1
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Pradhan B, Kanno T, Umeda Igarashi M, Loke MS, Baaske MD, Wong JSK, Jeppsson K, Björkegren C, Kim E. The Smc5/6 complex is a DNA loop-extruding motor. Nature 2023; 616:843-848. [PMID: 37076626 PMCID: PMC10132971 DOI: 10.1038/s41586-023-05963-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 03/16/2023] [Indexed: 04/21/2023]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes are essential for the spatial organization of chromosomes1. Whereas cohesin and condensin organize chromosomes by extrusion of DNA loops, the molecular functions of the third eukaryotic SMC complex, Smc5/6, remain largely unknown2. Using single-molecule imaging, we show that Smc5/6 forms DNA loops by extrusion. Upon ATP hydrolysis, Smc5/6 reels DNA symmetrically into loops at a force-dependent rate of one kilobase pair per second. Smc5/6 extrudes loops in the form of dimers, whereas monomeric Smc5/6 unidirectionally translocates along DNA. We also find that the subunits Nse5 and Nse6 (Nse5/6) act as negative regulators of loop extrusion. Nse5/6 inhibits loop-extrusion initiation by hindering Smc5/6 dimerization but has no influence on ongoing loop extrusion. Our findings reveal functions of Smc5/6 at the molecular level and establish DNA loop extrusion as a conserved mechanism among eukaryotic SMC complexes.
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Affiliation(s)
| | - Takaharu Kanno
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Miki Umeda Igarashi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Mun Siong Loke
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | | | - Kristian Jeppsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Camilla Björkegren
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
| | - Eugene Kim
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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2
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Katsumata K, Ichikawa Y, Fuse T, Kurumizaka H, Yanagida A, Urano T, Kato H, Shimizu M. Sequence-dependent nucleosome formation in trinucleotide repeats evaluated by in vivo chemical mapping. Biochem Biophys Res Commun 2021; 556:179-184. [PMID: 33839413 DOI: 10.1016/j.bbrc.2021.03.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 03/28/2021] [Indexed: 11/18/2022]
Abstract
Trinucleotide repeat sequences (TRSs), consisting of 10 unique classes of repeats in DNA, are members of microsatellites and abundantly and non-randomly distributed in many eukaryotic genomes. The lengths of TRSs are mutable, and the expansions of several TRSs are implicated in hereditary neurological diseases. However, the underlying causes of the biased distribution and the dynamic properties of TRSs in the genome remain elusive. Here, we examined the effects of TRSs on nucleosome formation in vivo by histone H4-S47C site-directed chemical cleavages, using well-defined yeast minichromosomes in which each of the ten TRS classes resided in the central region of a positioned nucleosome. We showed that (AAT)12 and (ACT)12 act as strong nucleosome-promoting sequences, while (AGG)12 and (CCG)12 act as nucleosome-excluding sequences in vivo. The local histone binding affinity scores support the idea that nucleosome formation in TRSs, except for (AGG)12, is mainly determined by the affinity for the histone octamers. Overall, our study presents a framework for understanding the nucleosome-forming abilities of TRSs.
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Affiliation(s)
- Koji Katsumata
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan
| | - Yuichi Ichikawa
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Tomohiro Fuse
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Akio Yanagida
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan
| | - Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan
| | - Mitsuhiro Shimizu
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan.
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3
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Guin K, Chen Y, Mishra R, Muzaki SRBM, Thimmappa BC, O'Brien CE, Butler G, Sanyal A, Sanyal K. Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres. eLife 2020; 9:e58556. [PMID: 32469306 PMCID: PMC7292649 DOI: 10.7554/elife.58556] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Centromeres of Candida albicans form on unique and different DNA sequences but a closely related species, Candida tropicalis, possesses homogenized inverted repeat (HIR)-associated centromeres. To investigate the mechanism of centromere type transition, we improved the fragmented genome assembly and constructed a chromosome-level genome assembly of C. tropicalis by employing PacBio sequencing, chromosome conformation capture sequencing (3C-seq), chromoblot, and genetic analysis of engineered aneuploid strains. Further, we analyzed the 3D genome organization using 3C-seq data, which revealed spatial proximity among the centromeres as well as telomeres of seven chromosomes in C. tropicalis. Intriguingly, we observed evidence of inter-centromeric translocations in the common ancestor of C. albicans and C. tropicalis. Identification of putative centromeres in closely related Candida sojae, Candida viswanathii and Candida parapsilosis indicates loss of ancestral HIR-associated centromeres and establishment of evolutionary new centromeres (ENCs) in C. albicans. We propose that spatial proximity of the homologous centromere DNA sequences facilitated karyotype rearrangements and centromere type transitions in human pathogenic yeasts of the CUG-Ser1 clade.
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Affiliation(s)
- Krishnendu Guin
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Yao Chen
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Radha Mishra
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | | | - Bhagya C Thimmappa
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Caoimhe E O'Brien
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Geraldine Butler
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
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4
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Dauban L, Montagne R, Thierry A, Lazar-Stefanita L, Bastié N, Gadal O, Cournac A, Koszul R, Beckouët F. Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners. Mol Cell 2020; 77:1279-1293.e4. [PMID: 32032532 DOI: 10.1016/j.molcel.2020.01.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 09/24/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Cohesin, a member of the SMC complex family, holds sister chromatids together but also shapes chromosomes by promoting the formation of long-range intra-chromatid loops, a process proposed to be mediated by DNA loop extrusion. Here we describe the roles of three cohesin partners, Pds5, Wpl1, and Eco1, in loop formation along either unreplicated or mitotic Saccharomyces cerevisiae chromosomes. Pds5 limits the size of DNA loops via two different pathways: the canonical Wpl1-mediated releasing activity and an Eco1-dependent mechanism. In the absence of Pds5, the main barrier to DNA loop expansion appears to be the centromere. Our data also show that Eco1 acetyl-transferase inhibits the translocase activity that powers loop formation and contributes to the positioning of loops through a mechanism that is distinguishable from its role in cohesion establishment. This study reveals that the mechanisms regulating cohesin-dependent chromatin loops are conserved among eukaryotes while promoting different functions.
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Affiliation(s)
- Lise Dauban
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Rémi Montagne
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Nathalie Bastié
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Axel Cournac
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France.
| | - Frédéric Beckouët
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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5
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Abstract
DNA-strand breaks influence structure and function of chromosomes in diverse ways, and it is essential to analyze the lesions to understand behaviors of genetic information. For researchers in a wide array of fields including recombination, repair, and DNA damage response, efficient and easy detection of DNA breaks is of paramount importance. Among several procedures suitable for this purpose, a method to directly observe broken chromosomes by pulsed-field gel electrophoresis, using the fission yeast Schizosaccharomyces pombe as a model organism, is described in this chapter. Because S. pombe chromosomes are megabase-size, careful attention should be paid to maintain DNA as intact as possible. The protocol includes induction of DNA breaks, preparation of chromosomes, and separation of chromosomal DNA by PFGE. This procedure can be applicable to other species as well as other experiments handling large-size DNA molecules.
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Affiliation(s)
- Takatomi Yamada
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan.
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Hiroshi Murakami
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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6
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Schalbetter SA, Fudenberg G, Baxter J, Pollard KS, Neale MJ. Principles of meiotic chromosome assembly revealed in S. cerevisiae. Nat Commun 2019; 10:4795. [PMID: 31641121 PMCID: PMC6805904 DOI: 10.1038/s41467-019-12629-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we use Saccharomyces cerevisiae to explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent in S. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process.
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Affiliation(s)
- Stephanie A Schalbetter
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Geoffrey Fudenberg
- Gladstone Institutes for Data Science and Biotechnology, San Francisco, USA.
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Katherine S Pollard
- Gladstone Institutes for Data Science and Biotechnology, San Francisco, USA.
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
| | - Matthew J Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
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7
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Socol M, Wang R, Jost D, Carrivain P, Vaillant C, Le Cam E, Dahirel V, Normand C, Bystricky K, Victor JM, Gadal O, Bancaud A. Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes. Nucleic Acids Res 2019; 47:6195-6207. [PMID: 31114898 PMCID: PMC6614813 DOI: 10.1093/nar/gkz374] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/25/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023] Open
Abstract
DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of -0.3 to -0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in 'theta' conditions, in which they are poised for compartmentalization and phase separation.
