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Ning Y, Shang D, Xin H, Ni R, Wang Z, Zhen Y, Liu G, Xi M. Establishing of 3D-FISH on frozen section and its applying in chromosome territories analysis in Populus trichocarpa. PLANT CELL REPORTS 2024; 43:255. [PMID: 39375198 DOI: 10.1007/s00299-024-03342-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 09/23/2024] [Indexed: 10/09/2024]
Abstract
KEY MESSAGE Fluorescence in situ hybridization with frozen sections of root tips showed difference of chromosome territories distribution between autosome and sex-chromosome homologous pairs in Populus trichocarpa. The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biologic processes. Three-dimensional fluorescence in situ hybridization (3D-FISH) is a powerful tool for analyzing CTs, but its application in plants is limited. In this study, we established a 3D-FISH technique using frozen sections of Populus trichocarpa root tips, which was an improvement over the use of paraffin sections and enabled us to acquire good FISH signals. Using chromosome-specific oligo probes, we were able to analyze CTs in interphase nuclei in three dimensions. The distribution of chromosome pairs 17 and 19 in the 3D-preserved nuclei of P. trichocarpa root tip cells were analyzed and showed that the autosome pair 17 associated more often than sex chromosome 19. This research lays a foundation for further study of the spatial position of chromosomes in the nucleus and the relationship between gene expression and spatial localization of chromosomes in poplar.
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Affiliation(s)
- Yihang Ning
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Daxin Shang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Haoyang Xin
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Runxin Ni
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Ziyue Wang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yan Zhen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Guangxin Liu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
| | - Mengli Xi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
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Schubert V, Weißleder A, Lermontova I. Simultaneous EYFP-CENH3/H2B-DsRed Expression Is Impaired Differentially in Meristematic and Differentiated Nuclei of Arabidopsis Double Transformants. Cytogenet Genome Res 2023; 163:74-80. [PMID: 37552957 DOI: 10.1159/000533317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Fluorescence live-cell microscopy is important in cell biology to perform artifact-free investigations. To analyze the dynamics of chromatin and centromeres at different stages of the cell cycle in nuclei and chromosomes, we performed simultaneous EYFP-CENH3/H2B-DsRed and single H2B-YFP transformations in Arabidopsis wild-type and cohesin T-DNA mutants. All constructs were under the control of the strong CaMV 35S promoter. While a strong silencing of fluorescence expression occurred differently in leaf and root tissues in the double transformants, nearly all single-transformed wild-type and most mutant cells showed H2B-YFP fluorescence. It seems that for an efficient co-expression of two fluorescence proteins, endogenous promoters and terminators should be used.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andrea Weißleder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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Shams I, Raskina O. Supernumerary B Chromosomes and Plant Genome Changes: A Snapshot of Wild Populations of Aegilops speltoides Tausch ( Poaceae, Triticeae). Int J Mol Sci 2020; 21:ijms21113768. [PMID: 32466617 PMCID: PMC7312783 DOI: 10.3390/ijms21113768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 01/12/2023] Open
Abstract
In various eukaryotes, supernumerary B chromosomes (Bs) are an optional genomic component that affect their integrity and functioning. In the present study, the impact of Bs on the current changes in the genome of goatgrass, Aegilops speltoides, was addressed. Individual plants from contrasting populations with and without Bs were explored using fluorescence in situ hybridization. In parallel, abundances of the Ty1-copia, Ty3-gypsy, and LINE retrotransposons (TEs), and the species-specific Spelt1 tandem repeat (TR) in vegetative and generative spike tissues were estimated by real-time quantitative PCR. The results revealed: (i) ectopic associations between Bs and the regular A chromosomes, and (ii) cell-specific rearrangements of Bs in both mitosis and microgametogenesis. Further, the copy numbers of TEs and TR varied significantly between (iii) genotypes and (iv) different spike tissues in the same plant(s). Finally, (v) in plants with and without Bs from different populations, genomic abundances and/or copy number dynamics of TEs and TR were similar. These findings indicate that fluctuations in TE and TR copy numbers are associated with DNA damage and repair processes during cell proliferation and differentiation, and ectopic recombination is one of the mechanisms by which Bs play a role in genome changes.
