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Cook D, Kozmin SG, Yeh E, Petes TD, Bloom K. Dicentric chromosomes are resolved through breakage and repair at their centromeres. Chromosoma 2024; 133:117-134. [PMID: 38165460 PMCID: PMC11180013 DOI: 10.1007/s00412-023-00814-6] [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: 11/07/2023] [Revised: 11/11/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Chromosomes with two centromeres provide a unique opportunity to study chromosome breakage and DNA repair using completely endogenous cellular machinery. Using a conditional transcriptional promoter to control the second centromere, we are able to activate the dicentric chromosome and follow the appearance of DNA repair products. We find that the rate of appearance of DNA repair products resulting from homology-based mechanisms exceeds the expected rate based on their limited centromere homology (340 bp) and distance from one another (up to 46.3 kb). In order to identify whether DNA breaks originate in the centromere, we introduced 12 single-nucleotide polymorphisms (SNPs) into one of the centromeres. Analysis of the distribution of SNPs in the recombinant centromeres reveals that recombination was initiated with about equal frequency within the conserved centromere DNA elements CDEII and CDEIII of the two centromeres. The conversion tracts range from about 50 bp to the full length of the homology between the two centromeres (340 bp). Breakage and repair events within and between the centromeres can account for the efficiency and distribution of DNA repair products. We propose that in addition to providing a site for kinetochore assembly, the centromere may be a point of stress relief in the face of genomic perturbations.
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Affiliation(s)
- Diana Cook
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - Stanislav G Kozmin
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Elaine Yeh
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - Thomas D Petes
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, 27599-3280, USA.
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2
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Pei D, Yu X, Fu W, Ma X, Fang J. The evolution and formation of centromeric repeats analysis in Vitis vinifera. PLANTA 2024; 259:99. [PMID: 38522063 DOI: 10.1007/s00425-024-04374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/03/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION Six grape centromere-specific markers for cytogenetics were mined by combining genetic and immunological assays, and the possible evolution mechanism of centromeric repeats was analyzed. Centromeric histone proteins are functionally conserved; however, centromeric repetitive DNA sequences may represent considerable diversity in related species. Therefore, studying the characteristics and structure of grape centromere repeat sequences contributes to a deeper understanding of the evolutionary process of grape plants, including their origin and mechanisms of polyploidization. Plant centromeric regions are mainly composed of repetitive sequences, including SatDNA and transposable elements (TE). In this research, the characterization of centromere sequences in the whole genome of grapevine (Vitis vinifera L.) has been conducted. Five centromeric tandem repeat sequences (Vv1, Vv2, Vv5, Vv6, and Vv8) and one long terminal repeat (LTR) sequence Vv24 were isolated. These sequences had different centromeric distributions, which indicates that grape centromeric sequences may undergo rapid evolution. The existence of extrachromosomal circular DNA (eccDNA) and gene expression in CenH3 subdomain region may provide various potential mechanisms for the generation of new centromeric regions.
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Affiliation(s)
- Dan Pei
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xue Yu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weihong Fu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xuhui Ma
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China.
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3
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Scelfo A, Angrisani A, Grillo M, Barnes BM, Muyas F, Sauer CM, Leung CWB, Dumont M, Grison M, Mazaud D, Garnier M, Guintini L, Nelson L, Esashi F, Cortés-Ciriano I, Taylor SS, Déjardin J, Wilhelm T, Fachinetti D. Specialized replication mechanisms maintain genome stability at human centromeres. Mol Cell 2024; 84:1003-1020.e10. [PMID: 38359824 DOI: 10.1016/j.molcel.2024.01.018] [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] [Received: 03/13/2023] [Revised: 12/12/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
The high incidence of whole-arm chromosome aneuploidy and translocations in tumors suggests instability of centromeres, unique loci built on repetitive sequences and essential for chromosome separation. The causes behind this fragility and the mechanisms preserving centromere integrity remain elusive. We show that replication stress, hallmark of pre-cancerous lesions, promotes centromeric breakage in mitosis, due to spindle forces and endonuclease activities. Mechanistically, we unveil unique dynamics of the centromeric replisome distinct from the rest of the genome. Locus-specific proteomics identifies specialized DNA replication and repair proteins at centromeres, highlighting them as difficult-to-replicate regions. The translesion synthesis pathway, along with other factors, acts to sustain centromere replication and integrity. Prolonged stress causes centromeric alterations like ruptures and translocations, as observed in ovarian cancer models experiencing replication stress. This study provides unprecedented insights into centromere replication and integrity, proposing mechanistic insights into the origins of centromere alterations leading to abnormal cancerous karyotypes.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR144, 26 rue d'Ulm, Paris 75005, France
| | - Annapaola Angrisani
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR144, 26 rue d'Ulm, Paris 75005, France
| | - Marco Grillo
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR144, 26 rue d'Ulm, Paris 75005, France
| | - Bethany M Barnes
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Carolin M Sauer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | | | - Marie Dumont
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR144, 26 rue d'Ulm, Paris 75005, France
| | - Marine Grison
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR144, 26 rue d'Ulm, Paris 75005, France
| | - David Mazaud
- Plateforme Imagerie PICT-IBiSA, Institut Curie, PSL Research University, Paris 75005, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR3664, 26 rue d'Ulm, Paris 75005, France
| | - Mickaël Garnier
- Plateforme Imagerie PICT-IBiSA, Institut Curie, PSL Research University, Paris 75005, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR3664, 26 rue d'Ulm, Paris 75005, France
| | - Laetitia Guintini
- Institute of Human Genetics, CNRS-Université de Montpellier, Montpellier 34396, France
| | - Louisa Nelson
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Jérôme Déjardin
- Institute of Human Genetics, CNRS-Université de Montpellier, Montpellier 34396, France
| | - Therese Wilhelm
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR144, 26 rue d'Ulm, Paris 75005, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR3664, 26 rue d'Ulm, Paris 75005, France.