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Affiliation(s)
- Marius Socol
- LAAS-CNRS, Université de Toulouse, CNRS, F-31400 Toulouse, France
- IRIM, CNRS, University of Montpellier, France
| | - Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
- Material Science & Engineering School, Henan University of Technology, 450001 Zhengzhou, P.R. China
| | - Daniel Jost
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Pascal Carrivain
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
| | - Cédric Vaillant
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
| | - Eric Le Cam
- Genome Maintenance and Molecular Microscopy UMR8126, CNRS, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex France
| | - Vincent Dahirel
- Sorbonne Université, CNRS, Physicochimie des Electrolytes et Nanosystèmes interfaciaux, laboratoire PHENIX, F-75005 Paris, France
| | - Christophe Normand
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Jean-Marc Victor
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, F-75005 Paris, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Aurélien Bancaud
- LAAS-CNRS, Université de Toulouse, CNRS, F-31400 Toulouse, France
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8
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Tan HL, Lim KK, Yang Q, Fan JS, Sayed AMM, Low LS, Ren B, Lim TK, Lin Q, Mok YK, Liou YC, Chen ES. Prolyl isomerization of the CENP-A N-terminus regulates centromeric integrity in fission yeast. Nucleic Acids Res 2019; 46:1167-1179. [PMID: 29194511 DOI: 10.1093/nar/gkx1180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/22/2017] [Indexed: 01/15/2023] Open
Abstract
Centromeric identity and chromosome segregation are determined by the precise centromeric targeting of CENP-A, the centromere-specific histone H3 variant. The significance of the amino-terminal domain (NTD) of CENP-A in this process remains unclear. Here, we assessed the functional significance of each residue within the NTD of CENP-A from Schizosaccharomyces pombe (SpCENP-A) and identified a proline-rich 'GRANT' (Genomic stability-Regulating site within CENP-A N-Terminus) motif that is important for CENP-A function. Through sequential mutagenesis, we show that GRANT proline residues are essential for coordinating SpCENP-A centromeric targeting. GRANT proline-15 (P15), in particular, undergoes cis-trans isomerization to regulate chromosome segregation fidelity, which appears to be carried out by two FK506-binding protein (FKBP) family prolyl cis-trans isomerases. Using proteomics analysis, we further identified the SpCENP-A-localizing chaperone Sim3 as a SpCENP-A NTD interacting protein that is dependent on GRANT proline residues. Ectopic expression of sim3+ complemented the chromosome segregation defect arising from the loss of these proline residues. Overall, cis-trans proline isomerization is a post-translational modification of the SpCENP-A NTD that confers precise propagation of centromeric integrity in fission yeast, presumably via targeting SpCENP-A to the centromere.
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Affiliation(s)
- Hwei Ling Tan
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
| | - Kim Kiat Lim
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
| | - Qiaoyun Yang
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | | | - Liy Sim Low
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
| | - Bingbing Ren
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Yu-Keung Mok
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456 Singapore
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456 Singapore
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9
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Abstract
The three-dimensional (3D) genome structure is highly ordered by a hierarchy of organizing events ranging from enhancer-promoter or gene-gene contacts to chromosomal territorial arrangement. It is becoming clear that the cohesin and condensin complexes are key molecular machines that organize the 3D genome structure. These complexes are highly conserved from simple systems, e.g., yeast cells, to the much more complex human system. Therefore, knowledge from the budding and fission yeast systems illuminates highly conserved molecular mechanisms of how cohesin and condensin establish the functional 3D genome structures. Here I discuss how these complexes are recruited across the yeast genomes, mediate distinct genome-organizing events such as gene contacts and topological domain formation, and participate in important nuclear activities including transcriptional regulation and chromosomal dynamics.
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Affiliation(s)
- Ken-Ichi Noma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA;
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10
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Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J. SMC complexes differentially compact mitotic chromosomes according to genomic context. Nat Cell Biol 2017; 19:1071-1080. [PMID: 28825700 PMCID: PMC5640152 DOI: 10.1038/ncb3594] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/19/2017] [Indexed: 12/26/2022]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae. The canonical role of cohesin is to co-align sister chromatids, while condensin generally compacts mitotic chromosomes. We find strikingly different roles for the two complexes in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion. Polymer simulations demonstrate that this role can be fully accounted for through cis-looping of chromatin. Second, condensin is generally dispensable for compaction along chromosome arms. Instead, it plays a targeted role compacting the rDNA proximal regions and promoting resolution of peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that distinct SMC-dependent looping activities are selectively deployed to appropriately compact chromosomes.
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MESH Headings
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Structures
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- Computer Simulation
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Mitosis
- Models, Genetic
- Models, Molecular
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Nucleic Acid Conformation
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Structure-Activity Relationship
- Cohesins
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Affiliation(s)
| | - Anton Goloborodko
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jon-Matthew Belton
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Catrina Miles
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Miao Yu
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Leonid Mirny
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jonathan Baxter
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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11
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Katsumata K, Nishi E, Afrin S, Narusawa K, Yamamoto A. Position matters: multiple functions of LINC-dependent chromosome positioning during meiosis. Curr Genet 2017; 63:1037-1052. [PMID: 28493118 DOI: 10.1007/s00294-017-0699-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/14/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022]
Abstract
Chromosome positioning is crucial for multiple chromosomal events, including DNA replication, repair, and recombination. The linker of nucleoskeleton and cytoskeleton (LINC) complexes, which consist of conserved nuclear membrane proteins, were shown to control chromosome positioning and facilitate various biological processes by interacting with the cytoskeleton. However, the precise functions and regulation of LINC-dependent chromosome positioning are not fully understood. During meiosis, the LINC complexes induce clustering of telomeres, forming the bouquet chromosome arrangement, which promotes homologous chromosome pairing. In fission yeast, the bouquet forms through LINC-dependent clustering of telomeres at the spindle pole body (SPB, the centrosome equivalent in fungi) and detachment of centromeres from the SPB-localized LINC. It was recently found that, in fission yeast, the bouquet contributes to formation of the spindle and meiotic centromeres, in addition to homologous chromosome pairing, and that centromere detachment is linked to telomere clustering, which is crucial for proper spindle formation. Here, we summarize these findings and show that the bouquet chromosome arrangement also contributes to nuclear fusion during karyogamy. The available evidence suggests that these functions are universal among eukaryotes. The findings demonstrate that LINC-dependent chromosome positioning performs multiple functions and controls non-chromosomal as well as chromosomal events, and that the chromosome positioning is stringently regulated for its functions. Thus, chromosome positioning plays a much broader role and is more strictly regulated than previously thought.
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Affiliation(s)
- Kazuhiro Katsumata
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Eriko Nishi
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Sadia Afrin
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Kaoru Narusawa
- Department of Chemistry, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Ayumu Yamamoto
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8529, Japan.
- Department of Chemistry, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8529, Japan.
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12
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Kulemzina I, Ang K, Zhao X, Teh JT, Verma V, Suranthran S, Chavda AP, Huber RG, Eisenhaber B, Eisenhaber F, Yan J, Ivanov D. A Reversible Association between Smc Coiled Coils Is Regulated by Lysine Acetylation and Is Required for Cohesin Association with the DNA. Mol Cell 2016; 63:1044-54. [PMID: 27618487 DOI: 10.1016/j.molcel.2016.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 03/07/2016] [Accepted: 08/05/2016] [Indexed: 12/16/2022]
Abstract
Cohesin is a ring-shaped protein complex that is capable of embracing DNA. Most of the ring circumference is comprised of the anti-parallel intramolecular coiled coils of the Smc1 and Smc3 proteins, which connect globular head and hinge domains. Smc coiled coil arms contain multiple acetylated and ubiquitylated lysines. To investigate the role of these modifications, we substituted lysines for arginines to mimic the unmodified state and uncovered genetic interaction between the Smc arms. Using scanning force microscopy, we show that wild-type Smc arms associate with each other when the complex is not on DNA. Deacetylation of the Smc1/Smc3 dimers promotes arms' dissociation. Smc arginine mutants display loose packing of the Smc arms and, although they dimerize at the hinges, fail to connect the heads and associate with the DNA. Our findings highlight the importance of a "collapsed ring," or "rod," conformation of cohesin for its loading on the chromosomes.
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MESH Headings
- Acetylation
- Amino Acid Substitution
- Animals
- Arginine/metabolism
- Baculoviridae/genetics
- Baculoviridae/metabolism
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromatids/chemistry
- Chromatids/metabolism
- Chromatids/ultrastructure
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/metabolism
- Chromosomes, Fungal/ultrastructure
- Cloning, Molecular
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- Gene Expression
- Gene Expression Regulation, Fungal
- Lysine/metabolism
- Protein Conformation, alpha-Helical
- Protein Interaction Domains and Motifs
- Protein Processing, Post-Translational
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sf9 Cells
- Signal Transduction
- Spodoptera
- Cohesins
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Affiliation(s)
- Irina Kulemzina
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore; Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen 72076, Germany
| | - Keven Ang
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Xiaodan Zhao
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Jun-Thing Teh
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Vikash Verma
- Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen 72076, Germany
| | | | - Alap P Chavda
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Roland G Huber
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | | | - Frank Eisenhaber
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore; School of Computer Engineering, Nanyang Technological University, Singapore 637553, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117597, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Physics, National University of Singapore, Singapore 117551, Singapore; Center for Bioimaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Dmitri Ivanov
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen 72076, Germany; Department of Physics, National University of Singapore, Singapore 117551, Singapore.