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Pollak Y, Zelinger E, Raskina O. Repetitive DNA in the Architecture, Repatterning, and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae). FRONTIERS IN PLANT SCIENCE 2018; 9:1779. [PMID: 30564259 PMCID: PMC6288716 DOI: 10.3389/fpls.2018.01779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
The genome's adaptability to environmental changes, especially during rapid climatic fluctuations, underlies the existence and evolution of species. In the wild, genetic and epigenetic genomic changes are accompanied by significant alterations in the complex nuclear repetitive DNA fraction. Current intraspecific polymorphism of repetitive DNA is closely related to ongoing chromosomal rearrangements, which typically result from erroneous DNA repair and recombination. In this study, we addressed tandem repeat patterns and interaction/reshuffling both in pollen mother cell (PMC) development and somatogenesis in the wild diploid cereal Aegilops speltoides, with a focus on genome repatterning and stabilization. Individual contrasting genotypes were investigated using the fluorescent in situ hybridization (FISH) approach by applying correlative fluorescence and electron microscopy. Species-specific Spelt1 and tribe-specific Spelt52 tandem repeats were used as the markers for monitoring somatic and meiotic chromosomal interactions and dynamics in somatic interphase nuclei. We found that, the number of tandem repeat clusters in nuclei is usually lower than the number on chromosomes due to the associations of clusters of the same type in common blocks. In addition, tightly associated Spelt1-Spelt52 clusters were revealed in different genotypes. The frequencies of nonhomologous/ectopic associations between tandem repeat clusters were revealed in a genotype-/population-specific manner. An increase in the number of tandem repeat clusters in the genome causes an increase in the frequencies of their associations. The distal/terminal regions of homologous chromosomes are separated in nuclear space, and nonhomologous chromosomes are often involved in somatic recombination as seen by frequently formed interchromosomal chromatin bridges. In both microgametogenesis and somatogenesis, inter- and intrachromosomal associations are likely to lead to DNA breaks during chromosome disjunction in the anaphase stage. Uncondensed/improperly packed DNA fibers, mainly in heterochromatic regions, were revealed in both the meiotic and somatic prophases that might be a result of broken associations. Altogether, the data obtained showed that intraorganismal dynamics of repetitive DNA under the conditions of natural out-crossing and artificial intraspecific hybridization mirrors the structural plasticity of the Ae. speltoides genome, which is interlinked with genetic diversity through the species distribution area in contrasting ecogeographical environments in and around the Fertile Crescent.
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Affiliation(s)
- Yulia Pollak
- The CSI Center for Scientific Imaging, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
- The Electron Microscopy Unit, Faculty of Natural Science, University of Haifa, Haifa, Israel
| | - Einat Zelinger
- The CSI Center for Scientific Imaging, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Olga Raskina
- Institute of Evolution, University of Haifa, Haifa, Israel
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5
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Pernickova K, Linc G, Gaal E, Kopecky D, Samajova O, Lukaszewski AJ. Out-of-position telomeres in meiotic leptotene appear responsible for chiasmate pairing in an inversion heterozygote in wheat (Triticum aestivum L.). Chromosoma 2018; 128:31-39. [PMID: 30483879 DOI: 10.1007/s00412-018-0686-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 11/26/2022]
Abstract
Chromosome pairing in meiosis usually starts in the vicinity of the telomere attachment to the nuclear membrane and congregation of telomeres in the leptotene bouquet is believed responsible for bringing homologue pairs together. In a heterozygote for an inversion of a rye (Secale cereale L.) chromosome arm in wheat, a distal segment of the normal homologue is capable of chiasmate pairing with its counterpart in the inverted arm, located near the centromere. Using 3D imaging confocal microscopy, we observed that some telomeres failed to be incorporated into the bouquet and occupied various positions throughout the entire volume of the nucleus, including the centromere pole. Rye telomeres appeared ca. 21 times more likely to fail to be included in the telomere bouquet than wheat telomeres. The frequency of the out-of-bouquet rye telomere position in leptotene was virtually identical to the frequency of telomeres deviating from Rabl's orientation in the nuclei of somatic cells, and was similar to the frequency of synapsis of the normal and inverted chromosome arms, but lower than the MI pairing frequency of segments of these two arms normally positioned across the volume of the nucleus. Out-of-position placement of the rye telomeres may be responsible for reduced MI pairing of rye chromosomes in hybrids with wheat and their disproportionate contribution to aneuploidy, but appears responsible for initiating chiasmate pairing of distantly positioned segments of homology in an inversion heterozygote.