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR144, 26 rue d'Ulm, Paris 75005, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR3664, 26 rue d'Ulm, Paris 75005, France.
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4
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Marcon F, Giunta S, Bignami M. Emerging roles of DNA repair factors in the stability of centromeres. Semin Cell Dev Biol 2024; 156:121-129. [PMID: 37852903 DOI: 10.1016/j.semcdb.2023.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Satellite DNA sequences are an integral part of centromeres, regions critical for faithful segregation of chromosomes during cell division. Because of their complex repetitive structure, satellite DNA may act as a barrier to DNA replication and other DNA based transactions ultimately resulting in chromosome breakage. Over the past two decades, several DNA repair proteins have been shown to bind and function at centromeres. While the importance of these repair factors is highlighted by various structural and numerical chromosome aberrations resulting from their inactivation, their roles in helping to maintain genome stability by solving the intrinsic difficulties of satellite DNA replication or promoting their repair are just starting to emerge. In this review, we summarize the current knowledge on the role of DNA repair and DNA damage response proteins in maintaining the structure and function of centromeres in different contexts. We also report the recent connection between the roles of specific DNA repair factors at these genomic loci with age-related increase of chromosomal instability under physiological and pathological conditions.
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Affiliation(s)
- Francesca Marcon
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Italy
| | - Margherita Bignami
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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5
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Kozmin SG, Dominska M, Zheng DQ, Petes TD. Splitting the yeast centromere by recombination. Nucleic Acids Res 2024; 52:690-707. [PMID: 37994724 PMCID: PMC10810202 DOI: 10.1093/nar/gkad1110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
Although fusions between the centromeres of different human chromosomes have been observed cytologically in cancer cells, since the centromeres are long arrays of satellite sequences, the details of these fusions have been difficult to investigate. We developed methods of detecting recombination within the centromeres of the yeast Saccharomyces cerevisiae (intercentromere recombination). These events occur at similar rates (about 10-8/cell division) between two active or two inactive centromeres. We mapped the breakpoints of most of the recombination events to a region of 43 base pairs of uninterrupted homology between the two centromeres. By whole-genome DNA sequencing, we showed that most (>90%) of the events occur by non-reciprocal recombination (gene conversion/break-induced replication). We also found that intercentromere recombination can involve non-homologous chromosome, generating whole-arm translocations. In addition, intercentromere recombination is associated with very frequent chromosome missegregation. These observations support the conclusion that intercentromere recombination generally has negative genetic consequences.
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Affiliation(s)
- Stanislav G Kozmin
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | | | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
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6
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Li Y, Wang J, Chen X, Czajkowsky DM, Shao Z. Quantitative Super-Resolution Microscopy Reveals the Relationship between CENP-A Stoichiometry and Centromere Physical Size. Int J Mol Sci 2023; 24:15871. [PMID: 37958853 PMCID: PMC10649757 DOI: 10.3390/ijms242115871] [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: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Centromeric chromatin is thought to play a critical role in ensuring the faithful segregation of chromosomes during mitosis. However, our understanding of this role is presently limited by our poor understanding of the structure and composition of this unique chromatin. The nucleosomal variant, CENP-A, localizes to narrow regions within the centromere, where it plays a major role in centromeric function, effectively serving as a platform on which the kinetochore is assembled. Previous work found that, within a given cell, the number of microtubules within kinetochores is essentially unchanged between CENP-A-localized regions of different physical sizes. However, it is unknown if the amount of CENP-A is also unchanged between these regions of different sizes, which would reflect a strict structural correspondence between these two key characteristics of the centromere/kinetochore assembly. Here, we used super-resolution optical microscopy to image and quantify the amount of CENP-A and DNA within human centromere chromatin. We found that the amount of CENP-A within CENP-A domains of different physical sizes is indeed the same. Further, our measurements suggest that the ratio of CENP-A- to H3-containing nucleosomes within these domains is between 8:1 and 11:1. Thus, our results not only identify an unexpectedly strict relationship between CENP-A and microtubules stoichiometries but also that the CENP-A centromeric domain is almost exclusively composed of CENP-A nucleosomes.
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Affiliation(s)
- Yaqian Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
| | - Jiabin Wang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Daniel M. Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
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7
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Litwin I, Nowicka M, Markowska K, Maciaszczyk-Dziubińska E, Tomaszewska P, Wysocki R, Kramarz K. ISW1a modulates cohesin distribution in centromeric and pericentromeric regions. Nucleic Acids Res 2023; 51:9101-9121. [PMID: 37486771 PMCID: PMC10516642 DOI: 10.1093/nar/gkad612] [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: 10/03/2022] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023] Open
Abstract
Cohesin is a highly conserved, multiprotein complex whose canonical function is to hold sister chromatids together to ensure accurate chromosome segregation. Cohesin association with chromatin relies on the Scc2-Scc4 cohesin loading complex that enables cohesin ring opening and topological entrapment of sister DNAs. To better understand how sister chromatid cohesion is regulated, we performed a proteomic screen in budding yeast that identified the Isw1 chromatin remodeler as a cohesin binding partner. In addition, we found that Isw1 also interacts with Scc2-Scc4. Lack of Isw1 protein, the Ioc3 subunit of ISW1a or Isw1 chromatin remodeling activity resulted in increased accumulation of cohesin at centromeres and pericentromeres, suggesting that ISW1a may promote efficient translocation of cohesin from the centromeric site of loading to neighboring regions. Consistent with the role of ISW1a in the chromatin organization of centromeric regions, Isw1 was found to be recruited to centromeres. In its absence we observed changes in the nucleosomal landscape at centromeres and pericentromeres. Finally, we discovered that upon loss of RSC functionality, ISW1a activity leads to reduced cohesin binding and cohesion defect. Taken together, our results support the notion of a key role of chromatin remodelers in the regulation of cohesin distribution on chromosomes.
