uncapping and the accumulation of ssDNA, which results in premature senescence in the absence of telomerase. We propose that Mph1 is able to direct repair towards HR (thereby inhibiting NHEJ) at telomeres by remodeling them into a nuclease-sensitive structure, which promotes the accumulation of a recombinogenic ssDNA intermediate. We thus put forward that Mph1 is a double-edge sword at the telomere, it prevents NHEJ, but promotes senescence in cells with dysfunctional telomeres by increasing the levels of ssDNA.
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Affiliation(s)
- Sarah Luke-Glaser
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Heidelberg, Germany
- * E-mail: (BL); (SLG)
| | - Brian Luke
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Heidelberg, Germany
- * E-mail: (BL); (SLG)
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Matot B, Le Bihan YV, Lescasse R, Pérez J, Miron S, David G, Castaing B, Weber P, Raynal B, Zinn-Justin S, Gasparini S, Le Du MH. The orientation of the C-terminal domain of the Saccharomyces cerevisiae Rap1 protein is determined by its binding to DNA. Nucleic Acids Res 2012; 40:3197-207. [PMID: 22139930 PMCID: PMC3326314 DOI: 10.1093/nar/gkr1166] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 11/10/2011] [Accepted: 11/11/2011] [Indexed: 11/22/2022] Open
Abstract
Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded regions, and comprising BRCT, Myb and RCT well-structured domains. Here, we present the architectures of Rap1 and a Rap1/DNA complex, built through a step-by-step integration of small angle X-ray scattering, X-ray crystallography and nuclear magnetic resonance data. Our results reveal Rap1 structural adjustment upon DNA binding that involves a specific orientation of the C-terminal (RCT) domain with regard to the DNA binding domain (DBD). Crystal structure of DBD in complex with a long DNA identifies an essential wrapping loop, which constrains the orientation of the RCT and affects Rap1 affinity to DNA. Based on our structural information, we propose a model for Rap1 assembly at telomere.
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Affiliation(s)
- Béatrice Matot
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Yann-Vaï Le Bihan
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Rachel Lescasse
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Javier Pérez
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Simona Miron
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Gabriel David
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Bertrand Castaing
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Patrick Weber
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Bertrand Raynal
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Sophie Zinn-Justin
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Sylvaine Gasparini
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
| | - Marie-Hélène Le Du
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et Technologie de Saclay, Laboratoire de Biologie Structurale et Radiobiologie, CNRS-URA2096, 91191 Gif-sur-Yvette, France, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télomère et Réparation du Chromosome, 92260 Fontenay-aux-roses, SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, Institut Pasteur, CNRS-URA2185, Plate-forme 6, Cristallogenèse et Diffraction des Rayons X, 25 Rue Dr. Roux, 75724 Paris and Institut Pasteur, Plateforme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, F-75015 Paris, France
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Sato H, Masuda F, Takayama Y, Takahashi K, Saitoh S. Epigenetic inactivation and subsequent heterochromatinization of a centromere stabilize dicentric chromosomes. Curr Biol 2012; 22:658-67. [PMID: 22464190 DOI: 10.1016/j.cub.2012.02.062] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 01/24/2012] [Accepted: 02/21/2012] [Indexed: 11/29/2022]
Abstract
BACKGROUND The kinetochore is a multiprotein complex that forms on a chromosomal locus designated as the centromere, which links the chromosome to the spindle during mitosis and meiosis. Most eukaryotes, with the exception of holocentric species, have a single distinct centromere per chromosome, and the presence of multiple centromeres on a single chromosome is predicted to cause breakage and/or loss of that chromosome. However, some stably maintained non-Robertsonian translocated chromosomes have been reported, suggesting that the excessive centromeres are inactivated by an as yet undetermined mechanism. RESULTS We have developed systems to generate dicentric chromosomes containing two centromeres by fusing two chromosomes in fission yeast. Although the majority of cells harboring the artificial dicentric chromosome are arrested with elongated cell morphology in a manner dependent on the DNA structure checkpoint genes, a portion of the cells survive by converting the dicentric chromosome into a stable functional monocentric chromosome; either centromere was inactivated epigenetically or by DNA rearrangement. Mutations compromising kinetochore formation increased the frequency of epigenetic centromere inactivation. The inactivated centromere is occupied by heterochromatin and frequently reactivated in heterochromatin- or histone deacetylase-deficient mutants. CONCLUSIONS Chromosomes with multiple centromeres are stabilized by epigenetic centromere inactivation, which is initiated by kinetochore disassembly. Consequent heterochromatinization and histone deacetylation expanding from pericentric repeats to the central domain prevent reactivation of the inactivated centromere.