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Affiliation(s)
- Katerina Pernickova
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, Olomouc, Czech Republic
| | - Gabriella Linc
- Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences, Martonvasar, 2462, Hungary
- National Food Chain Safety Office, Budaörsi Str. 141-145, Budapest, 1118, Hungary
| | - Eszter Gaal
- Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences, Martonvasar, 2462, Hungary
- National Food Chain Safety Office, Budaörsi Str. 141-145, Budapest, 1118, Hungary
| | - David Kopecky
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, Olomouc, Czech Republic
| | - Olga Samajova
- Faculty of Science, Centre of the Region Hana for Biotechnological and Agricultural Research, Department of Cell Biology, Palacky University Olomouc, Slechtitelu 27, Olomouc, Czech Republic
| | - Adam J Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
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6
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Sas-Nowosielska H, Bernas T. Spatial relationship between chromosomal domains in diploid and autotetraploid Arabidopsis thaliana nuclei. Nucleus 2017; 7:216-31. [PMID: 27310308 DOI: 10.1080/19491034.2016.1182277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Polyploids constitute more than 80% of angiosperm plant species. Their DNA content is often further increased by endoreplication, which occurs as a part of cell differentiation. Here, we explore the relationship between 3D chromatin architecture, number of genome copies and their origin in the model plant, Arabidopsis thaliana. Spatial proximity between pericentromeric, interstitial and subtelomeric domains of chromosomes 1 and 4 was quantified over a range of distances. The results indicate that average nuclear volume as well as chromatin density increase with the genome copy number. Similar dependence is observed when association of homologous chromosomes (in 2C/ endopolyploid nuclei) and sister chromatid separation (in endopolyploid nuclei) is studied. Moreover, clusters of chromosomal domains are detectable at the spatial scale above microscopy resolution. Subtelomeric, interstitial and pericentromeric chromosomal domains are affected to different extent by these processes, which are modulated by endopolyploidy. This factor influences fusion of heterochromatin as well. Nonetheless, local chromatin architecture of Arabidopsis thaliana depends mainly on endopolyploidy level, and to lesser extend on polyploidy.
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Affiliation(s)
- H Sas-Nowosielska
- a Laboratory of Imaging Tissue Structure and Function , Nencki Institute of Experimental Biology , Polish Academy of Sciences , Warszawa , Poland.,b Department of Plant Anatomy and Cytology , Faculty of Biology , University of Silesia , Katowice , Poland
| | - T Bernas
- b Department of Plant Anatomy and Cytology , Faculty of Biology , University of Silesia , Katowice , Poland
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Del Prete S, Arpón J, Sakai K, Andrey P, Gaudin V. Nuclear architecture and chromatin dynamics in interphase nuclei of Arabidopsis thaliana. Cytogenet Genome Res 2014; 143:28-50. [PMID: 24992956 DOI: 10.1159/000363724] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The interphase cell nucleus is extraordinarily complex, ordered, and dynamic. In the last decade, remarkable progress has been made in deciphering the functional organisation of the cell nucleus, and intricate relationships between genome functions (transcription, DNA repair, or replication) and various nuclear compartments have been revealed. In this review, we describe the architecture of the Arabidopsis thaliana interphase cell nucleus and discuss the dynamic nature of its organisation. We underline the need for further developments in quantitative and modelling approaches to nuclear organization.