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Affiliation(s)
- Ireneusz Litwin
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Małgorzata Nowicka
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Katarzyna Markowska
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubińska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Paulina Tomaszewska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Karol Kramarz
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
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8
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Mishra PK, Au WC, Castineira PG, Ali N, Stanton J, Boeckmann L, Takahashi Y, Costanzo M, Boone C, Bloom KS, Thorpe PH, Basrai MA. Misregulation of cell cycle-dependent methylation of budding yeast CENP-A contributes to chromosomal instability. Mol Biol Cell 2023; 34:ar99. [PMID: 37436802 PMCID: PMC10551700 DOI: 10.1091/mbc.e23-03-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/15/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2023] Open
Abstract
Centromere (CEN) identity is specified epigenetically by specialized nucleosomes containing evolutionarily conserved CEN-specific histone H3 variant CENP-A (Cse4 in Saccharomyces cerevisiae, CENP-A in humans), which is essential for faithful chromosome segregation. However, the epigenetic mechanisms that regulate Cse4 function have not been fully defined. In this study, we show that cell cycle-dependent methylation of Cse4-R37 regulates kinetochore function and high-fidelity chromosome segregation. We generated a custom antibody that specifically recognizes methylated Cse4-R37 and showed that methylation of Cse4 is cell cycle regulated with maximum levels of methylated Cse4-R37 and its enrichment at the CEN chromatin occur in the mitotic cells. Methyl-mimic cse4-R37F mutant exhibits synthetic lethality with kinetochore mutants, reduced levels of CEN-associated kinetochore proteins and chromosome instability (CIN), suggesting that mimicking the methylation of Cse4-R37 throughout the cell cycle is detrimental to faithful chromosome segregation. Our results showed that SPOUT methyltransferase Upa1 contributes to methylation of Cse4-R37 and overexpression of UPA1 leads to CIN phenotype. In summary, our studies have defined a role for cell cycle-regulated methylation of Cse4 in high-fidelity chromosome segregation and highlight an important role of epigenetic modifications such as methylation of kinetochore proteins in preventing CIN, an important hallmark of human cancers.
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Affiliation(s)
- Prashant K. Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Pedro G. Castineira
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Nazrin Ali
- Queen Mary University of London, E1 4NS, UK
| | - John Stanton
- University of North Carolina, Chapel Hill, NC 27599
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yoshimitsu Takahashi
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | | | | | - Munira A. Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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9
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Lustig AJ. Investigating the origin of subtelomeric and centromeric AT-rich elements in Aspergillus flavus. PLoS One 2023; 18:e0279148. [PMID: 36758027 PMCID: PMC9910759 DOI: 10.1371/journal.pone.0279148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
An in silico study of Aspergillus flavus genome stability uncovered significant variations in both coding and non-coding regions. The non-coding insertions uniformly consisted of AT-rich sequences that are evolutionarily maintained, albeit distributed at widely different sites in an array of A. flavus strains. A survey of ≥ 2kb AT-rich elements (AT ≥ 70%; ATEs) in non-centromeric regions uncovered two major categories of ATEs. The first category is composed of homologous insertions at ectopic, non-allelic sites that contain homology to transposable elements (TEs; Classes B, C, D, and E). Strains differed significantly in frequency, position, and TE type, but displayed a common enrichment in subtelomeric regions. The TEs were heavily mutated, with patterns consistent with the ancestral activity of repeat-induced point mutations (RIP). The second category consists of a conserved set of novel subtelomeric ATE repeats (Classes A, G, G, H, I and J) which lack discernible TEs and, unlike TEs, display a constant polarity relative to the telomere. Members of one of these classes are derivatives of a progenitor ATE that is predicted to have undergone extensive homologous recombination during evolution. A third category of ATEs consists of ~100 kb regions at each centromere. Centromeric ATEs and TE clusters within these centromeres display a high level of sequence identity between strains. These studies suggest that transposition and RIP are forces in the evolution of subtelomeric and centromeric structure and function.
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Affiliation(s)
- Arthur J. Lustig
- Department of Biochemistry and Molecular Biology, Tulane University Medical School, New Orleans, LA, United States of America
- * E-mail:
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10
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van Schaik T, Manzo SG, Vouzas AE, Liu NQ, Teunissen H, de Wit E, Gilbert DM, van Steensel B. Dynamic chromosomal interactions and control of heterochromatin positioning by Ki-67. EMBO Rep 2022; 23:e55782. [PMID: 36245428 PMCID: PMC9724667 DOI: 10.15252/embr.202255782] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Ki-67 is a chromatin-associated protein with a dynamic distribution pattern throughout the cell cycle and is thought to be involved in chromatin organization. The lack of genomic interaction maps has hampered a detailed understanding of its roles, particularly during interphase. By pA-DamID mapping in human cell lines, we find that Ki-67 associates with large genomic domains that overlap mostly with late-replicating regions. Early in interphase, when Ki-67 is present in pre-nucleolar bodies, it interacts with these domains on all chromosomes. However, later in interphase, when Ki-67 is confined to nucleoli, it shows a striking shift toward small chromosomes. Nucleolar perturbations indicate that these cell cycle dynamics correspond to nucleolar maturation during interphase, and suggest that nucleolar sequestration of Ki-67 limits its interactions with larger chromosomes. Furthermore, we demonstrate that Ki-67 does not detectably control chromatin-chromatin interactions during interphase, but it competes with the nuclear lamina for interaction with late-replicating DNA, and it controls replication timing of (peri)centromeric regions. Together, these results reveal a highly dynamic choreography of genome interactions and roles for Ki-67 in heterochromatin organization.