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13
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Sasano Y, Nagasawa K, Kaboli S, Sugiyama M, Harashima S. CRISPR-PCS: a powerful new approach to inducing multiple chromosome splitting in Saccharomyces cerevisiae. Sci Rep 2016; 6:30278. [PMID: 27530680 PMCID: PMC4987674 DOI: 10.1038/srep30278] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/27/2016] [Indexed: 12/31/2022] Open
Abstract
PCR-mediated chromosome splitting (PCS) was developed in the yeast Saccharomyces cerevisiae. It is based on homologous recombination and enables division of a chromosome at any point to form two derived and functional chromosomes. However, because of low homologous recombination activity, PCS is limited to a single site at a time, which makes the splitting of multiple loci laborious and time-consuming. Here we have developed a highly efficient and versatile chromosome engineering technology named CRISPR-PCS that integrates PCS with the novel genome editing CRISPR/Cas9 system. This integration allows PCS to utilize induced double strand breaks to activate homologous recombination. CRISPR-PCS enhances the efficiency of chromosome splitting approximately 200-fold and enables generation of simultaneous multiple chromosome splits. We propose that CRISPR-PCS will be a powerful tool for breeding novel yeast strains with desirable traits for specific industrial applications and for investigating genome function.
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Affiliation(s)
- Yu Sasano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Koki Nagasawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Saeed Kaboli
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Minetaka Sugiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Satoshi Harashima
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, Ikeda 4-22-1, Kumamoto, 860-0082, Japan
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14
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Ichikawa Y, Morohashi N, Tomita N, Mitchell AP, Kurumizaka H, Shimizu M. Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo. Biochem Biophys Res Commun 2016; 476:57-62. [PMID: 27208777 DOI: 10.1016/j.bbrc.2016.05.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022]
Abstract
Nucleosome-depleted regions (NDRs) (also called nucleosome-free regions or NFRs) are often found in the promoter regions of many yeast genes, and are formed by multiple mechanisms, including the binding of activators and enhancers, the actions of chromatin remodeling complexes, and the specific DNA sequences themselves. However, it remains unclear whether NDR formation per se is essential for transcriptional activation. Here, we examined the relationship between nucleosome organization and gene expression using a defined yeast reporter system, consisting of the CYC1 minimal core promoter and the lacZ gene. We introduced simple repeated sequences that should be either incorporated in nucleosomes or excluded from nucleosomes in the site upstream of the TATA boxes. The (CTG)12, (GAA)12 and (TGTAGG)6 inserts were incorporated into a positioned nucleosome in the core promoter region, and did not affect the reporter gene expression. In contrast, the insertion of (CGG)12, (TTAGGG)6, (A)34 or (CG)8 induced lacZ expression by 10-20 fold. Nucleosome mapping analyses revealed that the inserts that induced the reporter gene expression prevented nucleosome formation, and created an NDR upstream of the TATA boxes. Thus, our results demonstrated that NDR formation dictated by DNA sequences is sufficient for transcriptional activation from the core promoter in vivo.
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Affiliation(s)
- Yuichi Ichikawa
- Graduate School of Advanced Science and Engineering/RISE, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8640, Japan; Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Nobuyuki Morohashi
- Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Nobuyuki Tomita
- Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Aaron P Mitchell
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering/RISE, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Mitsuhiro Shimizu
- Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan.
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15
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Eeftens JM, Katan AJ, Kschonsak M, Hassler M, de Wilde L, Dief EM, Haering CH, Dekker C. Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic. Cell Rep 2016; 14:1813-8. [PMID: 26904946 PMCID: PMC4785793 DOI: 10.1016/j.celrep.2016.01.063] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/21/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022] Open
Abstract
Structural maintenance of chromosomes (SMC) protein complexes, including cohesin and condensin, play key roles in the regulation of higher-order chromosome organization. Even though SMC proteins are thought to mechanistically determine the function of the complexes, their native conformations and dynamics have remained unclear. Here, we probe the topology of Smc2-Smc4 dimers of the S. cerevisiae condensin complex with high-speed atomic force microscopy (AFM) in liquid. We show that the Smc2-Smc4 coiled coils are highly flexible polymers with a persistence length of only ∼ 4 nm. Moreover, we demonstrate that the SMC dimers can adopt various architectures that interconvert dynamically over time, and we find that the SMC head domains engage not only with each other, but also with the hinge domain situated at the other end of the ∼ 45-nm-long coiled coil. Our findings reveal structural properties that provide insights into the molecular mechanics of condensin complexes.
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Affiliation(s)
- Jorine M Eeftens
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands
| | - Allard J Katan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands
| | - Marc Kschonsak
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Markus Hassler
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Liza de Wilde
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands
| | - Essam M Dief
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands.
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16
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Gürsoy G, Xu Y, Liang J. Computational predictions of structures of multichromosomes of budding yeast. Annu Int Conf IEEE Eng Med Biol Soc 2015; 2014:3945-8. [PMID: 25570855 DOI: 10.1109/embc.2014.6944487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Knowledge of the global architecture of the cell nucleus and the spatial organization of genome is critical for understanding gene expression and nuclear function. Single-cell imaging techniques provide a wealth of information on the spatial organization of chromosomes. Computational tools for modelling chromosome structure have broad implications in studying the effect of cell nucleus on higher-order genome organization. Here we describe a multichromosome constrained self-avoiding chromatin model for studying ensembles of genome structural models of budding yeast nucleus. We successfully generated a large number of model genomes of yeast with appropriate chromatin fiber diameter, persistence length, and excluded volume under spatial confinement. By incorporating details of the constraints from single-cell imaging studies, our method can model the budding yeast genome realistically. The model developed here provides a general computational framework for studying the overall architecture of budding yeast genome.
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17
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Hsieh THS, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell 2015; 162:108-19. [PMID: 26119342 DOI: 10.1016/j.cell.2015.05.048] [Citation(s) in RCA: 413] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/23/2015] [Accepted: 04/29/2015] [Indexed: 11/18/2022]
Abstract
We describe a Hi-C-based method, Micro-C, in which micrococcal nuclease is used instead of restriction enzymes to fragment chromatin, enabling nucleosome resolution chromosome folding maps. Analysis of Micro-C maps for budding yeast reveals abundant self-associating domains similar to those reported in other species, but not previously observed in yeast. These structures, far shorter than topologically associating domains in mammals, typically encompass one to five genes in yeast. Strong boundaries between self-associating domains occur at promoters of highly transcribed genes and regions of rapid histone turnover that are typically bound by the RSC chromatin-remodeling complex. Investigation of chromosome folding in mutants confirms roles for RSC, "gene looping" factor Ssu72, Mediator, H3K56 acetyltransferase Rtt109, and the N-terminal tail of H4 in folding of the yeast genome. This approach provides detailed structural maps of a eukaryotic genome, and our findings provide insights into the machinery underlying chromosome compaction.
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Affiliation(s)
- Tsung-Han S Hsieh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Assaf Weiner
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Bryan Lajoie
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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18
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Abstract
We studied the 3D structural organization of the fission yeast genome, which emerges from the tethering of heterochromatic regions in otherwise randomly configured chromosomes represented as flexible polymer chains in an nuclear environment. This model is sufficient to explain in a statistical manner many experimentally determined distinctive features of the fission yeast genome, including chromatin interaction patterns from Hi-C experiments and the co-locations of functionally related and co-expressed genes, such as genes expressed by Pol-III. Our findings demonstrate that some previously described structure-function correlations can be explained as a consequence of random chromatin collisions driven by a few geometric constraints (mainly due to centromere-SPB and telomere-NE tethering) combined with the specific gene locations in the chromosome sequence. We also performed a comparative analysis between the fission and budding yeast genome structures, for which we previously detected a similar organizing principle. However, due to the different chromosome sizes and numbers, substantial differences are observed in the 3D structural genome organization between the two species, most notably in the nuclear locations of orthologous genes, and the extent of nuclear territories for genes and chromosomes. However, despite those differences, remarkably, functional similarities are maintained, which is evident when comparing spatial clustering of functionally related genes in both yeasts. Functionally related genes show a similar spatial clustering behavior in both yeasts, even though their nuclear locations are largely different between the yeast species.