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Affiliation(s)
- Stefania Del Prete
- INRA, UMR1318-AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), INRA-Centre de Versailles-Grignon, Versailles, France
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8
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Zamariola L, De Storme N, Vannerum K, Vandepoele K, Armstrong SJ, Franklin FCH, Geelen D. SHUGOSHINs and PATRONUS protect meiotic centromere cohesion in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:782-94. [PMID: 24506176 DOI: 10.1111/tpj.12432] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/20/2013] [Accepted: 01/07/2014] [Indexed: 05/23/2023]
Abstract
In meiosis, chromosome cohesion is maintained by the cohesin complex, which is released in a two-step manner. At meiosis I, the meiosis-specific cohesin subunit Rec8 is cleaved by the protease Separase along chromosome arms, allowing homologous chromosome segregation. Next, in meiosis II, cleavage of the remaining centromere cohesin results in separation of the sister chromatids. In eukaryotes, protection of centromeric cohesion in meiosis I is mediated by SHUGOSHINs (SGOs). The Arabidopsis genome contains two SGO homologs. Here we demonstrate that Atsgo1 mutants show a premature loss of cohesion of sister chromatid centromeres at anaphase I and that AtSGO2 partially rescues this loss of cohesion. In addition to SGOs, we characterize PATRONUS which is specifically required for the maintenance of cohesion of sister chromatid centromeres in meiosis II. In contrast to the Atsgo1 Atsgo2 double mutant, patronus T-DNA insertion mutants only display loss of sister chromatid cohesion after meiosis I, and additionally show disorganized spindles, resulting in defects in chromosome segregation in meiosis. This leads to reduced fertility and aneuploid offspring. Furthermore, we detect aneuploidy in sporophytic tissue, indicating a role for PATRONUS in chromosome segregation in somatic cells. Thus, ploidy stability is preserved in Arabidopsis by PATRONUS during both meiosis and mitosis.
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Affiliation(s)
- Linda Zamariola
- Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Ghent, 9000, Belgium
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Zamariola L, Tiang CL, De Storme N, Pawlowski W, Geelen D. Chromosome segregation in plant meiosis. FRONTIERS IN PLANT SCIENCE 2014; 5:279. [PMID: 24987397 PMCID: PMC4060054 DOI: 10.3389/fpls.2014.00279] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/28/2014] [Indexed: 05/18/2023]
Abstract
Faithful chromosome segregation in meiosis is essential for ploidy stability over sexual life cycles. In plants, defective chromosome segregation caused by gene mutations or other factors leads to the formation of unbalanced or unreduced gametes creating aneuploid or polyploid progeny, respectively. Accurate segregation requires the coordinated execution of conserved processes occurring throughout the two meiotic cell divisions. Synapsis and recombination ensure the establishment of chiasmata that hold homologous chromosomes together allowing their correct segregation in the first meiotic division, which is also tightly regulated by cell-cycle dependent release of cohesin and monopolar attachment of sister kinetochores to microtubules. In meiosis II, bi-orientation of sister kinetochores and proper spindle orientation correctly segregate chromosomes in four haploid cells. Checkpoint mechanisms acting at kinetochores control the accuracy of kinetochore-microtubule attachment, thus ensuring the completion of segregation. Here we review the current knowledge on the processes taking place during chromosome segregation in plant meiosis, focusing on the characterization of the molecular factors involved.
