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Sarıyer OS, Erbaş A. Polymer physics view of peripheral chromatin: de Gennes' self-similar carpet. Phys Rev E 2024; 109:054403. [PMID: 38907468 DOI: 10.1103/physreve.109.054403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/09/2024] [Indexed: 06/24/2024]
Abstract
Using scaling arguments to model peripheral chromatin localized near the inner surface of the nuclear envelope (NE) as a flexible polymer chain, we discuss the structural properties of the peripheral chromatin composed of alternating lamin-associated domains (LADs) and inter-LADs. Modeling the attraction of LADs to NE by de Gennes' self-similar carpet, which treats the chromatin layer as a polymer fractal, explains two major experimental observations. (i) The high density of chromatin close to the nuclear periphery decays to a constant density as the distance to the periphery increases. (ii) Due to the decreasing mesh size towards the nuclear periphery, the chromatin carpet inside NE excludes molecules (via nonspecific interactions) above a threshold size that depends on the distance from the nuclear periphery.
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Affiliation(s)
- Ozan S Sarıyer
- Pîrî Reis University, School of Arts and Sciences, Tuzla 34940, Istanbul, Turkey
| | - Aykut Erbaş
- UNAM National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey and University of Silesia, Institute of Physics, 41-500 Katowice, Poland
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2
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Abdelhady H, Aleanizy F, Alqahtani F, Bukhari A, Soliman S, Sau S, Iyer A. Visualizing the 4D Impact of Gold Nanoparticles on DNA. Int J Mol Sci 2023; 25:542. [PMID: 38203711 PMCID: PMC10778996 DOI: 10.3390/ijms25010542] [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: 11/27/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The genotoxicity of AuNPs has sparked a scientific debate, with one perspective attributing it to direct DNA damage and another to oxidative damage through reactive oxygen species (ROS) activation. This controversy poses challenges for the widespread use of AuNPs in biomedical applications. To address this debate, we employed four-dimensional atomic force microscopy (4DAFM) to examine the ability of AuNPs to damage DNA in vitro in the absence of ROS. To further examine whether the size and chemical coupling of these AuNPs are properties that control their toxicity, we exposed individual DNA molecules to three different types of AuNPs: small (average diameter = 10 nm), large (average diameter = 22 nm), and large conjugated (average diameter = 39 nm) AuNPs. We found that all types of AuNPs caused rapid (within minutes) and direct damage to the DNA molecules without the involvement of ROS. This research holds significant promise for advancing nanomedicines in diverse areas like viral therapy (including COVID-19), cancer treatment, and biosensor development for detecting DNA damage or mutations by resolving the ongoing debate regarding the genotoxicity mechanism. Moreover, it actively contributes to the continuous endeavors aimed at fully harnessing the capabilities of AuNPs across diverse biomedical fields, promising transformative healthcare solutions.
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Affiliation(s)
- Hosam Abdelhady
- Department of Physiology and Pharmacology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Fadilah Aleanizy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fulwah Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Bukhari
- College of Medicine, Taibah University, Medina 41477, Saudi Arabia
| | - Sahar Soliman
- Department of Physiology and Pharmacology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Samaresh Sau
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Arun Iyer
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI 48201, USA
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3
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Mondal S, Banerjee S, Dey D, Lahiri H, Mana T, Jana SS, Mukhopadhyay R. Impact of HMGB1 binding on the structural alterations of platinum drug-treated single dsDNA molecule. Biochimie 2023; 213:168-175. [PMID: 37211256 DOI: 10.1016/j.biochi.2023.05.012] [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: 02/15/2023] [Revised: 04/24/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
High mobility group B1 (HMGB1) is an architectural protein that recognizes the DNA damage sites formed by the platinum anticancer drugs. However, the impact of HMGB1 binding on the structural alterations of the platinum drug-treated single dsDNA molecules has remained largely unknown. Herein, the structural alterations induced by the platinum drugs, the mononuclear cisplatin and it's analog the trinuclear BBR3464, have been probed in presence of HMGB1, by atomic force microscopy (AFM) and AFM-based force spectroscopy. It is observed that the drug-induced DNA loop formation enhanced upon HMGB1 binding, most likely as a result of HMGB1-induced increase in DNA conformational flexibility that allowed the drug-binding sites to come close and form double adducts, thereby resulting in enhanced loop formation via inter-helix cross-linking. Since HMGB1 enhances DNA flexibility, the near-reversible structural transitions as observed in the force-extension curves (for 1 h drug treatment), generally occurred at lower forces in presence of HMGB1. The DNA structural integrity was largely lost after 24 h drug treatment as no reversible transition could be observed. The Young's modulus of the dsDNA molecules, as estimated from the force-extension analysis, increased upon drug treatment, due to formation of the drug-induced covalent cross-links and consequent reduction in DNA flexibility. The Young's modulus increased further in presence of HMGB1 due to HMGB1-induced enhancement in DNA flexibility that could ease formation of the drug-induced covalent cross-links. To our knowledge, this is the first report that shows an increase in the stiffness of the platinum drug-treated DNA molecules in presence of HMGB1.
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Affiliation(s)
- Sourav Mondal
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Siddhartha Banerjee
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Debapriya Dey
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Tanushree Mana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Siddhartha S Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India.
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4
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González L, Kolbin D, Trahan C, Jeronimo C, Robert F, Oeffinger M, Bloom K, Michnick SW. Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation. Nat Commun 2023; 14:1135. [PMID: 36854718 PMCID: PMC9975218 DOI: 10.1038/s41467-023-36391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Partitioning of active gene loci to the nuclear envelope (NE) is a mechanism by which organisms increase the speed of adaptation and metabolic robustness to fluctuating resources in the environment. In the yeast Saccharomyces cerevisiae, adaptation to nutrient depletion or other stresses, manifests as relocalization of active gene loci from nucleoplasm to the NE, resulting in more efficient transport and translation of mRNA. The mechanism by which this partitioning occurs remains a mystery. Here, we demonstrate that the yeast inositol depletion-responsive gene locus INO1 partitions to the nuclear envelope, driven by local histone acetylation-induced polymer-polymer phase separation from the nucleoplasmic phase. This demixing is consistent with recent evidence for chromatin phase separation by acetylation-mediated dissolution of multivalent histone association and fits a physical model where increased bending stiffness of acetylated chromatin polymer causes its phase separation from de-acetylated chromatin. Increased chromatin spring stiffness could explain nucleation of transcriptional machinery at active gene loci.
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Affiliation(s)
- Lidice González
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christian Trahan
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Marlene Oeffinger
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada.