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Affiliation(s)
- Ke Gong
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States of America
| | - Harianto Tjong
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States of America
| | - Xianghong Jasmine Zhou
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States of America
- * E-mail: (FA); (XJZ)
| | - Frank Alber
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States of America
- * E-mail: (FA); (XJZ)
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19
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Kruse K, Sewitz S, Babu MM. A complex network framework for unbiased statistical analyses of DNA-DNA contact maps. Nucleic Acids Res 2013; 41:701-10. [PMID: 23175602 PMCID: PMC3553935 DOI: 10.1093/nar/gks1096] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/17/2012] [Accepted: 10/19/2012] [Indexed: 01/08/2023] Open
Abstract
Experimental techniques for the investigation of three-dimensional (3D) genome organization are being developed at a fast pace. Currently, the associated computational methods are mostly specific to the individual experimental approach. Here we present a general statistical framework that is widely applicable to the analysis of genomic contact maps, irrespective of the data acquisition and normalization processes. Within this framework DNA-DNA contact data are represented as a complex network, for which a broad number of directly applicable methods already exist. In such a network representation, DNA segments and contacts between them are denoted as nodes and edges, respectively. Furthermore, we present a robust method for generating randomized contact networks that explicitly take into account the inherent 3D nature of the genome and serve as realistic null-models for unbiased statistical analyses. By integrating a variety of large-scale genome-wide datasets we demonstrate that meiotic crossover sites display enriched genomic contacts and that cohesin-bound genes are significantly colocalized in the yeast nucleus. We anticipate that the complex network framework in conjunction with the randomization of DNA-DNA contact networks will become a widely used tool in the study of nuclear architecture.
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Affiliation(s)
- Kai Kruse
- Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH and Department of Biochemistry, Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Sven Sewitz
- Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH and Department of Biochemistry, Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - M. Madan Babu
- Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH and Department of Biochemistry, Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
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21
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Perriches T, Singleton MR. Structure of yeast kinetochore Ndc10 DNA-binding domain reveals unexpected evolutionary relationship to tyrosine recombinases. J Biol Chem 2012; 287:5173-9. [PMID: 22215672 PMCID: PMC3281669 DOI: 10.1074/jbc.c111.318501] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/21/2011] [Indexed: 11/06/2022] Open
Abstract
We have solved the x-ray structure of the N-terminal half of the yeast kinetochore protein Ndc10 at 1.9 Å resolution. This essential protein is a key constituent of the budding yeast centromere and is essential for the recruitment of the centromeric nucleosome and establishment of the kinetochore. The fold of the protein shows unexpected similarities to the tyrosine recombinase/λ-integrase family of proteins, most notably Cre, with some variation in the relative position of the subdomains. This finding offers new insights into kinetochore evolution and the adaptation of a well studied protein fold to a novel role. By comparison with tyrosine recombinases and mutagenesis studies, we have been able to define some of the key DNA-binding motifs.
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Affiliation(s)
- Thibaud Perriches
- From the Macromolecular Structure and Function Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
| | - Martin R. Singleton
- From the Macromolecular Structure and Function Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
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22
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Abstract
Cohesin is a member of the Smc family of protein complexes that mediates higher-order chromosome structure by tethering different regions of chromatin. We present a new in vitro system that assembles cohesin-DNA complexes with in vivo properties. The assembly of these physiological salt-resistant complexes requires the cohesin holo-complex, its ability to bind ATP, the cohesin loader Scc2p and a closed DNA topology. Both the number of cohesin molecules bound to the DNA substrate and their distribution on the DNA substrate are limited. Cohesin and Scc2p bind preferentially to cohesin associated regions (CARs), DNA sequences with enriched cohesin binding in vivo. A subsequence of CARC1 promotes cohesin binding to neighboring sequences within CARC1. The enhancer-like function of this sequence is validated by in vivo deletion analysis. By demonstrating the physiological relevance of these in vitro assembled cohesin-DNA complexes, we establish our in vitro system as a powerful tool to elucidate the mechanism of cohesin and other Smc complexes.
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Affiliation(s)
- Itay Onn
- Howard Hughes Medical Institute
- Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, MD 21218; and
| | - Douglas Koshland
- Howard Hughes Medical Institute
- Department of Molecular and Cell Biology, University of California, Berkeley, 16 Barker Hall #3202, Berkeley, CA 94720-3202
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23
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Abstract
The evolutionarily conserved cohesin proteins Smc1, Smc3, Rad21 (Mcd1), and Scc3 function in the cohesin complex that provides the basis for chromosome cohesion and is involved in gene regulation. Understanding how these proteins link together the genome requires the use of whole-genome approaches to study the molecular mechanisms of these essential proteins. While chromatin immunoprecipitation followed by DNA microarray (ChIP-chip) studies have provided a snapshot in time of where these proteins associate with various genomes, the cohesin proteins are dynamic in their localization and interactions on chromatin. Study of the dynamic nature of these proteins requires approaches such as live cell imaging. We present evidence from fluorescence loss in photobleaching (FLIP) experiments in budding yeast that the decay constant of each cohesin subunit is approximately 60-90 s in interphase. The decay constant on chromatin increases from G(1) to S phase to metaphase, consistent with the interaction with chromatin becoming more stable once chromosomes are cohered. A small population of Smc3 at a position consistent with centromeric location has a longer decay constant than bulk Smc3. The characterization of the interaction of cohesin with chromatin, in terms of both its position and its dynamics, may be key to understanding how this protein complex contributes to chromosome segregation and gene regulation.
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Affiliation(s)
- Adrian J McNairn
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
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24
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Knoch TA, Göker M, Lohner R, Abuseiris A, Grosveld FG. Fine-structured multi-scaling long-range correlations in completely sequenced genomes--features, origin, and classification. Eur Biophys J 2009; 38:757-79. [PMID: 19533117 PMCID: PMC2701493 DOI: 10.1007/s00249-009-0489-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 05/05/2009] [Accepted: 05/13/2009] [Indexed: 11/26/2022]
Abstract
The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 × 106 to 3.0 × 107 bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens. The local correlation coefficients show a species-specific multi-scaling behaviour: close to random correlations on the scale of a few base pairs, a first maximum from 40 to 3,400 bp (for Arabidopsis thaliana and Drosophila melanogaster divided in two submaxima), and often a region of one or more second maxima from 105 to 3 × 105 bp. Within this multi-scaling behaviour, an additional fine-structure is present and attributable to codon usage in all except the human sequences, where it is related to nucleosomal binding. Computer-generated random sequences assuming a block organization of genomes, the codon usage, and nucleosomal binding explain these results. Mutation by sequence reshuffling destroyed all correlations. Thus, the stability of correlations seems to be evolutionarily tightly controlled and connected to the spatial genome organization, especially on large scales. In summary, genomes show a complex sequential organization related closely to their three-dimensional organization.
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MESH Headings
- Algorithms
- Animals
- Arabidopsis/genetics
- Chromosomes/chemistry
- Chromosomes/genetics
- Chromosomes/ultrastructure
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/ultrastructure
- Chromosomes, Human/chemistry
- Chromosomes, Human/genetics
- Chromosomes, Human/ultrastructure
- Chromosomes, Plant/chemistry
- Chromosomes, Plant/genetics
- Chromosomes, Plant/ultrastructure
- Codon/chemistry
- Computer Simulation
- DNA/chemistry
- Drosophila melanogaster/genetics
- Genome
- Humans
- Models, Genetic
- Mutation
- Nucleosomes/chemistry
- Saccharomyces cerevisiae/genetics
- Schizosaccharomyces/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Tobias A Knoch
- Biophysical Genomics, Cell Biology and Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
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25
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Schmidt CK, Brookes N, Uhlmann F. Conserved features of cohesin binding along fission yeast chromosomes. Genome Biol 2009; 10:R52. [PMID: 19454013 PMCID: PMC2718518 DOI: 10.1186/gb-2009-10-5-r52] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2008] [Revised: 03/06/2009] [Accepted: 05/19/2009] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Cohesin holds sister chromatids together to enable their accurate segregation in mitosis. How, and where, cohesin binds to chromosomes are still poorly understood, and recent genome-wide surveys have revealed an apparent disparity between its chromosomal association patterns in different organisms. RESULTS Here, we present the high-resolution analysis of cohesin localization along fission yeast chromosomes. This reveals that several determinants, thought specific for different organisms, come together to shape the overall distribution. Cohesin is detected at chromosomal loading sites, characterized by the cohesin loader Mis4/Ssl3, in regions of strong transcriptional activity. Cohesin also responds to transcription by downstream translocation and accumulation at convergent transcriptional terminators surrounding the loading sites. As cells enter mitosis, a fraction of cohesin leaves chromosomes in a cleavage-independent reaction, while a substantial pool of cohesin dissociates when it is cleaved at anaphase onset. We furthermore observe that centromeric cohesin spreads out onto chromosome arms during mitosis, dependent on Aurora B kinase activity, emphasizing the plasticity of cohesin behavior. CONCLUSIONS Our findings suggest that features that were thought to differentiate cohesin between organisms collectively define the overall behavior of fission yeast cohesin. Apparent differences between organisms might reflect an emphasis on different aspects, rather than different principles, of cohesin action.