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Affiliation(s)
- Linda Zamariola
- Department of Plant Production, Faculty of Bioscience Engineering, University of GhentGhent, Belgium
| | - Choon Lin Tiang
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Nico De Storme
- Department of Plant Production, Faculty of Bioscience Engineering, University of GhentGhent, Belgium
| | - Wojtek Pawlowski
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Danny Geelen
- Department of Plant Production, Faculty of Bioscience Engineering, University of GhentGhent, Belgium
- *Correspondence: Danny Geelen, Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium e-mail:
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10
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Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness. Chromosoma 2012; 121:369-87. [PMID: 22476443 DOI: 10.1007/s00412-012-0367-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 02/09/2012] [Accepted: 03/12/2012] [Indexed: 12/22/2022]
Abstract
The spatial chromatin organisation and molecular interactions within and between chromatin domains and chromosome territories (CTs) are essential for fundamental processes such as replication, transcription and DNA repair via homologous recombination. To analyse the distribution and interaction of whole CTs, centromeres, (sub)telomeres and ~100-kb interstitial chromatin segments in endopolyploid nuclei, specific FISH probes from Arabidopsis thaliana were applied to 2-64C differentiated leaf nuclei. Whereas CTs occupy a distinct and defined volume of the nucleus and do not obviously intermingle with each other in 2-64C nuclei, ~100-kb sister chromatin segments within these CTs become more non-cohesive with increasing endopolyploidy. Centromeres, preferentially located at the nuclear periphery, may show ring- or half-moon like shapes in 2C and 4C nuclei. Sister centromeres tend to associate up to the 8C level. From 16C nuclei on, they become progressively separated. The higher the polyploidy level gets, the more separate chromatids are present. Due to sister chromatid separation in highly endopolyploid nuclei, the centromeric histone variant CENH3, the 180-bp centromeric repeats and pericentromeric heterochromatin form distinct subdomains at adjacent but not intermingling positions. The (sub)telomeres are frequently associated with each other and with the nucleolus and less often with centromeres. The extent of chromatid separation and of chromatin decondensation at subtelomeric chromatin segments varies between chromosome arms. A mainly random distribution and similar shapes of CTs even at higher ploidy levels indicate that in general no substantial CT reorganisation occurs during endopolyploidisation. Non-cohesive sister chromatid regions at chromosome arms and at the (peri)centromere are accompanied by a less dense chromatin conformation in highly endopolyploid nuclei. We discuss the possible function of this conformation in comparison to transcriptionally active regions at insect polytene chromosomes.
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11
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Ashtiyani RK, Moghaddam AMB, Schubert V, Rutten T, Fuchs J, Demidov D, Blattner FR, Houben A. AtHaspin phosphorylates histone H3 at threonine 3 during mitosis and contributes to embryonic patterning in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:443-54. [PMID: 21749502 DOI: 10.1111/j.1365-313x.2011.04699.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Post-translational histone modifications regulate many aspects of chromosome activity. Threonine 3 of histone H3 is highly conserved, but the significance of its phosphorylation is unclear, and the identity of the corresponding kinase in plants is unknown. Therefore, we characterized the candidate kinase in Arabidopsis thaliana, called AtHaspin. Recombinant AtHaspin in vitro phosphorylates histone H3 at threonine 3. Reduction of H3 threonine 3 phosphorylation level and reduced chromatin condensation in interphase nuclei by AtHaspin RNAi supports the proposition that this kinase is involved in histone H3 phosphorylation in vivo in mitotic cells. In addition, we provide a developmental function for a Haspin kinase. At the whole plant level, altered expression of the kinase induced pleiotropic phenotypes with defects in floral organs and vascular tissue. It reduced fertility and modified adventitious shoot apical meristems that then gave rise to plants with multi-rosettes and multi-shoots. Haspin mutant embryos frequently showed alteration in division plane orientation that could be traced back to the earliest divisions of embryo development, thus Haspin contributes to embryonic patterning.
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Affiliation(s)
- Raheleh Karimi Ashtiyani
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466 Gatersleben, Germany
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12
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Similar rye A and B chromosome organization in meristematic and differentiated interphase nuclei. Chromosome Res 2011; 19:645-55. [PMID: 21674259 DOI: 10.1007/s10577-011-9224-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/26/2011] [Accepted: 05/26/2011] [Indexed: 12/28/2022]
Abstract
Supernumerary (B) chromosomes of rye are not required for plant development and exhibit a reduced transcription activity. These special features inspired us to analyse whether there are differences between A and B chromatin organization in interphase nuclei. Applying fluorescence in situ hybridization, we found that both rye A and B chromosomes added to hexaploid wheat showed in meristematic nuclei a string-like shape and a clear Rabl orientation. In 4C differentiated leaf nuclei, a more relaxed chromatin structure, round-shaped chromosome territories and a less pronounced Rabl configuration were found. Also, the observed random association of homologues in 2C and 4C nuclei indicated in general a similar behaviour of A and B chromosomes. Whereas in differentiated 4C nuclei A sister centromeres are separated, B sister centromeres align in nearly all nuclei. In short, despite the different transcription activity of A and B chromosomes, both types of chromosomes exhibit a similar organization in meristematic and differentiated interphase nuclei. But the deletion of a B chromosome segment responsible for non-disjunction during gametogenesis induces released sister centromeres also in some interphase nuclei of somatic tissue. Hence, the control of rye B chromosome non-disjunction is also active in sporophytic cells.