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Bunning AR, Gupta Jr. ML. The importance of microtubule-dependent tension in accurate chromosome segregation. Front Cell Dev Biol 2023; 11:1096333. [PMID: 36755973 PMCID: PMC9899852 DOI: 10.3389/fcell.2023.1096333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/11/2023] [Indexed: 01/24/2023] Open
Abstract
Accurate chromosome segregation is vital for cell and organismal viability. The mitotic spindle, a bipolar macromolecular machine composed largely of dynamic microtubules, is responsible for chromosome segregation during each cell replication cycle. Prior to anaphase, a bipolar metaphase spindle must be formed in which each pair of chromatids is attached to microtubules from opposite spindle poles. In this bipolar configuration pulling forces from the dynamic microtubules can generate tension across the sister kinetochores. The tension status acts as a signal that can destabilize aberrant kinetochore-microtubule attachments and reinforces correct, bipolar connections. Historically it has been challenging to isolate the specific role of tension in mitotic processes due to the interdependency of attachment and tension status at kinetochores. Recent technical and experimental advances have revealed new insights into how tension functions during mitosis. Here we summarize the evidence that tension serves as a biophysical signal that unifies multiple aspects of kinetochore and centromere function to ensure accurate chromosome segregation.
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6
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Nikitin AA, Ivanova AV, Semkina AS, Lazareva PA, Abakumov MA. Magneto-Mechanical Approach in Biomedicine: Benefits, Challenges, and Future Perspectives. Int J Mol Sci 2022; 23:11134. [PMID: 36232435 PMCID: PMC9569787 DOI: 10.3390/ijms231911134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
The magneto-mechanical approach is a powerful technique used in many different applications in biomedicine, including remote control enzyme activity, cell receptors, cancer-selective treatments, mechanically-activated drug releases, etc. This approach is based on the use of a combination of magnetic nanoparticles and external magnetic fields that have led to the movement of such nanoparticles with torques and forces (enough to change the conformation of biomolecules or even break weak chemical bonds). However, despite many theoretical and experimental works on this topic, it is difficult to predict the magneto-mechanical effects in each particular case, while the important results are scattered and often cannot be translated to other experiments. The main reason is that the magneto-mechanical effect is extremely sensitive to changes in any parameter of magnetic nanoparticles and the environment and changes in the parameters of the applied magnetic field. Thus, in this review, we (1) summarize and propose a simplified theoretical explanation of the main factors affecting the efficiency of the magneto-mechanical approach; (2) discuss the nature of the MNP-mediated mechanical forces and their order of magnitude; (3) show some of the main applications of the magneto-mechanical approach in the control over the properties of biological systems.
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Affiliation(s)
- Aleksey A. Nikitin
- Laboratory of Biomedical Nanomaterials, National University of Science and Technology (MISIS), 119049 Moscow, Russia
- Department of Medical Nanobiotechnology, N.I. Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anna V. Ivanova
- Department of Medical Nanobiotechnology, N.I. Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alevtina S. Semkina
- Department of Medical Nanobiotechnology, N.I. Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Polina A. Lazareva
- Department of Medical Nanobiotechnology, N.I. Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Maxim A. Abakumov
- Department of Medical Nanobiotechnology, N.I. Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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7
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Abstract
The centromere serves as the binding site for the kinetochore and is essential for the faithful segregation of chromosomes throughout cell division. The point centromere in yeast is encoded by a ∼115 bp specific DNA sequence, whereas regional centromeres range from 6-10 kbp in fission yeast to 5-10 Mbp in humans. Understanding the physical structure of centromere chromatin (pericentromere in yeast), defined as the chromatin between sister kinetochores, will provide fundamental insights into how centromere DNA is woven into a stiff spring that is able to resist microtubule pulling forces during mitosis. One hallmark of the pericentromere is the enrichment of the structural maintenance of chromosome (SMC) proteins cohesin and condensin. Based on studies from population approaches (ChIP-seq and Hi-C) and experimentally obtained images of fluorescent probes of pericentromeric structure, as well as quantitative comparisons between simulations and experimental results, we suggest a mechanism for building tension between sister kinetochores. We propose that the centromere is a chromatin bottlebrush that is organized by the loop-extruding proteins condensin and cohesin. The bottlebrush arrangement provides a biophysical means to transform pericentromeric chromatin into a spring due to the steric repulsion between radial loops. We argue that the bottlebrush is an organizing principle for chromosome organization that has emerged from multiple approaches in the field.
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8
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Chang RYK, Chow MY, Khanal D, Chen D, Chan HK. Dry powder pharmaceutical biologics for inhalation therapy. Adv Drug Deliv Rev 2021; 172:64-79. [PMID: 33705876 DOI: 10.1016/j.addr.2021.02.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/17/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
Therapeutic biologics such as genes, peptides, proteins, virus and cells provide clinical benefits and are becoming increasingly important tools in respiratory medicine. Pulmonary delivery of therapeutic biologics enables the potential for safe and effective treatment option for respiratory diseases due to high bioavailability while minimizing absorption into the systemic circulation, reducing off-target toxicity to other organs. Development of inhalable powder formulation requires stabilization of complex biological materials, and each type of biologics may present unique challenges and require different formulation strategy combined with manufacture process to ensure biological and physical stabilities during production and over shelf-life. This review examines key formulation strategies for stabilizing proteins, nucleic acids, virus (bacteriophages) and bacterial cells in inhalable powders. It also covers characterization methods used to assess physicochemical properties and aerosol performance of the powders, biological activity and structural integrity of the biologics, and chemical analysis at the nanoscale. Furthermore, the review includes manufacture technologies which are based on lyophilization and spray-drying as they have been applied to manufacture Food and Drug Administration (FDA)-approved protein powders. In perspective, formulation and manufacture of inhalable powders for biologic are highly challenging but attainable. The key requirements are the stability of both the biologics and the powder, along with the powder dispersibility. The formulation to be developed depends on the manufacture process as it will subject the biologics to different stresses (temperature, mechanical and chemical) which could lead to degradation by different pathways. Stabilizing excipients coupled with the suitable choice of process can alleviate the stability issues of inhaled powders of biologics.
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9
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Kilic Z, Sgouralis I, Pressé S. Residence time analysis of RNA polymerase transcription dynamics: A Bayesian sticky HMM approach. Biophys J 2021; 120:1665-1679. [PMID: 33705761 DOI: 10.1016/j.bpj.2021.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 01/09/2023] Open
Abstract
The time spent by a single RNA polymerase (RNAP) at specific locations along the DNA, termed "residence time," reports on the initiation, elongation, and termination stages of transcription. At the single-molecule level, this information can be obtained from dual ultrastable optical trapping experiments, revealing a transcriptional elongation of RNAP interspersed with residence times of variable duration. Successfully discriminating between long and short residence times was used by previous approaches to learn about RNAP's transcription elongation dynamics. Here, we propose an approach based on the Bayesian sticky hidden Markov model that treats all residence times for an Escherichia coli RNAP on an equal footing without a priori discriminating between long and short residence times. Furthermore, our method has two additional advantages: we provide full distributions around key point statistics and directly treat the sequence dependence of RNAP's elongation rate. By applying our approach to experimental data, we find assigned relative probabilities on long versus short residence times, force-dependent average residence time transcription elongation dynamics, ∼10% drop in the average backtracking durations in the presence of GreB, and ∼20% drop in the average residence time as a function of applied force in the presence of RNaseA.