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Affiliation(s)
- Christine K Schmidt
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, UK
- Current address: National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Neil Brookes
- Bioinformatics and Biostatistics Service, Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, UK
- Current address: Trinity Centre for High Performance Computing, Trinity College, Dublin 2, Ireland
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, UK
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26
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Abstract
The fission yeast Schizosaccharomyces pombe has provided a useful experimental system to study nuclear structures during meiosis. Unlike many higher animals in which meiosis takes place only in specialized tissues deep inside their bodies, S. pombe is a unicellular eukaryote and its meiosis can be induced simply by depleting nitrogen sources from the culture medium. The entire process of meiosis is completed within several hours, and thus can be followed in individual living cells. These features provide ease of microscopic observation. A more trivial merit is its rod-like cell shape, which aids microscopic observation, as the long axis of cells is kept in the microscope image plane. Here we describe methods for induction of meiosis and fluorescence microscopy observation in living cells of S. pombe.
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Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Suita, Japan
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27
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Abstract
The fission yeast, Schizosaccharomyces pombe, much like the budding yeast, is a particularly well-suited model organism for genetic research. However, the miniscule size of both yeasts' nuclei has hindered their success as research models for cytologists. A solution to this problem is provided by the spreading of nuclei, which increases their volume and allows for a better spatial resolution of nuclear contents. Here we describe nuclear spreading in fission yeast. Spreading of meiotic nuclei is particularly helpful in exposing the linear elements (LinEs), which are the fission yeasts' rudimentary version of the synaptonemal complex. Although the LinEs' role is still not fully understood, they serve as important meiotic hallmarks and their presence and morphology can be used in characterizing meiotic mutants. We first describe methods to induce meiosis in liquid cell cultures, then outline a method to break down cell and nuclear membranes by detergent treatment to release chromatin on cytological slides, and finally provide a set of protocols for analyzing these nuclei by immunostaining and fluorescence in situ hybridization (FISH), and by electron microscopy.
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Affiliation(s)
- Josef Loidl
- Department of Chromosome Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
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28
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Maruthachalam K, Nair V, Rho HS, Choi J, Kim S, Lee YH. Agrobacterium tumefaciens-mediated transformation in Colletotrichum falcatum and C. acutatum. J Microbiol Biotechnol 2008; 18:234-241. [PMID: 18309266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Agrobacterium tumefaciens-mediated transformation (ATMT) is becoming an effective system as an insertional mutagenesis tool in filamentous fungi. We developed and optimized ATMT for two Colletotrichum species, C. falcatum and C. acutatum, which are the causal agents of sugarcane red rot and pepper anthracnose, respectively. A. tumefaciens strain SK1044, carrying a hygromycin phosphotransferase gene (hph) and a green fluorescent protein (GFP) gene, was used to transform the conidia of these two Colletotrichum species. Transformation efficiency was correlated with cocultivation time and bacterial cell concentration and was higher in C. falcatum than in C. acutatum. Southern blot analysis indicated that about 65% of the transformants had a single copy of the T-DNA in both C. falcatum and C. acutatum and that T-DNA integrated randomly in both fungal genomes. T-DNA insertions were identified in transformants through thermal asymmetrical interlaced PCR (TAIL-PCR) followed by sequencing. Our results suggested that ATMT can be used as a molecular tool to identify and characterize pathogenicity-related genes in these two economically important Colletotrichum species.
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29
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van het Hoog M, Rast TJ, Martchenko M, Grindle S, Dignard D, Hogues H, Cuomo C, Berriman M, Scherer S, Magee BB, Whiteway M, Chibana H, Nantel A, Magee PT. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol 2007; 8:R52. [PMID: 17419877 PMCID: PMC1896002 DOI: 10.1186/gb-2007-8-4-r52] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 02/28/2007] [Accepted: 04/09/2007] [Indexed: 11/10/2022] Open
Abstract
For Assembly 20 of the Candida albicans genome, the sequence of each of the eight chromosomes was determined, revealing new insights into gene family creation and dispersion, subtelomere organization, and chromosome evolution. Background The 10.9× genomic sequence of Candida albicans, the most important human fungal pathogen, was published in 2004. Assembly 19 consisted of 412 supercontigs, of which 266 were a haploid set, since this fungus is diploid and contains an extensive degree of heterozygosity but lacks a complete sexual cycle. However, sequences of specific chromosomes were not determined. Results Supercontigs from Assembly 19 (183, representing 98.4% of the sequence) were assigned to individual chromosomes purified by pulse-field gel electrophoresis and hybridized to DNA microarrays. Nine Assembly 19 supercontigs were found to contain markers from two different chromosomes. Assembly 21 contains the sequence of each of the eight chromosomes and was determined using a synteny analysis with preliminary versions of the Candida dubliniensis genome assembly, bioinformatics, a sequence tagged site (STS) map of overlapping fosmid clones, and an optical map. The orientation and order of the contigs on each chromosome, repeat regions too large to be covered by a sequence run, such as the ribosomal DNA cluster and the major repeat sequence, and telomere placement were determined using the STS map. Sequence gaps were closed by PCR and sequencing of the products. The overall assembly was compared to an optical map; this identified some misassembled contigs and gave a size estimate for each chromosome. Conclusion Assembly 21 reveals an ancient chromosome fusion, a number of small internal duplications followed by inversions, and a subtelomeric arrangement, including a new gene family, the TLO genes. Correlations of position with relatedness of gene families imply a novel method of dispersion. The sequence of the individual chromosomes of C. albicans raises interesting biological questions about gene family creation and dispersion, subtelomere organization, and chromosome evolution.
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Affiliation(s)
- Marco van het Hoog
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | - Mikhail Martchenko
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | - Daniel Dignard
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - Hervé Hogues
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | | | | | - BB Magee
- University of Minnesota, Minneapolis, MN, 55455, USA
| | - Malcolm Whiteway
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - Hiroji Chibana
- Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University, Chiba, 260-8673, Japan
| | - André Nantel
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - PT Magee
- University of Minnesota, Minneapolis, MN, 55455, USA
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30
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Nimonkar AV, Amitani I, Baskin RJ, Kowalczykowski SC. Single molecule imaging of Tid1/Rdh54, a Rad54 homolog that translocates on duplex DNA and can disrupt joint molecules. J Biol Chem 2007; 282:30776-84. [PMID: 17704061 DOI: 10.1074/jbc.m704767200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Saccharomyces cerevisiae Tid1 protein is important for the recombinational repair of double-stranded DNA breaks during meiosis. Tid1 is a member of Swi2/Snf2 family of chromatin remodeling proteins and shares homology with Rad54. Members of this family hydrolyze ATP and promote 1) chromatin remodeling, 2) DNA topology alterations, and 3) displacement of proteins from DNA. All of these activities are presumed to require translocation of the protein on DNA. Here we use single-molecule visualization to provide direct evidence for the ability of Tid1 to translocate on DNA. Tid1 translocation is ATP-dependent, and the velocities are broadly distributed, with the average being 84 +/- 39 base pairs/s. Translocation is processive, with the average molecule traveling approximately 10,000 base pairs before pausing or dissociating. Many molecules display simple monotonic unidirectional translocation, but the majority display complex translocation behavior comprising intermittent pauses, direction reversals, and velocity changes. Finally, we demonstrate that translocation by Tid1 on DNA can result in disruption of three-stranded DNA structures. The ability of Tid1 translocation to clear DNA of proteins and to migrate recombination intermediates may be of critical importance for DNA repair and chromosome dynamics.
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Affiliation(s)
- Amitabh V Nimonkar
- Section of Microbiology, University of California, Davis, California 95616, USA
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31
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Naumova ES, Serpova EV, Korshunova IV, Naumov GI. [Molecular genetic characterization of the yeast Lachancea kluyveri]. Mikrobiologiia 2007; 76:361-8. [PMID: 17633411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A comparative study of Lachancea kluyveri strains isolated in Europe, North America, Japan, and the Russian Far East was performed using restriction analysis, sequencing of non-coding rDNA regions, molecular karyotyping, and the phylogenetic analysis of the alpha- galactosidase MEL genes. This study showed a close genetic relatedness of these L. kluyveri strains. The chromosomal DNAs of the L. kluyveri strains were found to range in size from 980 to 3100 kb. The haploid number of chromosomes is equal to eight. The IGS2 restriction patterns and single nucleotide substitutions in the ITS1/ITS2 rDNA region correlate neither with geographic origin nor with the source of the strains. The L. kluyveri strains isolated from different sources have a high degree of homology (79-100%) of their MEL genes. The phylogenetic analysis of all of the known alpha-galactosidases in the "Saccharomyces" clade showed that the MEL genes of the yeasts L. kluyveri. L. cidri, Saccharomyces cerevisiae, S. paradoxus, S. bayanus, and S. mikatae are species specific.