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Affiliation(s)
- Tom van Schaik
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Stefano G Manzo
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Athanasios E Vouzas
- Department of Biological ScienceThe Florida State UniversityTallahasseeFLUSA,San Diego Biomedical Research InstituteSan DiegoCAUSA
| | - Ning Qing Liu
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Hans Teunissen
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Elzo de Wit
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - David M Gilbert
- Department of Biological ScienceThe Florida State UniversityTallahasseeFLUSA,San Diego Biomedical Research InstituteSan DiegoCAUSA
| | - Bas van Steensel
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands,Department of Cell BiologyErasmus University Medical CentreRotterdamThe Netherlands
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11
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Susilowati S, Mustofa I, Wurlina W, Hernawati T, Oktanella Y, Soeharsono S, Purwanto DA. Green Tea Extract in the Extender Improved the Post-Thawed Semen Quality and Decreased Amino Acid Mutation of Kacang Buck Sperm. Vet Sci 2022; 9:vetsci9080403. [PMID: 36006318 PMCID: PMC9413626 DOI: 10.3390/vetsci9080403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
This study was the first to combine the addition of antioxidants to a skim milk–egg yolk (SM–EY) extender and different equilibration periods to obtain higher quality post-thawed Kacang buck semen. This study aimed to determine the effects of green tea extract (GTE) on the quality of frozen Kacang goat sperm equilibrated for one and two hours. The pool of Kacang buck ejaculate was equally divided into four portions and was diluted in an SM–EY extender that contained four doses of 0, 0.05, 0.10, and 0.15 mg of GTE/100 mL for T0, T1, T2, and T3 groups, respectively. The aliquots were treated for an equilibration period of 1–2 h before further processing as frozen semen. Post-thawed semen quality was evaluated for sperm quality. The Sanger method was used for DNA sequencing, and the amino acid sequence was read using MEGA v.7.0. The post-thawed semen of the T2 group that was equilibrated for one hour had the highest semen quality. Pre-freezing motility had the highest determination coefficient compared to post-thawed sperm motility. This study is the first to report amino acid mutation due to freeze–thawing. The frequency of amino acid mutations revealed that T2 was the least mutated amino acid. Glycine, valine, leucine, serine, and asparagine strongly correlated to post-thawed sperm motility. It can be concluded that a combination of 0.1 mg GTE/100 mL extender as an antioxidant and one-hour equilibration period resulted in the best post-thawed Kacang buck semen quality.
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Affiliation(s)
- Suherni Susilowati
- Division of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia; (S.S.); (W.W.); (T.H.)
| | - Imam Mustofa
- Division of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia; (S.S.); (W.W.); (T.H.)
- Correspondence: ; Tel.: +62-812-356-1540; Fax: +62-31-599-3015
| | - Wurlina Wurlina
- Division of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia; (S.S.); (W.W.); (T.H.)
| | - Tatik Hernawati
- Division of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia; (S.S.); (W.W.); (T.H.)
| | - Yudit Oktanella
- Division of Veterinary Reproduction, Faculty of Veterinary Medicine, Brawijaya University, Malang City 65145, Indonesia;
| | - Soeharsono Soeharsono
- Division of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia;
| | - Djoko Agus Purwanto
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia;
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12
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Mitotic drive in asymmetric epigenetic inheritance. Biochem Soc Trans 2022; 50:675-688. [PMID: 35437581 PMCID: PMC9162470 DOI: 10.1042/bst20200267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 01/14/2023]
Abstract
Asymmetric cell division (ACD) produces two daughter cells with distinct cell fates. This division mode is widely used during development and by adult stem cells during tissue homeostasis and regeneration, which can be regulated by both extrinsic cues such as signaling molecules and intrinsic factors such as epigenetic information. While the DNA replication process ensures that the sequences of sister chromatids are identical, how epigenetic information is re-distributed during ACD has remained largely unclear in multicellular organisms. Studies of Drosophila male germline stem cells (GSCs) have revealed that sister chromatids incorporate pre-existing and newly synthesized histones differentially and segregate asymmetrically during ACD. To understand the underlying molecular mechanisms of this phenomenon, two key questions must be answered: first, how and when asymmetric histone information is established; and second, how epigenetically distinct sister chromatids are distinguished and segregated. Here, we discuss recent advances which help our understanding of this interesting and important cell division mode.
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13
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Chardon F, Japaridze A, Witt H, Velikovsky L, Chakraborty C, Wilhelm T, Dumont M, Yang W, Kikuti C, Gangnard S, Mace AS, Wuite G, Dekker C, Fachinetti D. CENP-B-mediated DNA loops regulate activity and stability of human centromeres. Mol Cell 2022; 82:1751-1767.e8. [PMID: 35320753 DOI: 10.1016/j.molcel.2022.02.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/25/2022]
Abstract
Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.