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13
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Schubert I, Shaw P. Organization and dynamics of plant interphase chromosomes. TRENDS IN PLANT SCIENCE 2011; 16:273-81. [PMID: 21393049 DOI: 10.1016/j.tplants.2011.02.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/01/2011] [Accepted: 02/05/2011] [Indexed: 05/23/2023]
Abstract
Eukaryotic chromosomes occupy distinct territories within interphase nuclei. The arrangement of chromosome territories (CTs) is important for replication, transcription, repair and recombination processes. Our knowledge about interphase chromatin arrangement is mainly based on results from in situ labeling approaches. The phylogenetic affiliation of a species, cell cycle, differentiation status and environmental factors are all likely to influence interphase nuclear architecture. In this review we survey current data about relative positioning of CTs, somatic pairing of homologs, and sister chromatid alignment in meristematic and differentiated tissues, using data derived mainly from Arabidopsis thaliana, wheat (Triticum aestivum) and their relatives. We discuss morphological constraints and epigenetic impacts on nuclear architecture, the evolutionary stability of CT arrangements, and alterations of nuclear architecture during transcription and repair.
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Affiliation(s)
- Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D06466 Gatersleben, Germany.
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14
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Takahashi N, Quimbaya M, Schubert V, Lammens T, Vandepoele K, Schubert I, Matsui M, Inzé D, Berx G, De Veylder L. The MCM-binding protein ETG1 aids sister chromatid cohesion required for postreplicative homologous recombination repair. PLoS Genet 2010; 6:e1000817. [PMID: 20090939 PMCID: PMC2806904 DOI: 10.1371/journal.pgen.1000817] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 12/16/2009] [Indexed: 11/22/2022] Open
Abstract
The DNA replication process represents a source of DNA stress that causes potentially spontaneous genome damage. This effect might be strengthened by mutations in crucial replication factors, requiring the activation of DNA damage checkpoints to enable DNA repair before anaphase onset. Here, we demonstrate that depletion of the evolutionarily conserved minichromosome maintenance helicase-binding protein ETG1 of Arabidopsis thaliana resulted in a stringent late G2 cell cycle arrest. This arrest correlated with a partial loss of sister chromatid cohesion. The lack-of-cohesion phenotype was intensified in plants without functional CTF18, a replication fork factor needed for cohesion establishment. The synergistic effect of the etg1 and ctf18 mutants on sister chromatid cohesion strengthened the impact on plant growth of the replication stress caused by ETG1 deficiency because of inefficient DNA repair. We conclude that the ETG1 replication factor is required for efficient cohesion and that cohesion establishment is essential for proper development of plants suffering from endogenous DNA stress. Cohesion defects observed upon knockdown of its human counterpart suggest an equally important developmental role for the orthologous mammalian ETG1 protein. DNA replication is a highly complex process and the source of potential DNA damage. It is of utmost importance that the damaged DNA is repaired before cells proceed through mitosis, because the genome holds all the information required for correct development. DNA replication results in two identical sister chromatids. A trick applied by cells to overcome damaged DNA is homologous recombination, using the undamaged copy of the sister chromatid as a template to repair the damaged one. This process is aided by keeping the two sister chromatids in close proximity after the replication process by the deposition of a molecular glue, called cohesin. In the present work, we identified the Arabidopsis thaliana ETG1 protein as a novel evolutionarily conserved replication factor that is needed for maintaining the sister chromatids physically aligned. In plants without ETG1, DNA damage builds up due to inefficient DNA repair. As a consequence, cell division is impaired with a huge impact on plant growth, highlighting the importance of cohesin for the correct development of eukaryotic organisms. Cohesion phenotypes observed upon the depletion of the orthologous human ETG1 protein indicate equally prominent roles for this particular factor during mammalian development.