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32
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McArthur M, Bibb M. In vivo DNase I sensitivity of the Streptomyces coelicolor chromosome correlates with gene expression: implications for bacterial chromosome structure. Nucleic Acids Res 2006; 34:5395-401. [PMID: 17012277 PMCID: PMC1636467 DOI: 10.1093/nar/gkl649] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
For a bacterium, Streptomyces coelicolor A3(2) contains a relatively large genome (8.7 Mb) with a complex and adaptive pattern of gene regulation. We discovered a correlation between the physical structure of the S.coelicolor genome and the transcriptional activity of the genes therein. Twelve genes were surveyed throughout 72 h of growth for both in vivo sensitivity to DNase I digestion and levels of transcription. DNase I-sensitivity correlated positively with transcript levels, implying that it was predictive of gene expression, and indicating increased accessibility of transcribed DNA. The genome was fractionated based on the sensitivity to DNase I digestion, with the low molecular weight (frequently cut) fraction highly enriched for actively transcribed sequences when compared to the infrequently cut fraction, which was representative of the entire genome. This approach will allow comparison of nucleoid proteins, and any modifications thereof, associated with transcriptionally active and inactive regions of the bacterial genome.
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Affiliation(s)
- Michael McArthur
- To whom correspondence should be addressed. Tel: +44 1603 450757; Fax: +44 1603 450778;
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33
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Abstract
Most organisms form protein-rich, linear, ladder-like structures associated with chromosomes during early meiosis, the synaptonemal complex. In Schizosaccharomyces pombe, linear elements (LinEs) are thread-like, proteinacious chromosome-associated structures that form during early meiosis. LinEs are related to axial elements, the synaptonemal complex precursors of other organisms. Previous studies have led to the suggestion that axial structures are essential to mediate meiotic recombination. Rec10 protein is a major component of S. pombe LinEs and is required for their development. In this report we study recombination in a number of rec10 mutants, one of which (rec10-155) does not form LinEs, but is predicted to encode a truncated Rec10 protein. This mutant has levels of crossing over and gene conversion substantially higher than a rec10 null mutant (rec10-175) and forms cytologically detectable Rad51 foci indicative of meiotic recombination intermediates. These data demonstrate that while Rec10 is required for meiotic recombination, substantial meiotic recombination can occur in rec10 mutants that do not form LinEs, indicating that LinEs per se are not essential for all meiotic recombination.
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Affiliation(s)
- Jennifer L Wells
- North West Research Fund Institute, University of Wales, Bangor, UK
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34
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Rehmeyer C, Li W, Kusaba M, Kim YS, Brown D, Staben C, Dean R, Farman M. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucleic Acids Res 2006; 34:4685-701. [PMID: 16963777 PMCID: PMC1635262 DOI: 10.1093/nar/gkl588] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Eukaryotic pathogens of humans often evade the immune system by switching the expression of surface proteins encoded by subtelomeric gene families. To determine if plant pathogenic fungi use a similar mechanism to avoid host defenses, we sequenced the 14 chromosome ends of the rice blast pathogen, Magnaporthe oryzae. One telomere is directly joined to ribosomal RNA-encoding genes, at the end of the ∼2 Mb rDNA array. Two are attached to chromosome-unique sequences, and the remainder adjoin a distinct subtelomere region, consisting of a telomere-linked RecQ-helicase (TLH) gene flanked by several blocks of tandem repeats. Unlike other microbes, M.oryzae exhibits very little gene amplification in the subtelomere regions—out of 261 predicted genes found within 100 kb of the telomeres, only four were present at more than one chromosome end. Therefore, it seems unlikely that M.oryzae uses switching mechanisms to evade host defenses. Instead, the M.oryzae telomeres have undergone frequent terminal truncation, and there is evidence of extensive ectopic recombination among transposons in these regions. We propose that the M.oryzae chromosome termini play more subtle roles in host adaptation by promoting the loss of terminally-positioned genes that tend to trigger host defenses.
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Affiliation(s)
- Cathryn Rehmeyer
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Weixi Li
- Department of Biology, University of KentuckyLexington, KY 40546 USA
| | - Motoaki Kusaba
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Yun-Sik Kim
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Doug Brown
- Center for Integrated Fungal Research, North Carolina State UniversityRaleigh, NC 27695 USA
| | - Chuck Staben
- Department of Biology, University of KentuckyLexington, KY 40546 USA
| | - Ralph Dean
- Center for Integrated Fungal Research, North Carolina State UniversityRaleigh, NC 27695 USA
| | - Mark Farman
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
- To whom correspondence should be addressed. Tel: 859 257 7445, ext. 80728; Fax: 859 323 1961;
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Bowring FJ, Yeadon PJ, Stainer RG, Catcheside DEA. Chromosome pairing and meiotic recombination in Neurospora crassa spo11 mutants. Curr Genet 2006; 50:115-23. [PMID: 16758206 DOI: 10.1007/s00294-006-0066-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Accepted: 02/21/2006] [Indexed: 10/24/2022]
Abstract
Some organisms, such as mammals, green plants and fungi, require double-strand breaks in DNA (DSBs) for synapsis of homologous chromosomes at pachynema. Drosophila melanogaster and Caenorhabditis elegans are exceptions, achieving synapsis independently of DSB. SPO11 is responsible for generating DSBs and perhaps for the initiation of recombination in all organisms. Although it was previously suggested that Neurospora may not require DSBs for synapsis, we report here that mutation of Neurospora spo11 disrupts meiosis, abolishing synapsis of homologous chromosomes during pachynema and resulting in ascospores that are frequently aneuploid and rarely viable. Alignment of homologues is partially restored after exposure of spo11 perithecia to ionising radiation. Crossing over in a spo11 mutant is reduced in two regions of the Neurospora genome as expected, but is unaffected in a third.
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Seringhaus M, Kumar A, Hartigan J, Snyder M, Gerstein M. Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucleic Acids Res 2006; 34:e57. [PMID: 16648358 PMCID: PMC1450332 DOI: 10.1093/nar/gkl184] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transposons are widely employed as tools for gene disruption. Ideally, they should display unbiased insertion behavior, and incorporate readily into any genomic DNA to which they are exposed. However, many transposons preferentially insert at specific nucleotide sequences. It is unclear to what extent such bias affects their usefulness as mutagenesis tools. Here, we examine insertion site specificity and global insertion behavior of two mini-transposons previously used for large-scale gene disruption in Saccharomyces cerevisiae: Tn3 and Tn7. Using an expanded set of insertion data, we confirm that Tn3 displays marked preference for the AT-rich 5 bp consensus site TA[A/T]TA, whereas Tn7 displays negligible target site preference. On a genome level, both transposons display marked non-uniform insertion behavior: certain sites are targeted far more often than expected, and both distributions depart drastically from Poisson. Thus, to compare their insertion behavior on a genome level, we developed a windowed Kolmogorov–Smirnov (K–S) test to analyze transposon insertion distributions in sequence windows of various sizes. We find that when scored in large windows (>300 bp), both Tn3 and Tn7 distributions appear uniform, whereas in smaller windows, Tn7 appears uniform while Tn3 does not. Thus, both transposons are effective tools for gene disruption, but Tn7 does so with less duplication and a more uniform distribution, better approximating the behavior of the ideal transposon.
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Affiliation(s)
- Michael Seringhaus
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT 06520, USA
| | - Anuj Kumar
- Department of Molecular, Cellular and Developmental Biology and Life Sciences Institute, University of MichiganAnn Arbor, MI 48109-2216, USA
| | - John Hartigan
- Department of Statistics, Yale UniversityNew Haven, CT 06520, USA
| | - Michael Snyder
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew Haven, CT 06520, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, Yale UniversityNew Haven, CT 06520, USA
- To whom correspondence should be addressed: Tel: 203 432 6105; Fax: 203 432 6946;
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Coïc E, Richard GF, Haber JE. Saccharomyces cerevisiae donor preference during mating-type switching is dependent on chromosome architecture and organization. Genetics 2006; 173:1197-206. [PMID: 16624909 PMCID: PMC1526691 DOI: 10.1534/genetics.106.055392] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces mating-type (MAT) switching occurs by gene conversion using one of two donors, HMLalpha and HMRa, located near the ends of the same chromosome. MATa cells preferentially choose HMLalpha, a decision that depends on the recombination enhancer (RE) that controls recombination along the left arm of chromosome III (III-L). When RE is inactive, the two chromosome arms constitute separate domains inaccessible to each other; thus HMRa, located on the same arm as MAT, becomes the default donor. Activation of RE increases HMLalpha usage, even when RE is moved 50 kb closer to the centromere. If MAT is inserted into the same domain as HML, RE plays little or no role in activating HML, thus ruling out any role for RE in remodeling the silent chromatin of HML in regulating donor preference. When the donors MAT and RE are moved to chromosome V, RE increases HML usage, but the inaccessibility of HML without RE apparently depends on other chromosome III-specific sequences. Similar conclusions were reached when RE was placed adjacent to leu2 or arg4 sequences engaged in spontaneous recombination. We propose that RE's targets are anchor sites that tether chromosome III-L in MATalpha cells thus reducing its mobility in the nucleus.