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Affiliation(s)
- Florian Chardon
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Hannes Witt
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Camellia Chakraborty
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Therese Wilhelm
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carlos Kikuti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Stephane Gangnard
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Anne-Sophie Mace
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Gijs Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France.
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14
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El Dika M, Fritz AJ, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Fidelity of Mechanisms Governing the Cell Cycle. Results Probl Cell Differ 2022; 70:375-396. [PMID: 36348115 PMCID: PMC9703624 DOI: 10.1007/978-3-031-06573-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cell cycle is governed by stringent epigenetic mechanisms that, in response to intrinsic and extrinsic regulatory cues, support fidelity of DNA replication and cell division. We will focus on (1) the complex and interdependent processes that are obligatory for control of proliferation and compromised in cancer, (2) epigenetic and topological domains that are associated with distinct phases of the cell cycle that may be altered in cancer initiation and progression, and (3) the requirement for mitotic bookmarking to maintain intranuclear localization of transcriptional regulatory machinery to reinforce cell identity throughout the cell cycle to prevent malignant transformation.
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Affiliation(s)
- Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
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15
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Hagemeijer YP, Guryev V, Horvatovich P. Accurate Prediction of Protein Sequences for Proteogenomics Data Integration. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:233-260. [PMID: 34905178 DOI: 10.1007/978-1-0716-1936-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This book chapter discusses proteogenomics data integration and provides an overview into the different omics layer involved in defining the proteome of a living organism. Various aspects of genome variability affecting either the sequence or abundance level of proteins are discussed in this book chapter, such as the effect of single-nucleotide variants or larger genomic structural variants on the proteome. Next, various sequencing technologies are introduced and discussed from a proteogenomics data integration perspective such as those providing short- and long-read sequencing and listing their respective advantages and shortcomings for accurate protein variant prediction using genomic/transcriptomics sequencing data. Finally, the various bioinformatics tools used to process and analyze DNA/RNA sequencing data are discussed with the ultimate goal of obtaining accurately predicted sample-specific protein sequences that can be used as a drop-in replacement in existing approaches for peptide and protein identification using popular database search engines such as MSFragger, SearchGUI/PeptideShaker.
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Affiliation(s)
- Yanick Paco Hagemeijer
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands.
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16
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Zhang S, Xie Y, Tian T, Yang Q, Zhou Y, Qiu J, Xu L, Wen N, Lv Q, Du Z. High expression levels of centromere protein A plus upregulation of the phosphatidylinositol 3-kinase/Akt/mammalian target of rapamycin signaling pathway affect chemotherapy response and prognosis in patients with breast cancer. Oncol Lett 2021; 21:410. [PMID: 33841571 PMCID: PMC8020387 DOI: 10.3892/ol.2021.12671] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 02/16/2021] [Indexed: 02/05/2023] Open
Abstract
Centromere proteins (CENPs) are involved in mitosis, and CENP gene expression levels are associated with chemotherapy responses in patients with breast cancer. The present study aimed to examine the roles and underlying mechanisms of the effects of CENP genes on chemotherapy responses and breast cancer prognosis. Using data obtained from the Gene Expression Omnibus (GEO) database, correlation and Cox multivariate regression analyses were used to determine the CENP genes associated with chemotherapy responses and survival in patients with breast cancer. Weighted gene co-expression network and correlation analyses were used to determine the gene modules co-expressed with the identified genes and the differential expression of gene modules associated with the pathological complete response (PCR) and residual disease (RD) subgroups. CENPA, CENPE, CENPF, CENPI, CENPJ and CENPN were associated with a high nuclear grade and low estrogen and progesterone receptor expression levels. In addition, CENPA, CENPB, CENPC and CENPO were independent factors affecting the distant relapse-free survival (DRFS) rates in patients with breast cancer. Patients with high expression levels of CENPA or CENPO exhibited poor prognoses, whereas those with high expression levels of CENPB or CENPC presented with favorable prognoses. For validation between databases, the Cancer Genome Atlas (TCGA) database analysis also revealed that CENPA, CENPB and CENPO exerted similar effects on overall survival. However, according to the multivariate analyses, only CENPA was an independent risk factor associated with DRFS in GEO database. In addition, in the RD subgroup, patients with higher CENPA expression levels had a worse prognosis compared with those with lower CENPA expression levels. Among patients with high expression levels of CENPA, the PI3K/Akt/mTOR pathway was more likely to be activated in the RD compared with the PCR subgroup. The same trend was observed in TCGA data. These results suggested that high CENPA expression levels plus upregulation of the PI3K/Akt/mTOR signaling pathway may affect DRFS in patients with breast cancer.
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Affiliation(s)
- Songbo Zhang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yanyan Xie
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ting Tian
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Qianru Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuting Zhou
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Juanjuan Qiu
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Li Xu
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Nan Wen
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Qing Lv
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Zhenggui Du
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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17
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Nagpal H, Fierz B. The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity? J Mol Biol 2021; 433:166676. [PMID: 33065112 DOI: 10.1016/j.jmb.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023]
Abstract
The centromere is an essential chromatin domain required for kinetochore recruitment and chromosome segregation in eukaryotes. To perform this role, centro-chromatin adopts a unique structure that provides access to kinetochore proteins and maintains stability under tension during mitosis. This is achieved by the presence of nucleosomes containing the H3 variant CENP-A, which also acts as the epigenetic mark defining the centromere. In this review, we discuss the role of CENP-A on the structure and dynamics of centromeric chromatin. We further discuss the impact of the CENP-A binding proteins CENP-C, CENP-N, and CENP-B on modulating centro-chromatin structure. Based on these findings we provide an overview of the higher order structure of the centromere.