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Affiliation(s)
- Hiroshi Sato
- Division of Cell Biology, Institute of Life Science, Kurume University, Hyakunen-kohen 1-1, Kurume, Fukuoka 839-0864, Japan.
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Abstract
This chapter focuses on the three-dimensional organization of the nucleus in normal, early genomically unstable, and tumor cells. A cause-consequence relationship is discussed between nuclear alterations and the resulting genomic rearrangements. Examples are presented from studies on conditional Myc deregulation, experimental tumorigenesis in mouse plasmacytoma, nuclear remodeling in Hodgkin's lymphoma, and in adult glioblastoma. A model of nuclear remodeling is proposed for cancer progression in multiple myeloma. Current models of nuclear remodeling are described, including our model of altered nuclear architecture and the onset of genomic instability.
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Mackinnon RN, Campbell LJ. The role of dicentric chromosome formation and secondary centromere deletion in the evolution of myeloid malignancy. GENETICS RESEARCH INTERNATIONAL 2011; 2011:643628. [PMID: 22567363 PMCID: PMC3335544 DOI: 10.4061/2011/643628] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/20/2011] [Indexed: 01/16/2023]
Abstract
Dicentric chromosomes have been identified as instigators of the genome instability associated with cancer, but this instability is often resolved by one of a number of different secondary events. These include centromere inactivation, inversion, and intercentromeric deletion. Deletion or excision of one of the centromeres may be a significant occurrence in myeloid malignancy and other malignancies but has not previously been widely recognized, and our reports are the first describing centromere deletion in cancer cells. We review what is known about dicentric chromosomes and the mechanisms by which they can undergo stabilization in both constitutional and cancer genomes. The failure to identify centromere deletion in cancer cells until recently can be partly explained by the standard approaches to routine diagnostic cancer genome analysis, which do not identify centromeres in the context of chromosome organization. This hitherto hidden group of primary dicentric, secondary monocentric chromosomes, together with other unrecognized dicentric chromosomes, points to a greater role for dicentric chromosomes in cancer initiation and progression than is generally acknowledged. We present a model that predicts and explains a significant role for dicentric chromosomes in the formation of unbalanced translocations in malignancy.