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Affiliation(s)
- Eric Coïc
- Department of Biology and Rosenstiel Center, Brandeis University, Waltham, Massachusetts 02254-9110, USA
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38
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Abstract
The separation of chromosome-size DNA molecules by pulsed-field gel electrophoresis (PFGE) has become a well-established technique in recent years. Although it has very wide-ranging applications, it made a real breakthrough for fungal genome analysis. Because of the small size of fungal chromosomes, their investigation was not possible earlier. Different PFGE approaches allowed the separation of DNA molecules larger than 10 megabase pairs in size, and electrophoretic karyotypes for numerous previously genetically uncharacterized fungal species could be established. This review discusses the applicability of these electrophoretic karyotypes for the investigation of genome structure, for strain identification and for species delimitation.
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Affiliation(s)
- Gyöngyi Lukácsi
- Department of Microbiology, Faculty of Sciences, University of Szeged, P.O. Box 533, H-6701 Szeged, Hungary.
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Sohn K, Roehm M, Urban C, Saunders N, Rothenstein D, Lottspeich F, Schröppel K, Brunner H, Rupp S. Identification and characterization of Cor33p, a novel protein implicated in tolerance towards oxidative stress in Candida albicans. Eukaryot Cell 2006; 4:2160-9. [PMID: 16339733 PMCID: PMC1317491 DOI: 10.1128/ec.4.12.2160-2169.2005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We applied two-dimensional gel electrophoresis to identify downstream effectors of CPH1 and EFG1 under hypha-inducing conditions in Candida albicans. Among the proteins that were expressed in wild-type cells but were strongly downregulated in a cph1Delta/efg1Delta double mutant in alpha-minimal essential medium at 37 degrees C, we could identify not-yet-characterized proteins, including Cor33-1p and Cor33-2p. The two proteins are almost identical (97% identity) and represent products of allelic isoforms of the same gene. Cor33p is highly similar to Cip1p from Candida sp. but lacks any significant homology to proteins from Saccharomyces cerevisiae. Strikingly, both proteins share homology with phenylcoumaran benzylic ether reductases and isoflavone reductases from plants. For other hypha-inducing media, like yeast-peptone-dextrose (YPD) plus serum at 37 degrees C, we could not detect any transcription for COR33 in wild-type cells, indicating that Cor33p is not hypha specific. In contrast, we found a strong induction for COR33 when cells were treated with 5 mM hydrogen peroxide. However, under oxidative conditions, transcription of COR33 was not dependent on EFG1, indicating that other regulatory factors are involved. In fact, upregulation depends on CAP1 at least, as transcript levels were clearly reduced in a Deltacap1 mutant strain under oxidative conditions. Unlike in wild-type cells, transcription of COR33 in a tsa1Delta mutant can be induced by treatment with 0.1 mM hydrogen peroxide. This suggests a functional link between COR33 and thiol-specific antioxidant-like proteins that are important in the oxidative-stress response in yeasts. Concordantly, cor33Delta deletion mutants show retarded growth on YPD plates supplemented with hydrogen peroxide, indicating that COR33 in general is implicated in conferring tolerance toward oxidative stress on Candida albicans.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Candida albicans/chemistry
- Candida albicans/genetics
- Candida albicans/growth & development
- Candida albicans/metabolism
- Cell Extracts/chemistry
- Chromosomes, Fungal/chemistry
- DNA, Fungal/chemistry
- DNA, Fungal/isolation & purification
- Databases, Genetic
- Down-Regulation
- Electrophoresis, Gel, Two-Dimensional
- Fungal Proteins/chemistry
- Fungal Proteins/genetics
- Fungal Proteins/isolation & purification
- Fungal Proteins/metabolism
- Gene Deletion
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Heat-Shock Proteins/chemistry
- Heat-Shock Proteins/genetics
- Heat-Shock Proteins/isolation & purification
- Hydrogen Peroxide/pharmacology
- Molecular Sequence Data
- Oxidants/pharmacology
- Oxidative Stress
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/isolation & purification
- Protein Isoforms/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/isolation & purification
- Sequence Homology, Amino Acid
- Transcription, Genetic/drug effects
- Up-Regulation
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Affiliation(s)
- K Sohn
- Fraunhofer, IGP, Inst. f. Grenzflächen- und Bioverfahrenstechnik, Nobelstr. 12, 70569 Stuttgart, Germany
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40
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Abstract
Pulsed-field gel electrophoresis (PFGE) can be used to separate the 16 budding yeast chromosomes on the basis of size. Here we describe a detailed, practical protocol that will allow a novice to perform informative PFGE experiments. We first describe the culture of yeast prior to analysis, along with details of embedding cells in agarose before removal of cell walls. We then detail the procedure to remove protein and RNA from chromosomes and how naked chromosomes are loaded into agarose gels before being subjected to electrophoresis. Finally, we describe how the separated chromosomes can be visualized and photographed.
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Affiliation(s)
- Laura Maringele
- University of Newcastle, School of Clinical Medical Sciences--Newcastle General Hospital, Newcastle upon Tyne, UK
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41
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Abstract
The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. We developed a tiled microarray approach to identify at high resolution the translational positions of 2278 nucleosomes over 482 kilobases of Saccharomyces cerevisiae DNA, including almost all of chromosome III and 223 additional regulatory regions. The majority of the nucleosomes identified were well-positioned. We found a stereotyped chromatin organization at Pol II promoters consisting of a nucleosome-free region approximately 200 base pairs upstream of the start codon flanked on both sides by positioned nucleosomes. The nucleosome-free sequences were evolutionarily conserved and were enriched in poly-deoxyadenosine or poly-deoxythymidine sequences. Most occupied transcription factor binding motifs were devoid of nucleosomes, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access.
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Affiliation(s)
- Guo-Cheng Yuan
- Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
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42
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Bystricky K, Heun P, Gehlen L, Langowski J, Gasser SM. Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. Proc Natl Acad Sci U S A 2004; 101:16495-500. [PMID: 15545610 PMCID: PMC534505 DOI: 10.1073/pnas.0402766101] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Little is known about how chromatin folds in its native state. Using optimized in situ hybridization and live imaging techniques have determined compaction ratios and fiber flexibility for interphase chromatin in budding yeast. Unlike previous studies, ours examines nonrepetitive chromatin at intervals short enough to be meaningful for yeast chromosomes and functional domains in higher eukaryotes. We reconcile high-resolution fluorescence in situ hybridization data from intervals of 14-100 kb along single chromatids with measurements of whole chromosome arms (122-623 kb in length), monitored in intact cells through the targeted binding of bacterial repressors fused to GFP derivatives. The results are interpreted with a flexible polymer model and suggest that interphase chromatin exists in a compact higher-order conformation with a persistence length of 170-220 nm and a mass density of approximately 110-150 bp/nm. These values are equivalent to 7-10 nucleosomes per 11-nm turn within a 30-nm-like fiber structure. Comparison of long and short chromatid arm measurements demonstrates that chromatin fiber extension is also influenced by nuclear geometry. The observation of this surprisingly compact chromatin structure for transcriptionally competent chromatin in living yeast cells suggests that the passage of RNA polymerase II requires a very transient unfolding of higher-order chromatin structure.
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Affiliation(s)
- Kerstin Bystricky
- Department of Molecular Biology and National Center of Competence in Research Frontiers in Genetics, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland
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43
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Haraguchi T, Ding DQ, Yamamoto A, Kaneda T, Koujin T, Hiraoka Y. Multiple-color fluorescence imaging of chromosomes and microtubules in living cells. Cell Struct Funct 2004; 24:291-8. [PMID: 15216885 DOI: 10.1247/csf.24.291] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Microscopic observation of fluorescently-stained intracellular molecules within a living cell provides a straightforward approach to understanding their temporal and spatial relationships. However, exposure to the excitation light used to visualize these fluorescently-stained molecules can be toxic to the cells. Here we describe several important considerations in microscope instrumentation and experimental conditions for avoiding the toxicity associated with observing living fluorescently-stained cells. Using a computer-controlled fluorescence microscope system designed for live observation, we recorded time-lapse, multi-color images of chromosomes and microtubules in living human and fission yeast cells. In HeLa cells, a human cell line, microtubules were stained with rhodamine-conjugated tubulin, and chromosomes were stained with a DNA-specific fluorescent dye, Hoechst33342, or with rhodamine-conjugated histone. In fission yeast cells, microtubules were stained with alpha-tubulin fused with the jellyfish green fluorescent protein (GFP), and chromosomes were stained with Hoechst33342.