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Affiliation(s)
- Zeliha Kilic
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee
| | - Steve Pressé
- Center for Biological Physics, Department of Physics and School of Molecular Sciences, Arizona State University, Tempe, Arizona. spresse@%20asu.edu
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Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041885] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.
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He Y, Lawrimore J, Cook D, Van Gorder EE, De Larimat SC, Adalsteinsson D, Forest MG, Bloom K. Statistical mechanics of chromosomes: in vivo and in silico approaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and chromatin substrate properties. Nucleic Acids Res 2020; 48:11284-11303. [PMID: 33080019 PMCID: PMC7672462 DOI: 10.1093/nar/gkaa871] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/14/2022] Open
Abstract
The revolution in understanding higher order chromosome dynamics and organization derives from treating the chromosome as a chain polymer and adapting appropriate polymer-based physical principles. Using basic principles, such as entropic fluctuations and timescales of relaxation of Rouse polymer chains, one can recapitulate the dominant features of chromatin motion observed in vivo. An emerging challenge is to relate the mechanical properties of chromatin to more nuanced organizational principles such as ubiquitous DNA loops. Toward this goal, we introduce a real-time numerical simulation model of a long chain polymer in the presence of histones and condensin, encoding physical principles of chromosome dynamics with coupled histone and condensin sources of transient loop generation. An exact experimental correlate of the model was obtained through analysis of a model-matching fluorescently labeled circular chromosome in live yeast cells. We show that experimentally observed chromosome compaction and variance in compaction are reproduced only with tandem interactions between histone and condensin, not from either individually. The hierarchical loop structures that emerge upon incorporation of histone and condensin activities significantly impact the dynamic and structural properties of chromatin. Moreover, simulations reveal that tandem condensin–histone activity is responsible for higher order chromosomal structures, including recently observed Z-loops.
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Affiliation(s)
- Yunyan He
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Diana Cook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - David Adalsteinsson
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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12
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Lawrimore CJ, Lawrimore J, He Y, Chavez S, Bloom K. Polymer perspective of genome mobilization. Mutat Res 2020; 821:111706. [PMID: 32516654 DOI: 10.1016/j.mrfmmm.2020.111706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
Chromosome motion is an intrinsic feature of all DNA-based metabolic processes and is a particularly well-documented response to both DNA damage and repair. By using both biological and polymer physics approaches, many of the contributing factors of chromatin motility have been elucidated. These include the intrinsic properties of chromatin, such as stiffness, as well as the loop modulators condensin and cohesin. Various biological factors such as external tethering to nuclear domains, ATP-dependent processes, and nucleofilaments further impact chromatin motion. DNA damaging agents that induce double-stranded breaks also cause increased chromatin motion that is modulated by recruitment of repair and checkpoint proteins. Approaches that integrate biological experimentation in conjunction with models from polymer physics provide mechanistic insights into the role of chromatin dynamics in biological function. In this review we discuss the polymer models and the effects of both DNA damage and repair on chromatin motion as well as mechanisms that may underlie these effects.
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Affiliation(s)
- Colleen J Lawrimore
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Josh Lawrimore
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Yunyan He
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Sergio Chavez
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Kerry Bloom
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States.
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13
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Chromatin Viscoelasticity Measured by Local Dynamic Analysis. Biophys J 2020; 118:2258-2267. [PMID: 32320676 PMCID: PMC7203068 DOI: 10.1016/j.bpj.2020.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 12/25/2022] Open
Abstract
The nucleus in eukaryotic cells is a crowded environment that consists of genetic code along the DNA, together with a condensed solution of proteins, RNA, and other molecules. It is subjected to highly dynamic processes, including cell division, transcription, and DNA repair. In addition, the genome in the nucleus is subjected to external forces applied by the cytoplasmic skeleton and neighboring cells, as well as to internal nuclear forces. These forces oppose the need to maintain the genome order, which may be compensated by the internal nuclear viscoelastic properties that can restrain these forces. The structural and mechanical properties of chromatin inside the nucleus are still not fully clear; however, their importance for the proper functioning of the cells is unquestionable. Different approaches have been developed for this aim, ranging from directly measuring the dynamic and elastic properties of chromatin to studying the interactions of chromatin with the surrounding envelope and nuclear bodies. Although the elasticity of naked DNA in vitro is well characterized, the elasticity of chromatin in live cells is more complex and is still not fully understood. Here, we studied the elastic properties of chromatin by dynamic measurements in live cells, followed by viscoelastic modeling. We measured the trajectories of single chromatin loci, centromeres, and telomeres in live cells and analyzed their dynamics using the Langevin formalism. We assumed that the overall effect of the chromatin network forces can be modeled for each locus by a local harmonic potential and calculated the effective force constant. In addition, we assumed that this harmonic force results from the chromatin network formed by the internal polymer structure together with cross-links formed by the protein complex. We show that lamin A has the greatest effect on chromatin viscoelasticity and that its removal leads to a significant reduction in the local harmonic force.
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14
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Smith KB, Wehrli M, Japaridze A, Assenza S, Dekker C, Mezzenga R. Interplay between Confinement and Drag Forces Determine the Fate of Amyloid Fibrils. PHYSICAL REVIEW LETTERS 2020; 124:118102. [PMID: 32242730 DOI: 10.1103/physrevlett.124.118102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/26/2020] [Indexed: 06/11/2023]
Abstract
The fine interplay between the simultaneous stretching and confinement of amyloid fibrils is probed by combining a microcapillary setup with atomic force microscopy. Single-molecule statistics reveal how the stretching of fibrils changed from force to confinement dominated at different length scales. System order, however, is solely ruled by confinement. Coarse-grained simulations support the results and display the potential to tailor system properties by tuning the two effects. These findings may further help shed light on in vivo amyloid fibril growth and transport in highly confined environments such as blood vessels.