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Affiliation(s)
- Harsh Nagpal
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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18
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Mishra PK, Chakraborty A, Yeh E, Feng W, Bloom KS, Basrai MA. R-loops at centromeric chromatin contribute to defects in kinetochore integrity and chromosomal instability in budding yeast. Mol Biol Cell 2020; 32:74-89. [PMID: 33147102 PMCID: PMC8098821 DOI: 10.1091/mbc.e20-06-0379] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
R-loops, the byproduct of DNA–RNA hybridization and the displaced single-stranded DNA (ssDNA), have been identified in bacteria, yeasts, and other eukaryotic organisms. The persistent presence of R-loops contributes to defects in DNA replication and repair, gene expression, and genomic integrity. R-loops have not been detected at centromeric (CEN) chromatin in wild-type budding yeast. Here we used an hpr1∆ strain that accumulates R-loops to investigate the consequences of R-loops at CEN chromatin and chromosome segregation. We show that Hpr1 interacts with the CEN-histone H3 variant, Cse4, and prevents the accumulation of R-loops at CEN chromatin for chromosomal stability. DNA–RNA immunoprecipitation (DRIP) analysis showed an accumulation of R-loops at CEN chromatin that was reduced by overexpression of RNH1 in hpr1∆ strains. Increased levels of ssDNA, reduced levels of Cse4 and its assembly factor Scm3, and mislocalization of histone H3 at CEN chromatin were observed in hpr1∆ strains. We determined that accumulation of R-loops at CEN chromatin contributes to defects in kinetochore biorientation and chromosomal instability (CIN) and these phenotypes are suppressed by RNH1 overexpression in hpr1∆ strains. In summary, our studies provide mechanistic insights into how accumulation of R-loops at CEN contributes to defects in kinetochore integrity and CIN.
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Affiliation(s)
- Prashant K Mishra
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | | | - Elaine Yeh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Wenyi Feng
- SUNY Upstate Medical University, Syracuse, NY 13210
| | - Kerry S Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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19
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Susilowati S, Triana IN, Sardjito T, Suprayogi TW, Wurlina W, Mustofa I. Effect of Simmental bull seminal plasma protein in egg yolk-citrate extender on Kacang buck semen fertility. Cryobiology 2020; 97:20-27. [PMID: 33121627 DOI: 10.1016/j.cryobiol.2020.10.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/15/2020] [Accepted: 10/21/2020] [Indexed: 12/18/2022]
Abstract
The genetic resources of Indonesia's indigenous Kacang goat require preservation. Artificial insemination is expected to accelerate population increases and preserve genetic resources simultaneously. The present study was the maiden attempt for cryopreservation of Kacang buck sperm. The objectives of this study were to determine whether the supplementation of superior Simmental bull seminal plasma protein in egg yolk-citrate extender could improve the quality of post-thawed Kacang buck sperm, increase conceptions rates, and improve kidding rates. Buck semen was diluted without supplementation (T0) and with supplementation of 2.5 mg (T1) and 5 mg (T2) of Simmental bull seminal plasma protein per mL egg yolk-citrate extender. Extended semen was packed in 0.25 mL straw as cryopreserved frozen semen. Post-thawed semen samples were evaluated for viability, motility, intact plasma membranes, malondialdehyde level, and DNA fragmentation. Estrus was synchronized for sixty Kacang does, which were divided randomly into three groups and inseminated using post-thawed semen. The progesterone serum concentration of the does was measured 7 and 22 days post-insemination to detect ovulation and conception. Pregnancy was confirmed using abdominal palpation at 43 days post-insemination and by observing birth. The T1 group showed the highest (P < 0.05) post-thawed viability, motility, and intact plasma membrane. Conception, pregnancy and kidding rates were also higher in T1 than other treatment groups. In conclusion, the 2.5 mg Simmental bull seminal plasma protein supplementation per mL egg yolk-citrate extender provided the best seminal quality and fertility of post-thawed Kacang buck semen.
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Affiliation(s)
| | | | - Trilas Sardjito
- Laboratory of Veterinary Artificial Insemination, Indonesia.
| | | | - Wurlina Wurlina
- Laboratory of Veterinary Infertility and Sterility, Indonesia.
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20
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Trivedi P, Stukenberg PT. A Condensed View of the Chromosome Passenger Complex. Trends Cell Biol 2020; 30:676-687. [PMID: 32684321 PMCID: PMC10714244 DOI: 10.1016/j.tcb.2020.06.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 02/02/2023]
Abstract
The inner centromere is a region on the mitotic chromosome that serves as a platform for mitotic signaling and possesses unique biophysical properties that enable it to withstand relatively large pulling forces that are generated by kinetochores (KTs) during chromosome segregation. The chromosomal passenger complex (CPC) localizes to and is the key regulator of inner centromere organization and function during mitosis. Recently, we demonstrated that in addition to its kinase and histone code-reading activities, the CPC also can undergo liquid-liquid phase separation (LLPS) and proposed that the inner centromere is a membraneless organelle scaffolded by the CPC. In this perspective, we explore mechanisms that can allow the formation and dissolution of this membraneless body. The cell-cycle-regulated spatially defined assembly and disassembly of the CPC condensate at the inner centromere can reveal general principles about how histone modifications control chromatin-bound membraneless organelles. We further explore how the ability of the CPC to undergo LLPS may contribute to the organization and function of the inner centromere during mitosis.
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Affiliation(s)
- Prasad Trivedi
- Department of Cell Biology, University of Virginia, School of Medicine, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, USA
| | - P Todd Stukenberg
- Department of Cell Biology, University of Virginia, School of Medicine, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, USA.