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Affiliation(s)
- Naoki Takahashi
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Mauricio Quimbaya
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
- Department for Molecular Biomedical Research, Molecular and Cellular Oncology Unit, Flanders Institute for Biotechnology (VIB), Gent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Gent, Belgium
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Tim Lammens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Minami Matsui
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Dirk Inzé
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
| | - Geert Berx
- Department for Molecular Biomedical Research, Molecular and Cellular Oncology Unit, Flanders Institute for Biotechnology (VIB), Gent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
- * E-mail:
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15
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Schubert V, Weissleder A, Ali H, Fuchs J, Lermontova I, Meister A, Schubert I. Cohesin gene defects may impair sister chromatid alignment and genome stability in Arabidopsis thaliana. Chromosoma 2009; 118:591-605. [PMID: 19533160 DOI: 10.1007/s00412-009-0220-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 05/22/2009] [Indexed: 12/19/2022]
Abstract
In contrast to yeast, plant interphase nuclei often display incomplete alignment (cohesion) along sister chromatid arms. Sister chromatid cohesion mediated by the multi-subunit cohesin complex is essential for correct chromosome segregation during nuclear divisions and for DNA recombination repair. The cohesin complex consists of the conserved proteins SMC1, SMC3, SCC3, and an alpha-kleisin subunit. Viable homozygous mutants could be selected for the Arabidopsis thaliana alpha-kleisins SYN1, SYN2, and SYN4, which can partially compensate each other. For the kleisin SYN3 and for the single-copy genes SMC1, SMC3, and SCC3, only heterozygous mutants were obtained that displayed between 77% and 97% of the wild-type transcript level. Compared to wild-type nuclei, sister chromatid alignment was significantly decreased along arms in 4C nuclei of the homozygous syn1 and syn4 and even of the heterozygous smc1, smc3, scc3, and syn3 mutants. Knocking out SYN1 and SYN4 additionally impaired sister centromere cohesion. Homozygous mutants of SWITCH1 (required for meiotic sister chromatid alignment) displayed sterility and decreased sister arm alignment. For the cohesin loading complex subunit SCC2, only heterozygous mutants affecting sister centromere alignment were obtained. Defects of the alpha-kleisin SYN4, which impair sister chromatid alignment in 4C differentiated nuclei, do apparently not disturb alignment during prometaphase nor cause aneuploidy in meristematic cells. The syn2, 3, 4 scc3 and swi1 mutants display a high frequency of anaphases with bridges (~10% to >20% compared to 2.6% in wild type). Our results suggest that (a) already a slight reduction of the average transcript level in heterozygous cohesin mutants may cause perturbation of cohesion, at least in some leaf cells at distinct loci; (b) the decreased sister chromatid alignment in cohesin mutants can obviously not fully be compensated by other cohesion mechanisms such as DNA concatenation; (c) some cohesin genes, in addition to cohesion, might have further essential functions (e.g., for genome stability, apparently by facilitating correct recombination repair of double-strand breaks).
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany.
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16
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Watanabe K, Pacher M, Dukowic S, Schubert V, Puchta H, Schubert I. The STRUCTURAL MAINTENANCE OF CHROMOSOMES 5/6 complex promotes sister chromatid alignment and homologous recombination after DNA damage in Arabidopsis thaliana. THE PLANT CELL 2009; 21:2688-99. [PMID: 19737979 PMCID: PMC2768936 DOI: 10.1105/tpc.108.060525] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/13/2009] [Accepted: 08/24/2009] [Indexed: 05/18/2023]
Abstract
Sister chromatids are often arranged as incompletely aligned entities in interphase nuclei of Arabidopsis thaliana. The STRUCTURAL MAINTENANCE OF CHROMOSOMES (SMC) 5/6 complex, together with cohesin, is involved in double-strand break (DSB) repair by sister chromatid recombination in yeasts and mammals. Here, we analyzed the function of genes in Arabidopsis. The wild-type allele of SMC5 is essential for seed development. Each of the two SMC6 homologs of Arabidopsis is required for efficient repair of DNA breakage via intermolecular homologous recombination in somatic cells. Alignment of sister chromatids is enhanced transiently after X-irradiation (and mitomycin C treatment) in wild-type nuclei. In the smc5/6 mutants, the x-ray-mediated increase in sister chromatid alignment is much lower and delayed. The reduced S phase-established cohesion caused by a knockout mutation in one of the alpha-kleisin genes, SYN1, also perturbed enhancement of sister chromatid alignment after irradiation, suggesting that the S phase-established cohesion is a prerequisite for correct DSB-dependent cohesion. The radiation-sensitive51 mutant, deficient in heteroduplex formation during DSB repair, showed wild-type frequencies of sister chromatid alignment after X-irradiation, implying that the irradiation-mediated increase in sister chromatid alignment is a prerequisite for, rather than a consequence of, DNA strand exchange between sister chromatids. Our results suggest that the SMC5/6 complex promotes sister chromatid cohesion after DNA breakage and facilitates homologous recombination between sister chromatids.