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Affiliation(s)
- Kathleen Beth Smith
- Department of Health Sciences and Technology, Swiss Federal Institute of Technology in Zurich, 8092 Zurich, Switzerland
| | - Monika Wehrli
- Department of Health Sciences and Technology, Swiss Federal Institute of Technology in Zurich, 8092 Zurich, Switzerland
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Salvatore Assenza
- Department of Health Sciences and Technology, Swiss Federal Institute of Technology in Zurich, 8092 Zurich, Switzerland
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, Swiss Federal Institute of Technology in Zurich, 8092 Zurich, Switzerland
- Department of Materials, Swiss Federal Institute of Technology, Zurich, 8093, Zurich, Switzerland
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15
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Job Opening for Nucleosome Mechanic: Flexibility Required. Cells 2020; 9:cells9030580. [PMID: 32121488 PMCID: PMC7140402 DOI: 10.3390/cells9030580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/21/2022] Open
Abstract
The nucleus has been studied for well over 100 years, and chromatin has been the intense focus of experiments for decades. In this review, we focus on an understudied aspect of chromatin biology, namely the chromatin fiber polymer’s mechanical properties. In recent years, innovative work deploying interdisciplinary approaches including computational modeling, in vitro manipulations of purified and native chromatin have resulted in deep mechanistic insights into how the mechanics of chromatin might contribute to its function. The picture that emerges is one of a nucleus that is shaped as much by external forces pressing down upon it, as internal forces pushing outwards from the chromatin. These properties may have evolved to afford the cell a dynamic and reversible force-induced communication highway which allows rapid coordination between external cues and internal genomic function.
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16
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Basavalingappa V, Bera S, Xue B, Azuri I, Tang Y, Tao K, Shimon LJW, Sawaya MR, Kolusheva S, Eisenberg DS, Kronik L, Cao Y, Wei G, Gazit E. Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid. Nat Commun 2019; 10:5256. [PMID: 31748568 PMCID: PMC6868146 DOI: 10.1038/s41467-019-13250-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/23/2019] [Indexed: 01/25/2023] Open
Abstract
The variety and complexity of DNA-based structures make them attractive candidates for nanotechnology, yet insufficient stability and mechanical rigidity, compared to polyamide-based molecules, limit their application. Here, we combine the advantages of polyamide materials and the structural patterns inspired by nucleic-acids to generate a mechanically rigid fluorenylmethyloxycarbonyl (Fmoc)-guanine peptide nucleic acid (PNA) conjugate with diverse morphology and photoluminescent properties. The assembly possesses a unique atomic structure, with each guanine head of one molecule hydrogen bonded to the Fmoc carbonyl tail of another molecule, generating a non-planar cyclic quartet arrangement. This structure exhibits an average stiffness of 69.6 ± 6.8 N m-1 and Young's modulus of 17.8 ± 2.5 GPa, higher than any previously reported nucleic acid derived structure. This data suggests that the unique cation-free "basket" formed by the Fmoc-G-PNA conjugate can serve as an attractive component for the design of new materials based on PNA self-assembly for nanotechnology applications.
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Affiliation(s)
- Vasantha Basavalingappa
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Santu Bera
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, 210093, Nanjing, People's Republic of China
| | - Ido Azuri
- Department of Materials and Interfaces, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, 200433, Shanghai, People's Republic of China
| | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - David S Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, 210093, Nanjing, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, 200433, Shanghai, People's Republic of China
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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17
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Guérin TM, Béneut C, Barinova N, López V, Lazar-Stefanita L, Deshayes A, Thierry A, Koszul R, Dubrana K, Marcand S. Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis. Mol Cell 2019; 75:131-144.e3. [PMID: 31204167 DOI: 10.1016/j.molcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/12/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins.
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Affiliation(s)
- Thomas M Guérin
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Claire Béneut
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Natalja Barinova
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Virginia López
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Alice Deshayes
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Karine Dubrana
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Stéphane Marcand
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France.
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18
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Pawłowska S, Nakielski P, Pierini F, Piechocka IK, Zembrzycki K, Kowalewski TA. Lateral migration of electrospun hydrogel nanofilaments in an oscillatory flow. PLoS One 2017; 12:e0187815. [PMID: 29141043 PMCID: PMC5687761 DOI: 10.1371/journal.pone.0187815] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/26/2017] [Indexed: 12/31/2022] Open
Abstract
The recent progress in bioengineering has created great interest in the dynamics and manipulation of long, deformable macromolecules interacting with fluid flow. We report experimental data on the cross-flow migration, bending, and buckling of extremely deformable hydrogel nanofilaments conveyed by an oscillatory flow into a microchannel. The changes in migration velocity and filament orientation are related to the flow velocity and the filament's initial position, deformation, and length. The observed migration dynamics of hydrogel filaments qualitatively confirms the validity of the previously developed worm-like bead-chain hydrodynamic model. The experimental data collected may help to verify the role of hydrodynamic interactions in molecular simulations of long molecular chains dynamics.
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Affiliation(s)
- Sylwia Pawłowska
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Nakielski
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Filippo Pierini
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Izabela K. Piechocka
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Krzysztof Zembrzycki
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz A. Kowalewski
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
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19
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Volokh OI, Bozdaganyan ME, Shaitan KV. Assessment of the DNA-binding properties of actinomycin and its derivatives by molecular dynamics simulation. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350915060275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Measuring the elasticity of ribonucleotide(s)-containing DNA molecules using AFM. Methods Mol Biol 2016; 1297:43-57. [PMID: 25895994 DOI: 10.1007/978-1-4939-2562-9_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribonucleotides, ribonucleoside monophosphates (rNMPs), have been revealed as possibly the most noncanonical nucleotides in genomic DNA. rNMPs, either not removed from Okazaki fragments during DNA replication or incorporated and scattered throughout the genome, pose a perturbation to the structure and a threat to the stability of DNA. The instability of DNA is mainly due to the extra 2'-hydroxyl (OH) group of rNMPs which give rise to local structural effects, which may disturb various molecular interactions in cells. As a result of these structural perturbations by rNMPs, the elastic properties of DNA are also affected. Here, we show the approach to test whether the presence of rNMPs in DNA duplexes could alter the elasticity of DNA by implementing atomic force microscopy (AFM)-based single molecule force-measurements of short rNMP(s)-containing oligonucleotides (oligos).
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21
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Lawrimore J, Aicher JK, Hahn P, Fulp A, Kompa B, Vicci L, Falvo M, Taylor RM, Bloom K. ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin. Mol Biol Cell 2016; 27:153-66. [PMID: 26538024 PMCID: PMC4694754 DOI: 10.1091/mbc.e15-08-0575] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/27/2015] [Accepted: 10/27/2015] [Indexed: 12/12/2022] Open
Abstract
ChromoShake is a three-dimensional simulator designed to find the thermodynamically favored states for given chromosome geometries. The simulator has been applied to a geometric model based on experimentally determined positions and fluctuations of DNA and the distribution of cohesin and condensin in the budding yeast centromere. Simulations of chromatin in differing initial configurations reveal novel principles for understanding the structure and function of a eukaryotic centromere. The entropic position of DNA loops mirrors their experimental position, consistent with their radial displacement from the spindle axis. The barrel-like distribution of cohesin complexes surrounding the central spindle in metaphase is a consequence of the size of the DNA loops within the pericentromere to which cohesin is bound. Linkage between DNA loops of different centromeres is requisite to recapitulate experimentally determined correlations in DNA motion. The consequences of radial loops and cohesin and condensin binding are to stiffen the DNA along the spindle axis, imparting an active function to the centromere in mitosis.