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Affiliation(s)
- Ruth N Mackinnon
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital (Melbourne) Ltd., P.O. Box 2900, Fitzroy, VIC 3065, Australia
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Gordon JL, Byrne KP, Wolfe KH. Mechanisms of chromosome number evolution in yeast. PLoS Genet 2011; 7:e1002190. [PMID: 21811419 PMCID: PMC3141009 DOI: 10.1371/journal.pgen.1002190] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 06/03/2011] [Indexed: 12/25/2022] Open
Abstract
The whole-genome duplication (WGD) that occurred during yeast evolution changed the basal number of chromosomes from 8 to 16. However, the number of chromosomes in post-WGD species now ranges between 10 and 16, and the number in non-WGD species (Zygosaccharomyces, Kluyveromyces, Lachancea, and Ashbya) ranges between 6 and 8. To study the mechanism by which chromosome number changes, we traced the ancestry of centromeres and telomeres in each species. We observe only two mechanisms by which the number of chromosomes has decreased, as indicated by the loss of a centromere. The most frequent mechanism, seen 8 times, is telomere-to-telomere fusion between two chromosomes with the concomitant death of one centromere. The other mechanism, seen once, involves the breakage of a chromosome at its centromere, followed by the fusion of the two arms to the telomeres of two other chromosomes. The only mechanism by which chromosome number has increased in these species is WGD. Translocations and inversions have cycled telomere locations, internalizing some previously telomeric genes and creating novel telomeric locations. Comparison of centromere structures shows that the length of the CDEII region is variable between species but uniform within species. We trace the complete rearrangement history of the Lachancea kluyveri genome since its common ancestor with Saccharomyces and propose that its exceptionally low level of rearrangement is a consequence of the loss of the non-homologous end joining (NHEJ) DNA repair pathway in this species. The number of chromosomes in organisms often changes over evolutionary time. To study how the number changes, we compare several related species of yeast that share a common ancestor roughly 150 million years ago and have varying numbers of chromosomes. By inferring ancestral genome structures, we examine the changes in location of centromeres and telomeres, key elements that biologically define chromosomes. Their locations change over time by rearrangements of chromosome segments. By following these rearrangements, we trace an evolutionary path between existing centromeres and telomeres to those in the ancestral genomes, allowing us to identify the specific evolutionary events that caused changes in chromosome number. We show that, in these yeasts, chromosome number has generally decreased over time except for one notable exception: an event in an ancestor of several species where the whole genome was duplicated. Chromosome number reduction occurs by the simultaneous removal of a centromere from a chromosome and fusion of the rest of the chromosome to another that contains a working centromere. This process also results in telomere removal and the movement of genes from the ends of chromosomes to new locations in the middle of chromosomes.
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Affiliation(s)
- Jonathan L Gordon
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
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Baker NM, Zeitlin SG, Shi LZ, Shah J, Berns MW. Chromosome tips damaged in anaphase inhibit cytokinesis. PLoS One 2010; 5:e12398. [PMID: 20811641 PMCID: PMC2928297 DOI: 10.1371/journal.pone.0012398] [Citation(s) in RCA: 10] [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: 05/17/2010] [Accepted: 07/27/2010] [Indexed: 12/21/2022] Open
Abstract
Genome maintenance is ensured by a variety of biochemical sensors and pathways that repair accumulated damage. During mitosis, the mechanisms that sense and resolve DNA damage remain elusive. Studies have demonstrated that damage accumulated on lagging chromosomes can activate the spindle assembly checkpoint. However, there is little known regarding damage to DNA after anaphase onset. In this study, we demonstrate that laser-induced damage to chromosome tips (presumptive telomeres) in anaphase of Potorous tridactylis cells (PtK2) inhibits cytokinesis. In contrast, equivalent irradiation of non-telomeric chromosome regions or control irradiations in either the adjacent cytoplasm or adjacent to chromosome tips near the spindle midzone during anaphase caused no change in the eventual completion of cytokinesis. Damage to only one chromosome tip caused either complete absence of furrow formation, a prolonged delay in furrow formation, or furrow regression. When multiple chromosome tips were irradiated in the same cell, the cytokinesis defects increased, suggesting a potential dose-dependent mechanism. These results suggest a mechanism in which dysfunctional telomeres inhibit mitotic exit.
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Affiliation(s)
- Norman M. Baker
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, United States of America
| | - Samantha G. Zeitlin
- Laboratory for Cell Biology, Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, California, United States of America
| | - Linda Z. Shi
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Jagesh Shah
- Department of Systems Biology, Harvard Medical School and Renal Division, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- * E-mail: (MWB); (JS)
| | - Michael W. Berns
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- Beckman Laser Institute, University of California Irvine, Irvine, California, United States of America
- * E-mail: (MWB); (JS)
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