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Affiliation(s)
- T Haraguchi
- Kansai Advanced Research Center, Communications Research Laboratory, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2401, Japan
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44
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Abstract
Electrophoretic karyotype analysis was applied to obtain information on the organisation and intrageneric variability of the nuclear genome in three Micromucor isolates of two different species (M. isabellina and M. ramanniana). A protoplast formation protocol, conditions for the preparation of highly-intact chromosome-size DNA molecules and for the separation of DNA molecules were established. The chromosomal banding patterns revealed substantial variability among the isolates: 11 to 14 chromosomal mobility groups were resolved. The DNA in the Micromucor chromosomes were rather small; their estimated sizes were calculated to be between 2.60 and 0.4 Mb. Using Saccharomyces cerevisiae and Schizosaccharomyces pombe as size standard, the minimum total genome sizes were estimated to be between 24.19 and 24.9 Mb.
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Affiliation(s)
- Agnes Nagy
- Department of General and Environmental Microbiology, Faculty of Sciences, University of Pécs, Pécs, P.O. Box 266, H-7624, Hungary
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45
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Shimizu M, Fujita R, Tomita N, Shindo H, Wells RD. Chromatin structure of yeast minichromosomes containing triplet repeat sequences associated with human hereditary neurological diseases. Nucleic Acids Res Suppl 2003:71-2. [PMID: 12836269 DOI: 10.1093/nass/1.1.71] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Expansion of triplet repeat sequences such as (CTG)n, (CGG)n, and (GAA)n causes human genetic diseases. Since DNA is packaged into arrays of nucleosomes in eukaryotic cells, chromatin may be involved in the mechanism of triplet repeat diseases. To elucidate this issue, we have examined effects of triplet repeat sequences on the chromatin organization in vivo using well defined yeast minichromosomes. We show here that (CGG)12 disrupts an array of positioned nucleosomes, whereas (CTG)12 promotes the nucleosome formation. Thus, triplet repeat sequences can affect the chromatin organization in vivo, which may contribute to the triplet repeat expansion or alterations in the expression of genes associated with triplet repeat diseases.
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Affiliation(s)
- M Shimizu
- Department of Chemistry, Meisei University, Hino, Tokyo 191-8506, Japan
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46
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Coral G, Omer C, Unaldi MN. Separation of megabased-sized DNA molecules of Aspergillus niger using pulsed field gel electrophoresis. Folia Biol (Praha) 2003; 50:49-52. [PMID: 12597534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
In this study, the chromosomal DNAs were extracted from Aspergillus niger Z10 wild type strain and these DNAs were separated using the contour clamped homogeneous electric field gel electrophoresis (CHEF) system. This system is laboratory-made and is operated by a computer program. Total DNAs resolved into five distinct chromosomal bands. The size of the chromosomes was estimated as being between 3.3 Mb to 6.4 Mb.
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Affiliation(s)
- Gökhan Coral
- University, Faculty of Arts and Sciences, Department of Biology 33342 Ciftliköy-Mersin, Turkey.
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47
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Rincones J, Meinhardt LW, Vidal BC, Pereira GA. Electrophoretic karyotype analysis of Crinipellis perniciosa, the causal agent of witches' broom disease of Theobroma cacao. Mycol Res 2003; 107:452-8. [PMID: 12825518 DOI: 10.1017/s0953756203007597] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pulse-field gel electrophoresis (PFGE) was used to determine the genome size and characterize karyotypic differences in isolates of the cacao biotype of Crinipellis perniciosa (C-biotype). The karyotype analysis of four isolates from Brazil revealed that this biotype could be divided into two genotypes: one presenting six chromosomal bands and the other presenting eight. The size of the chromosomes ranged from 2.7 to 5.3 Mb. The different genotypes correlate with telomere-based PCR analysis. The isolates with six chromosomal bands had two that appeared to be doublets, as shown by densitometric analysis, indicating that the haploid chromosome number for this biotype is eight. The size of the haploid genomes was estimated at approximately 30 Mb by both PFGE and Feulgen-image analysis. DNA hybridization revealed that the rDNA sequences are clustered on a single chromosome and these sequences were located on different chromosomes in an isolate dependent manner. This is the first report of genome size and chromosomal polymorphism for the C-biotype of C. perniciosa.
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Affiliation(s)
- Johana Rincones
- Laboratório de Genômica e Biotecnologia, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Caixa Postal 6109, CEP 13083-970 Campinas, São Paulo, Brazil
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48
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Abstract
The cohesin complex is essential for sister chromatid cohesion during mitosis. Its Smc1 and Smc3 subunits are rod-shaped molecules with globular ABC-like ATPases at one end and dimerization domains at the other connected by long coiled coils. Smc1 and Smc3 associate to form V-shaped heterodimers. Their ATPase heads are thought to be bridged by a third subunit, Scc1, creating a huge triangular ring that could trap sister DNA molecules. We address here whether cohesin forms such rings in vivo. Proteolytic cleavage of Scc1 by separase at the onset of anaphase triggers its dissociation from chromosomes. We show that N- and C-terminal Scc1 cleavage fragments remain connected due to their association with different heads of a single Smc1/Smc3 heterodimer. Cleavage of the Smc3 coiled coil is sufficient to trigger cohesin release from chromosomes and loss of sister cohesion, consistent with a topological association with chromatin.
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Affiliation(s)
- Stephan Gruber
- Research Institute of Molecular Pathology, Dr Bohr-Gasse 7, 1030 Vienna, Austria
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49
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Mazheĭka IS, Kolomiets OL. [A method for preparation of synaptonemal complexes of meiotic chromosomes from basidial protoplasts of the common mushroom Agaricus bisporus (Lange) Imbach]. Genetika 2003; 39:357-361. [PMID: 12722635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
For the first time, preparations of synaptonemal complexes (SCs) were made from meiotic chromosomes of white button mushroom (Agaricus bisporus) basidia. It is the first experience of obtaining SC preparations of filamentous fungi from isolated meiosporangium protoplasts. Previously, only yeast SC preparations were obtained following this approach. The method includes four major stages: isolation of basidium protoplasts by treatment of basidia with lytic enzymes, spreading of protoplast nuclei on a filmy support by osmotic shock, staining the preparations with silver nitrate, and examination under light and electron microscopes. The structures of spread premeiotic nuclei, axial elements of chromosomes, SCs, chromatin, and nucleoli were studied at the leptotene-diplotene stage of meiotic prophase I.
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Affiliation(s)
- I S Mazheĭka
- Department of Mycology and Algology, Lomonosov Moscow State University, Moscow, 119899 Russia
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50
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Abstract
Many yeast strains isolated from the wild show karyotype instability during vegetative growth, with rearrangement rates of up to 10(-2) chromosomal changes per generation. Physical isolation and analysis of several chromosome I size variants of one of these strains revealed that they differed only in their subtelomeric regions, leaving the central 150 Kb unaltered. Fine mapping of these subtelomeric variable regions revealed gross alterations of two very similar loci, FLO1 and FLO9. These loci are located on the right and left arms, respectively, of chromosome I and encompass internal repetitive DNA sequences. Furthermore, some chromosome I variants lacking the FLO1 locus showed evidence of recombination at a DNA region on their right arm that is enriched in repeated sequences, including Ty LTRs. We propose that repetitive sequences in many subtelomeric regions in S. cerevisiae play a key role in karyotype hypervariability. As these regions encode several membrane-associated proteins, subtelomeric plasticity may allow rapid adaptive changes of the yeast strain to specific substrates. This pattern of semi-conservative chromosomal rearrangement may have profound implications, both in terms of evolution of wild strains and for biotechnological processes.
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MESH Headings
- Blotting, Southern
- Chromosome Mapping
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/physiology
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- Electrophoresis, Gel, Pulsed-Field
- Evolution, Molecular
- Genetic Variation/genetics
- Genetic Variation/physiology
- Karyotyping
- Nucleic Acid Hybridization
- Oligonucleotide Array Sequence Analysis
- Polymerase Chain Reaction
- Recombination, Genetic/genetics
- Recombination, Genetic/physiology
- Repetitive Sequences, Nucleic Acid/genetics
- Repetitive Sequences, Nucleic Acid/physiology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/physiology
- Sequence Analysis, DNA
- Telomere/genetics
- Telomere/physiology
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Affiliation(s)
- David Carro
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi Girona 18, 08034 Barcelona, Spain
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