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Affiliation(s)
- Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Joseph K Aicher
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Patrick Hahn
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Alyona Fulp
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Ben Kompa
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Leandra Vicci
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Michael Falvo
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Russell M Taylor
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
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22
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Lee S, Wang C, Song J, Kim DG, Oh Y, Ko W, Lee J, Park J, Lee HS, Jo K. Investigation of various fluorescent protein–DNA binding peptides for effectively visualizing large DNA molecules. RSC Adv 2016. [DOI: 10.1039/c6ra08683g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-molecule DNA visualization with fluorescent protein DNA binding peptides.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Cong Wang
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Junghyun Song
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Do-geun Kim
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Yeeun Oh
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Wooseok Ko
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jinyong Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jungyul Park
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Hyun Soo Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
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23
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Brodin JD, Smith SJ, Carr JR, Tezcan FA. Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block. J Am Chem Soc 2015; 137:10468-71. [PMID: 26256820 PMCID: PMC6855837 DOI: 10.1021/jacs.5b05755] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Due to their structural and mechanical properties, 1D helical protein assemblies represent highly attractive design targets for biomolecular engineering and protein design. Here we present a designed, tetrameric protein building block, Zn8R4, which assembles via Zn coordination interactions into a series of crystalline, helical nanotubes whose widths can be controlled by solution conditions. X-ray crystallography and transmission electron microscopy (TEM) measurements indicate that all classes of protein nanotubes are constructed through the same 2D arrangement of Zn8R4 tetramers held together by Zn coordination. The mechanical properties of these nanotubes are correlated with their widths. All Zn8R4 nanotubes are found to be highly flexible despite possessing crystalline order, owing to their minimal interbuilding-block interactions mediated solely by metal coordination.
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Affiliation(s)
| | | | - Jessica R. Carr
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0356
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0356
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24
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Li Y, Sheiko SS. Molecular Mechanochemistry: Engineering and Implications of Inherently Strained Architectures. Top Curr Chem (Cham) 2015; 369:1-36. [PMID: 25805145 DOI: 10.1007/128_2015_627] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Mechanical activation of chemical bonds is usually achieved by applying external forces. However, nearly all molecules exhibit inherent strain of their chemical bonds and angles as a result of constraints imposed by covalent bonding and interactions with the surrounding environment. Particularly strong deformation of bonds and angles is observed in hyperbranched macromolecules caused by steric repulsion of densely grafted polymer branches. In addition to the tension amplification, macromolecular architecture allows for accurate control of strain distribution, which enables focusing of the internal mechanical tension to specific chemical bonds and angles. As such, chemically identical bonds in self-strained macromolecules become physically distinct because the difference in bond tension leads to the corresponding difference in the electronic structure and chemical reactivity of individual bonds within the same macromolecule. In this review, we outline different approaches to the design of strained macromolecules along with physical principles of tension management, including generation, amplification, and focusing of mechanical tension at specific chemical bonds.
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Affiliation(s)
- Yuanchao Li
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599-3290, USA
| | - Sergei S Sheiko
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599-3290, USA.
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25
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Abstract
Centromeres are specialized domains of heterochromatin that provide the foundation for the kinetochore. Centromeric heterochromatin is characterized by specific histone modifications, a centromere-specific histone H3 variant (CENP-A), and the enrichment of cohesin, condensin, and topoisomerase II. Centromere DNA varies orders of magnitude in size from 125 bp (budding yeast) to several megabases (human). In metaphase, sister kinetochores on the surface of replicated chromosomes face away from each other, where they establish microtubule attachment and bi-orientation. Despite the disparity in centromere size, the distance between separated sister kinetochores is remarkably conserved (approximately 1 μm) throughout phylogeny. The centromere functions as a molecular spring that resists microtubule-based extensional forces in mitosis. This review explores the physical properties of DNA in order to understand how the molecular spring is built and how it contributes to the fidelity of chromosome segregation.
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Affiliation(s)
- Kerry S Bloom
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280;
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26
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Chiu HC, Koh KD, Evich M, Lesiak AL, Germann MW, Bongiorno A, Riedo E, Storici F. RNA intrusions change DNA elastic properties and structure. NANOSCALE 2014; 6:10009-17. [PMID: 24992674 DOI: 10.1039/c4nr01794c] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The units of RNA, termed ribonucleoside monophosphates (rNMPs), have been recently found as the most abundant defects present in DNA. Despite the relevance, it is largely unknown if and how rNMPs embedded in DNA can change the DNA structure and mechanical properties. Here, we report that rNMPs incorporated in DNA can change the elastic properties of DNA. Atomic force microscopy (AFM)-based single molecule elasticity measurements show that rNMP intrusions in short DNA duplexes can decrease--by 32%--or slightly increase the stretch modulus of DNA molecules for two sequences reported in this study. Molecular dynamics simulations and nuclear magnetic resonance spectroscopy identify a series of significant local structural alterations of DNA containing embedded rNMPs, especially at the rNMPs and nucleotide 3' to the rNMP sites. The demonstrated ability of rNMPs to locally alter DNA mechanical properties and structure may help in understanding how such intrusions impact DNA biological functions and find applications in structural DNA and RNA nanotechnology.
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Affiliation(s)
- Hsiang-Chih Chiu
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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27
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Centromere tethering confines chromosome domains. Mol Cell 2013; 52:819-31. [PMID: 24268574 DOI: 10.1016/j.molcel.2013.10.021] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/10/2013] [Accepted: 10/14/2013] [Indexed: 12/20/2022]
Abstract
The organization of chromosomes into territories plays an important role in a wide range of cellular processes, including gene expression, transcription, and DNA repair. Current understanding has largely excluded the spatiotemporal dynamic fluctuations of the chromatin polymer. We combine in vivo chromatin motion analysis with mathematical modeling to elucidate the physical properties that underlie the formation and fluctuations of territories. Chromosome motion varies in predicted ways along the length of the chromosome, dependent on tethering at the centromere. Detachment of a tether upon inactivation of the centromere results in increased spatial mobility. A confined bead-spring chain tethered at both ends provides a mechanism to generate observed variations in local mobility as a function of distance from the tether. These predictions are realized in experimentally determined higher effective spring constants closer to the centromere. The dynamic fluctuations and territorial organization of chromosomes are, in part, dictated by tethering at the centromere.