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21
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Fan X, Kraynak J, Knisely JPS, Formenti SC, Shen WH. PTEN as a Guardian of the Genome: Pathways and Targets. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036194. [PMID: 31932469 DOI: 10.1101/cshperspect.a036194] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Faithful transmission of genetic information is only possible with the structural and functional integrity of the genome. PTEN has been recognized as a guardian of the genome since the identification of its noncanonical localization and function in the nucleus. Yet, the role of PTEN in guarding the genome relies on integration of diverse mechanisms elicited by its canonical activity in antagonizing PI3K as well as emerging noncanonical functions. In the nucleus, PTEN maintains the structural integrity of chromosomes and the architecture of heterochromatin by physically interacting with chromosomal and nucleosomal components. PTEN also controls the functional integrity of key genetic transmission machineries by promoting proper assembly of the replisome and mitotic spindles. Deregulation of PTEN signaling impairs genome integrity, leading to spontaneous replication/mitotic stress and subsequent stress tolerance. Identification of novel targets of PTEN signaling and illumination of the interplay of diverse PTEN pathways in genome maintenance will help us better understand mechanisms underlying tumor evolution and therapeutic resistance.
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Affiliation(s)
- Xinyi Fan
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Jeffrey Kraynak
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Jonathan P S Knisely
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Silvia C Formenti
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Wen H Shen
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
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22
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Schizosaccharomyces pombe Assays to Study Mitotic Recombination Outcomes. Genes (Basel) 2020; 11:genes11010079. [PMID: 31936815 PMCID: PMC7016768 DOI: 10.3390/genes11010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 01/16/2023] Open
Abstract
The fission yeast—Schizosaccharomyces pombe—has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
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Martino F, Costa A. A Different Twist on Centromeric Chromatin. Structure 2020; 28:3-5. [PMID: 31951537 DOI: 10.1016/j.str.2019.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Nucleosomes at the centromere contain CENP-A, a histone H3 variant that establishes a specific, yet poorly defined centromeric chromatin architecture. In this issue of Structure, Takizawa et al. (2019) describe an untwisted configuration for an H3-CENP-A-H3 tri-nucleosome that mimics centromeric chromatin. Untwisting may increase centromeric-protein accessibility to CENP-A in compacted chromatin.
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Affiliation(s)
- Fabrizio Martino
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Scelfo A, Fachinetti D. Keeping the Centromere under Control: A Promising Role for DNA Methylation. Cells 2019; 8:cells8080912. [PMID: 31426433 PMCID: PMC6721688 DOI: 10.3390/cells8080912] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 01/22/2023] Open
Abstract
In order to maintain cell and organism homeostasis, the genetic material has to be faithfully and equally inherited through cell divisions while preserving its integrity. Centromeres play an essential task in this process; they are special sites on chromosomes where kinetochores form on repetitive DNA sequences to enable accurate chromosome segregation. Recent evidence suggests that centromeric DNA sequences, and epigenetic regulation of centromeres, have important roles in centromere physiology. In particular, DNA methylation is abundant at the centromere, and aberrant DNA methylation, observed in certain tumors, has been correlated to aneuploidy and genomic instability. In this review, we evaluate past and current insights on the relationship between centromere function and the DNA methylation pattern of its underlying sequences.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75005 Paris, France.
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75005 Paris, France.
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25
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Large-scale chromatin organisation in interphase, mitosis and meiosis. Biochem J 2019; 476:2141-2156. [DOI: 10.1042/bcj20180512] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/17/2023]
Abstract
AbstractThe spatial configuration of chromatin is fundamental to ensure any given cell can fulfil its functional duties, from gene expression to specialised cellular division. Significant technological innovations have facilitated further insights into the structure, function and regulation of three-dimensional chromatin organisation. To date, the vast majority of investigations into chromatin organisation have been conducted in interphase and mitotic cells leaving meiotic chromatin relatively unexplored. In combination, cytological and genome-wide contact frequency analyses in mammalian germ cells have recently demonstrated that large-scale chromatin structures in meiotic prophase I are reminiscent of the sequential loop arrays found in mitotic cells, although interphase-like segmentation of transcriptionally active and inactive regions are also evident along the length of chromosomes. Here, we discuss the similarities and differences of such large-scale chromatin architecture, between interphase, mitotic and meiotic cells, as well as their functional relevance and the proposed modulatory mechanisms which underlie them.
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Lawrimore J, Bloom K. The regulation of chromosome segregation via centromere loops. Crit Rev Biochem Mol Biol 2019; 54:352-370. [PMID: 31573359 PMCID: PMC6856439 DOI: 10.1080/10409238.2019.1670130] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/02/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
Biophysical studies of the yeast centromere have shown that the organization of the centromeric chromatin plays a crucial role in maintaining proper tension between sister kinetochores during mitosis. While centromeric chromatin has traditionally been considered a simple spring, recent work reveals the centromere as a multifaceted, tunable shock absorber. Centromeres can differ from other regions of the genome in their heterochromatin state, supercoiling state, and enrichment of structural maintenance of chromosomes (SMC) protein complexes. Each of these differences can be utilized to alter the effective stiffness of centromeric chromatin. In budding yeast, the SMC protein complexes condensin and cohesin stiffen chromatin by forming and cross-linking chromatin loops, respectively, into a fibrous structure resembling a bottlebrush. The high density of the loops compacts chromatin while spatially isolating the tension from spindle pulling forces to a subset of the chromatin. Paradoxically, the molecular crowding of chromatin via cohesin and condensin also causes an outward/poleward force. The structure allows the centromere to act as a shock absorber that buffers the variable forces generated by dynamic spindle microtubules. Based on the distribution of SMCs from bacteria to human and the conserved distance between sister kinetochores in a wide variety of organisms (0.4 to 1 micron), we propose that the bottlebrush mechanism is the foundational principle for centromere function in eukaryotes.