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Affiliation(s)
- Koichi Watanabe
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Michael Pacher
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Stefanie Dukowic
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Holger Puchta
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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17
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Arabidopsis sister chromatids often show complete alignment or separation along a 1.2-Mb euchromatic region but no cohesion "hot spots". Chromosoma 2008; 117:261-6. [PMID: 18193258 DOI: 10.1007/s00412-007-0141-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 11/21/2007] [Accepted: 11/30/2007] [Indexed: 12/22/2022]
Abstract
Sister chromatid cohesion is a prerequisite for correct segregation and possibly other functions of replicated chromosomes. Except for yeast, no details are known about arrangement of cohesion sites along interphase chromosomes. Within nuclei of several higher plants, sister chromatids are frequently not aligned at various positions along chromosome arms. Therefore, we tested whether preferential alignment positions ("cohesion hot spots") and constant extension of and distances between aligned sites occur in plants. Along a approximately 1.2-Mb contig from the bottom arm of chromosome 1, the sister chromatid positions of 13 individual BAC inserts were found to be aligned for approximately 67-77% of homologues in 4C Arabidopsis thaliana nuclei. The differences between the 13 BAC positions were not significant at the P < 0.01 level. This suggests variability of alignment positions between cells and indicates the absence of cohesion "hot spots". Similar as for single BACs, FISH with the entire contig indicated complete alignment for approximately 69% and complete separation of sister chromatids for approximately 31% of homologues in 4C nuclei. Partial alignment or separation was barely detectable. When three BAC inserts from a 760-kb region were tested simultaneously, alignment or separation of only the central BAC occurred in 3.3% and 3.5% of replicated chromosomes, respectively. Thus, we assume that sister chromatids can be separated or aligned within a Mb range in differentiated cells. However, the minimum extension of aligned sites or distances between them may (in rare cases) fall below ~500 kb.
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18
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Barzel A, Kupiec M. Finding a match: how do homologous sequences get together for recombination? Nat Rev Genet 2008; 9:27-37. [PMID: 18040271 DOI: 10.1038/nrg2224] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Decades of research into homologous recombination have unravelled many of the details concerning the transfer of information between two homologous sequences. By contrast, the processes by which the interacting molecules initially colocalize are largely unknown. How can two homologous needles find each other in the genomic haystack? Is homologous pairing the result of a damage-induced homology search, or is it an enduring and general feature of the genomic architecture that facilitates homologous recombination whenever and wherever damage occurs? This Review presents the homologous-pairing enigma, delineates our current understanding of the process and offers guidelines for future research.
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Affiliation(s)
- Adi Barzel
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
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Bozza C, Pawlowski W. The cytogenetics of homologous chromosome pairing in meiosis in plants. Cytogenet Genome Res 2008; 120:313-9. [DOI: 10.1159/000121080] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2007] [Indexed: 11/19/2022] Open
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20
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Ribeiro T, Barão A, Viegas W, Morais-Cecíli L. Molecular cytogenetics of forest trees. Cytogenet Genome Res 2008; 120:220-7. [DOI: 10.1159/000121070] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2007] [Indexed: 01/03/2023] Open
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