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28
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Rago F, Cheeseman IM. Review series: The functions and consequences of force at kinetochores. ACTA ACUST UNITED AC 2013; 200:557-65. [PMID: 23460675 PMCID: PMC3587826 DOI: 10.1083/jcb.201211113] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Chromosome segregation requires the generation of force at the kinetochore—the multiprotein structure that facilitates attachment of chromosomes to spindle microtubules. This force is required both to move chromosomes and to signal the formation of proper bioriented attachments. To understand the role of force in these processes, it is critical to define how force is generated at kinetochores, the contributions of this force to chromosome movement, and how the kinetochore is structured and organized to withstand and respond to force. Classical studies and recent work provide a framework to dissect the mechanisms, functions, and consequences of force at kinetochores.
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Affiliation(s)
- Florencia Rago
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 0214, USA
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29
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Abstract
Cellular defects that impair the fidelity of mitosis promote chromosome missegregation and aneuploidy. Increasing evidence reveals that errors in mitosis can also promote the direct and indirect acquisition of DNA damage and chromosome breaks. Consequently, deregulated cell division can devastate the integrity of the normal genome and unleash a variety of oncogenic stimuli that may promote transformation. Recent work has shed light on the mechanisms that link abnormal mitosis with the development of DNA damage, how cells respond to such affronts, and the potential impact on tumorigenesis.
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Affiliation(s)
- Neil J Ganem
- Howard Hughes Medical Institute, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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30
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Qiu R, Zhang J, Xiang X. Identification of a novel site in the tail of dynein heavy chain important for dynein function in vivo. J Biol Chem 2012; 288:2271-80. [PMID: 23212922 DOI: 10.1074/jbc.m112.412403] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The minus end-directed microtubule motor cytoplasmic dynein is responsible for the intracellular movements of many organelles, including nuclei and endosomes. The dynein heavy chain contains a C-terminal motor domain and an N-terminal tail domain. The tail binds other dynein subunits and the cargo-interacting dynactin complex but is dispensable for movement of single dynein molecules in vitro. Here, we identified a mutation in the Aspergillus nidulans heavy chain tail domain, nudA(F208V), which causes obvious defects in dynein-mediated nuclear positioning and early endosome movement. Astonishingly, the nudA(F208I) mutation in the same position does not cause the same defects, suggesting that a subtle difference in the size of the amino acid side chain at this position has a significant consequence. Importantly, our biochemical analyses indicate that the nudA(F208V) mutation does not affect dynein subunit interactions and the mutant dynein is also able to bind dynactin and another dynein regulator, NUDF/LIS1. The mutant dynein is able to physically interact with the early endosome cargo, but dynein-mediated early endosome movement away from the hyphal tip occurs at a significantly reduced frequency. Within the small group of early endosomes that move away from the hyphal tip in the mutant, the average speed of movement is lower than that in the wild type. Given the dispensability of the dynein tail in dynein motility in vitro, our results support the notion that the structural integrity of the dynein tail is critical in vivo for the coordination of dynein force production and movement when the motor is heavily loaded.
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Affiliation(s)
- Rongde Qiu
- Department of Biochemistry and Molecular Biology, the Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
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31
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Topoisomerase II- and condensin-dependent breakage of MEC1ATR-sensitive fragile sites occurs independently of spindle tension, anaphase, or cytokinesis. PLoS Genet 2012; 8:e1002978. [PMID: 23133392 PMCID: PMC3486896 DOI: 10.1371/journal.pgen.1002978] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/08/2012] [Indexed: 11/24/2022] Open
Abstract
Fragile sites are loci of recurrent chromosome breakage in the genome. They are found in organisms ranging from bacteria to humans and are implicated in genome instability, evolution, and cancer. In budding yeast, inactivation of Mec1, a homolog of mammalian ATR, leads to chromosome breakage at fragile sites referred to as replication slow zones (RSZs). RSZs are proposed to be homologous to mammalian common fragile sites (CFSs) whose stability is regulated by ATR. Perturbation during S phase, leading to elevated levels of stalled replication forks, is necessary but not sufficient for chromosome breakage at RSZs or CFSs. To address the nature of additional event(s) required for the break formation, we examined involvement of the currently known or implicated mechanisms of endogenous chromosome breakage, including errors in replication fork restart, premature mitotic chromosome condensation, spindle tension, anaphase, and cytokinesis. Results revealed that chromosome breakage at RSZs is independent of the RAD52 epistasis group genes and of TOP3, SGS1, SRS2, MMS4, or MUS81, indicating that homologous recombination and other recombination-related processes associated with replication fork restart are unlikely to be involved. We also found spindle force, anaphase, or cytokinesis to be dispensable. RSZ breakage, however, required genes encoding condensin subunits (YCG1, YSC4) and topoisomerase II (TOP2). We propose that chromosome break formation at RSZs following Mec1 inactivation, a model for mammalian fragile site breakage, is mediated by internal chromosomal stress generated during mitotic chromosome condensation. Chromosome breakage can occur during normal cell division. When it occurs, the breaks do not arise randomly throughout the genome, but at preferred locations referred to as fragile sites. Chromosome breakage at fragile sites is an evolutionarily conserved phenomenon, implicated in evolution and speciation. In humans, fragile site instability is also implicated in mental retardation and cancer. Despite its biological and clinical relevance, the mechanism(s) by which breaks are introduced at mammalian fragile sites remains unresolved. Although several plausible models have been proposed, it has not been possible to ascertain their contribution, largely due to the lack of a suitable experimental system. Here, we study a yeast model system that closely recapitulates the phenomenon of chromosome breakage at mammalian fragile sites. We eliminate all but one of the currently considered models—premature compaction of the incompletely replicated genome in preparation for their segregation during cell division. We also find that the breakage required functions of three proteins involved in the genome compaction, an essential process that is evolutionarily conserved from bacteria to humans. Our findings suggest that a fundamental chromosomal process required for normal cell division can paradoxically cause genome instability and/or cell death, by triggering chromosome breakage at fragile sites.
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Shi L, Carn F, Boué F, Mosser G, Buhler E. Nanorods of Well-Defined Length and Monodisperse Cross-Section Obtained from Electrostatic Complexation of Nanoparticles with a Semiflexible Biopolymer. ACS Macro Lett 2012; 1:857-861. [PMID: 35607133 DOI: 10.1021/mz300200y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We show by combining small-angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (cryo-TEM) that anionic silica nanoparticles (SiNPs) assemble into well-defined 1D cluster when mixed with a dilute solution of semiflexible chitosan polycation. The nanorods are stable in excess of SiNPs and composed of 10 SiNPs well-ordered into straight single strands with length Lrod ≈ 184.0 nm and radius Rrod = 9.2 nm = RSiNPs. We point out that the ratio between the chitosan persistence length and the SiNP radius, which is here equal to 1, can be the determining condition to obtain such original objects.