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Affiliation(s)
- Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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27
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Zhao H, Winogradoff D, Dalal Y, Papoian GA. The Oligomerization Landscape of Histones. Biophys J 2019; 116:1845-1855. [PMID: 31005236 DOI: 10.1016/j.bpj.2019.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 12/29/2022] Open
Abstract
In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here, we investigate canonical histone assembly and that of the centromere-specific histone variant, centromere protein A (CENP-A), using molecular dynamics simulations. We quantitatively characterize their thermodynamical and dynamical features, showing that two H3/H4 dimers form a structurally floppy, weakly bound complex, the latter exhibiting large instability around the central interface manifested via a swiveling motion of two halves. This finding is consistent with the recently observed DNA handedness flipping of the tetrasome. In contrast, the variant CENP-A encodes distinctive stability to its tetramer with a rigid but twisted interface compared to the crystal structure, implying diverse structural possibilities of the histone variant. Interestingly, the observed tetramer dynamics alter significantly and appear to reach a new balance when H2A/H2B dimers are present. Furthermore, we found that the preferred structure for the (CENP-A/H4)2 tetramer is incongruent with the octameric structure, explaining many of the unusual dynamical behaviors of the CENP-A nucleosome. In all, these data reveal key mechanistic insights and structural details for the assembly of canonical and variant histone tetramers and octamers, providing theoretical quantifications and physical interpretations for longstanding and recent experimental observations. Based on these findings, we propose different chaperone-assisted binding and nucleosome assembly mechanisms for the canonical and CENP-A histone oligomers.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Winogradoff
- Chemical Physics Program, Institute for Physical Science and Technology
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Garegin A Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Chemical Physics Program, Institute for Physical Science and Technology; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.
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28
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Smurova K, De Wulf P. Centromere and Pericentromere Transcription: Roles and Regulation … in Sickness and in Health. Front Genet 2018; 9:674. [PMID: 30627137 PMCID: PMC6309819 DOI: 10.3389/fgene.2018.00674] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/04/2018] [Indexed: 12/26/2022] Open
Abstract
The chromosomal loci known as centromeres (CEN) mediate the equal distribution of the duplicated genome between both daughter cells. Specifically, centromeres recruit a protein complex named the kinetochore, that bi-orients the replicated chromosome pairs to the mitotic or meiotic spindle structure. The paired chromosomes are then separated, and the individual chromosomes segregate in opposite direction along the regressing spindle into each daughter cell. Erroneous kinetochore assembly or activity produces aneuploid cells that contain an abnormal number of chromosomes. Aneuploidy may incite cell death, developmental defects (including genetic syndromes), and cancer (>90% of all cancer cells are aneuploid). While kinetochores and their activities have been preserved through evolution, the CEN DNA sequences have not. Hence, to be recognized as sites for kinetochore assembly, CEN display conserved structural themes. In addition, CEN nucleosomes enclose a CEN-exclusive variant of histone H3, named CENP-A, and carry distinct epigenetic labels on CENP-A and the other CEN histone proteins. Through the cell cycle, CEN are transcribed into non-coding RNAs. After subsequent processing, they become key components of the CEN chromatin by marking the CEN locus and by stably anchoring the CEN-binding kinetochore proteins. CEN transcription is tightly regulated, of low intensity, and essential for differentiation and development. Under- or overexpression of CEN transcripts, as documented for myriad cancers, provoke chromosome missegregation and aneuploidy. CEN are genetically stable and fully competent only when they are insulated from the surrounding, pericentromeric chromatin, which must be silenced. We will review CEN transcription and its contribution to faithful kinetochore function. We will further discuss how pericentromeric chromatin is silenced by RNA processing and transcriptionally repressive chromatin marks. We will report on the transcriptional misregulation of (peri)centromeres during stress, natural aging, and disease and reflect on whether their transcripts can serve as future diagnostic tools and anti-cancer targets in the clinic.
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Affiliation(s)
- Ksenia Smurova
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Peter De Wulf
- Centre for Integrative Biology, University of Trento, Trento, Italy
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Yan K, Zhang Z, Yang J, McLaughlin SH, Barford D. Architecture of the CBF3-centromere complex of the budding yeast kinetochore. Nat Struct Mol Biol 2018; 25:1103-1110. [PMID: 30478265 PMCID: PMC6292502 DOI: 10.1038/s41594-018-0154-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023]
Abstract
Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4. Deposition of Cse4 at CEN loci is dependent on the CBF3 complex that engages CDEIII to direct Cse4 nucleosomes to CDEII. To understand how CBF3 recognizes CDEIII and positions Cse4, we determined a cryo-EM structure of a CBF3-CEN complex. CBF3 interacts with CEN DNA as a head-to-head dimer that includes the whole of CDEIII and immediate 3' regions. Specific CEN-binding of CBF3 is mediated by a Cep3 subunit of one of the CBF3 protomers that forms major groove interactions with the conserved and essential CCG and TGT motifs of CDEIII. We propose a model for a CBF3-Cse4-CEN complex with implications for understanding CBF3-directed deposition of the Cse4 nucleosome at CEN loci.
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Affiliation(s)
- Kaige Yan
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge, UK
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