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Affiliation(s)
- Li Shi
- Laboratoire Matière
et
Systèmes Complexes (MSC), UMR 7057, Université Paris Diderot-Paris 7, Bâtiment Condorcet, 75205
Paris cedex 13, France
- Laboratoire Léon Brillouin, UMR 12 CEA-CNRS, CEA Saclay, 91191 Gif-sur-Yvette,
France
| | - Florent Carn
- Laboratoire Matière
et
Systèmes Complexes (MSC), UMR 7057, Université Paris Diderot-Paris 7, Bâtiment Condorcet, 75205
Paris cedex 13, France
| | - François Boué
- Laboratoire Léon Brillouin, UMR 12 CEA-CNRS, CEA Saclay, 91191 Gif-sur-Yvette,
France
| | - Gervaise Mosser
- Laboratoire Chimie
de la Matière
Condensée de Paris, UMR 7574, UPMC, Collège de France, 11 place Marcelin Berthelot, 75005 Paris,
France
| | - Eric Buhler
- Laboratoire Matière
et
Systèmes Complexes (MSC), UMR 7057, Université Paris Diderot-Paris 7, Bâtiment Condorcet, 75205
Paris cedex 13, France
- Laboratoire Léon Brillouin, UMR 12 CEA-CNRS, CEA Saclay, 91191 Gif-sur-Yvette,
France
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Charlebois BD, Kollu S, Schek HT, Compton DA, Hunt AJ. Spindle pole mechanics studied in mitotic asters: dynamic distribution of spindle forces through compliant linkages. Biophys J 2011; 100:1756-64. [PMID: 21463589 DOI: 10.1016/j.bpj.2011.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 01/15/2011] [Accepted: 02/08/2011] [Indexed: 02/05/2023] Open
Abstract
During cell division, chromosomes must faithfully segregate to maintain genome integrity, and this dynamic mechanical process is driven by the macromolecular machinery of the mitotic spindle. However, little is known about spindle mechanics. For example, spindle microtubules are organized by numerous cross-linking proteins yet the mechanical properties of those cross-links remain unexplored. To examine the mechanical properties of microtubule cross-links we applied optical trapping to mitotic asters that form in mammalian mitotic extracts. These asters are foci of microtubules, motors, and microtubule-associated proteins that reflect many of the functional properties of spindle poles and represent centrosome-independent spindle-pole analogs. We observed bidirectional motor-driven microtubule movements, showing that microtubule linkages within asters are remarkably compliant (mean stiffness 0.025 pN/nm) and mediated by only a handful of cross-links. Depleting the motor Eg5 reduced this stiffness, indicating that Eg5 contributes to the mechanical properties of microtubule asters in a manner consistent with its localization to spindle poles in cells. We propose that compliant linkages among microtubules provide a mechanical architecture capable of accommodating microtubule movements and distributing force among microtubules without loss of pole integrity-a mechanical paradigm that may be important throughout the spindle.
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Affiliation(s)
- Blake D Charlebois
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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Nakai W, Westmoreland J, Yeh E, Bloom K, Resnick MA. Chromosome integrity at a double-strand break requires exonuclease 1 and MRX. DNA Repair (Amst) 2010; 10:102-10. [PMID: 21115410 DOI: 10.1016/j.dnarep.2010.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 09/09/2010] [Accepted: 10/11/2010] [Indexed: 12/16/2022]
Abstract
The continuity of duplex DNA is generally considered a prerequisite for chromosome continuity. However, as previously shown in yeast as well as human cells, the introduction of a double-strand break (DSB) does not generate a chromosome break (CRB) in yeast or human cells. The transition from DSB to CRB was found to be under limited control by the tethering function of the RAD50/MRE11/XRS2 (MRX) complex. Using a system for differential fluorescent marking of both sides of an endonuclease-induced DSB in single cells, we found that nearly all DSBs are converted to CRBs in cells lacking both exonuclease 1 (EXO1) activity and MRX complex. Thus, it appears that some feature of exonuclease processing or resection at a DSB is critical for maintaining broken chromosome ends in close proximity. In addition, we discovered a thermal sensitive (cold) component to CRB formation in an MRX mutant that has implications for chromosome end mobility and/or end-processing.
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Affiliation(s)
- Wataru Nakai
- National Institute of Environmental Health Sciences, NIH, Laboratory of Molecular Genetics, Research Triangle Park, NC 27709, USA
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Zhang J, Zhuang L, Lee Y, Abenza JF, Peñalva MA, Xiang X. The microtubule plus-end localization of Aspergillus dynein is important for dynein-early-endosome interaction but not for dynein ATPase activation. J Cell Sci 2010; 123:3596-604. [PMID: 20876661 DOI: 10.1242/jcs.075259] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cytoplasmic dynein in filamentous fungi accumulates at microtubule plus-ends near the hyphal tip, which is important for minus-end-directed transport of early endosomes. It was hypothesized that dynein is switched on at the plus-end by cargo association. Here, we show in Aspergillus nidulans that kinesin-1-dependent plus-end localization is not a prerequisite for dynein ATPase activation. First, the Walker A and Walker B mutations in the dynein heavy chain AAA1 domain implicated in blocking different steps of the ATPase cycle cause different effects on dynein localization to microtubules, arguing against the suggestion that ATPase is inactive before arriving at the plus-end. Second, dynein from ΔkinA (kinesin 1) mutant cells has normal ATPase activity despite the absence of dynein plus-end accumulation. In ΔkinA hyphae, dynein localizes along microtubules and does not colocalize with abnormally accumulated early endosomes at the hyphal tip. This is in contrast to the colocalization of dynein and early endosomes in the absence of NUDF/LIS1. However, the Walker B mutation allows dynein to colocalize with the hyphal-tip-accumulated early endosomes in the ΔkinA background. We suggest that the normal ability of dyenin to interact with microtubules as an active minus-end-directed motor demands kinesin-1-mediated plus-end accumulation for effective interactions with early endosomes.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, USUHS, Bethesda, MD 20814, USA
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Centromere replication timing determines different forms of genomic instability in Saccharomyces cerevisiae checkpoint mutants during replication stress. Genetics 2009; 183:1249-60. [PMID: 19805819 DOI: 10.1534/genetics.109.107508] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Yeast replication checkpoint mutants lose viability following transient exposure to hydroxyurea, a replication-impeding drug. In an effort to understand the basis for this lethality, we discovered that different events are responsible for inviability in checkpoint-deficient cells harboring mutations in the mec1 and rad53 genes. By monitoring genomewide replication dynamics of cells exposed to hydroxyurea, we show that cells with a checkpoint deficient allele of RAD53, rad53K227A, fail to duplicate centromeres. Following removal of the drug, however, rad53K227A cells recover substantial DNA replication, including replication through centromeres. Despite this recovery, the rad53K227A mutant fails to achieve biorientation of sister centromeres during recovery from hydroxyurea, leading to secondary activation of the spindle assembly checkpoint (SAC), aneuploidy, and lethal chromosome segregation errors. We demonstrate that cell lethality from this segregation defect could be partially remedied by reinforcing bipolar attachment. In contrast, cells with the mec1-1 sml1-1 mutations suffer from severely impaired replication resumption upon removal of hydroxyurea. mec1-1 sml1-1 cells can, however, duplicate at least some of their centromeres and achieve bipolar attachment, leading to abortive segregation and fragmentation of incompletely replicated chromosomes. Our results highlight the importance of replicating yeast centromeres early and reveal different mechanisms of cell death due to differences in replication fork progression.
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Abstract
The mitotic spindle assembles to a steady-state length at metaphase through the integrated action of molecular mechanisms that generate and respond to mechanical forces. While molecular mechanisms that produce force have been described, our understanding of how they integrate with each other, and with the assembly/disassembly mechanisms that regulate length, is poor. We review current understanding of the basic architecture and dynamics of the metaphase spindle, and some of the elementary force-producing mechanisms. We then discuss models for force integration and spindle length determination. We also emphasize key missing data that notably include absolute values of forces and how they vary as a function of position within the spindle.
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Affiliation(s)
- Sophie Dumont
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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Mre11-Rad50-Nbs complex is required to cap telomeres during Drosophila embryogenesis. Proc Natl Acad Sci U S A 2009; 106:10728-33. [PMID: 19520832 DOI: 10.1073/pnas.0902707106] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using Drosophila as a model system, we identified here a stringent requirement for Mre11-Rad50-Nbs (MRN) function in telomere protection during early embryonic development. Animals homozygous for hypomorphic mutations in either mre11 or nbs develop normally with minimal telomere dysfunction. However, they produce inviable embryos that succumb to failure of mitosis caused by covalent fusion of telomeric DNA. Interestingly, the molecular defect is not the absence of MRN interaction or of Mre11 nuclease activities, but the depletion of the maternal pool of Nbs protein in these embryos. Because of Nbs depletion, Mre11 and Rad50 (MR) are excluded from chromatin. This maternal effect lethality in Drosophila is similar to that seen in mice carrying hypomorphic mrn mutations found in human patients, suggesting a common defect in telomere maintenance because of the loss of MRN integrity.
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Abstract
Centromeres are the discrete sites of spindle microtubule attachment on chromosomes during mitosis and meiosis in all eukaryotes. These highly specialized chromatin structures typically occupy the same site for thousands of generations, yet the mechanism by which centromeres are established, maintained, and function remain a mystery. In metazoans, centromeric DNA sequence has proven not to be the key determinant of centromeric identity; therefore, centromeres are thought to be epigenetically specified by their specialized chromatin structure. In all eukaryotes, the centromere-specific histone H3 variant CenH3 replaces canonical H3 within nucleosomes at centric chromatin. This specialized nucleosome is the building block upon which all other centromere-associated proteins depend. This review highlights exciting new findings that have resulted in a paradigm shift in our understanding of CenH3 assembly into centromeric chromatin, CenH3 nucleosomal structure, CenH3 chromatin folding, the contribution of these factors to centromeric identity, and finally, the intimate role cell-cycle-regulated transcription and pericentric heterochromatin play in the maintenance and integrity of centromeres.
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Affiliation(s)
- Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms Unit, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Kelly AE, Funabiki H. Correcting aberrant kinetochore microtubule attachments: an Aurora B-centric view. Curr Opin Cell Biol 2009; 21:51-8. [PMID: 19185479 DOI: 10.1016/j.ceb.2009.01.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 12/19/2008] [Accepted: 01/06/2009] [Indexed: 01/16/2023]
Abstract
The directed movement of chromosomes during mitosis and meiosis relies on microtubule-mediated connections between spindle poles and kinetochores assembled on chromosomes. The molecular basis for the dynamic interaction between microtubules and kinetochores is just beginning to be unveiled. Here, focusing on the mitotic centromere kinase Aurora B, we review our current understanding of the signaling pathways that correct erroneous microtubule attachment at kinetochores. We evaluate several potential models that may explain how maloriented attachments are recognized and processed by the Aurora B pathway.
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Affiliation(s)
- Alexander E Kelly
- The Rockefeller University, Laboratory of Chromosome and Cell Biology, 1230 York Avenue, New York, NY 10065, USA
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Shin MK, Kim SH, Jung SI, Kim SI, Kim SJ, Kim BJ, So I. The effect of DNA on mechanical properties of nanofiber hydrogels. APPLIED PHYSICS LETTERS 2008; 93. [DOI: 10.1063/1.3009204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Uniform poly(vinyl alcohol) (PVA) nanofiber gels incorporating double-stranded deoxyribonucleic acid (DNA) were fabricated without the aid of cross-linkers employing electrospinning. Creep and tensile tests of the DNA/PVA nanofiber gels were carried out in an aqueous medium to analyze interactions between the DNA and PVA. The DNA/PVA gels had a higher elastic modulus than the PVA gel. The viscosity with increasing external load was calculated by applying the Burger model to the creep curves. We conclude that DNA is relatively weakly bound with the PVA chains, although the elastic modulus of the DNA/PVA gels was higher than that of PVA gel.
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Affiliation(s)
- Min Kyoon Shin
- Hanyang University 1 Center for Bio-Artificial Muscle and Department of Biomedical Engineering, , Seoul 133-791, Republic of Korea
| | - Shi Hyeong Kim
- Hanyang University 1 Center for Bio-Artificial Muscle and Department of Biomedical Engineering, , Seoul 133-791, Republic of Korea
| | - Sung-il Jung
- Hanyang University 1 Center for Bio-Artificial Muscle and Department of Biomedical Engineering, , Seoul 133-791, Republic of Korea
| | - Sun I. Kim
- Hanyang University 1 Center for Bio-Artificial Muscle and Department of Biomedical Engineering, , Seoul 133-791, Republic of Korea
| | - Seon Jeong Kim
- Hanyang University 1 Center for Bio-Artificial Muscle and Department of Biomedical Engineering, , Seoul 133-791, Republic of Korea
| | - Byung Joo Kim
- Seoul National University 2 Center for Bio-Artificial Muscle and Department of Physiology, , Seoul 110-744, Republic of Korea
| | - Insuk So
- Seoul National University 2 Center for Bio-Artificial Muscle and Department of Physiology, , Seoul 110-744, Republic of Korea
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