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Brackley CA, Lips A, Morozov A, Poon WCK, Marenduzzo D. Mechanisms for destabilisation of RNA viruses at air-water and liquid-liquid interfaces. Nat Commun 2021; 12:6812. [PMID: 34819516 PMCID: PMC8613244 DOI: 10.1038/s41467-021-27052-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 10/22/2021] [Indexed: 11/19/2022] Open
Abstract
Understanding the interactions between viruses and surfaces or interfaces is important, as they provide the principles underpinning the cleaning and disinfection of contaminated surfaces. Yet, the physics of such interactions is currently poorly understood. For instance, there are longstanding experimental observations suggesting that the presence of air-water interfaces can generically inactivate and kill viruses, yet the mechanism underlying this phenomenon remains unknown. Here we use theory and simulations to show that electrostatics may provide one such mechanism, and that this is very general. Thus, we predict that the electrostatic free energy of an RNA virus should increase by several thousands of kBT as the virion breaches an air-water interface. We also show that the fate of a virus approaching a generic liquid-liquid interface depends strongly on the detailed balance between interfacial and electrostatic forces, which can be tuned, for instance, by choosing different media to contact a virus-laden respiratory droplet. Tunability arises because both the electrostatic and interfacial forces scale similarly with viral size. We propose that these results can be used to design effective strategies for surface disinfection. We know that air-water interfaces can generically inactivate viruses, but the mechanisms behind this observation are unclear. Here the authors use simulations to uncover those mechanisms and find that the electrostatic repulsive free energy of an RNA virus increases by several thousands of kBT as it approaches an air-water interface, providing a mechanism for viral destabilization which may induce inactivation.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - A Lips
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - A Morozov
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - W C K Poon
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK.
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2
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Brackley CA, Gilbert N, Michieletto D, Papantonis A, Pereira MCF, Cook PR, Marenduzzo D. Complex small-world regulatory networks emerge from the 3D organisation of the human genome. Nat Commun 2021; 12:5756. [PMID: 34599163 PMCID: PMC8486811 DOI: 10.1038/s41467-021-25875-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/30/2021] [Indexed: 01/01/2023] Open
Abstract
The discovery that overexpressing one or a few critical transcription factors can switch cell state suggests that gene regulatory networks are relatively simple. In contrast, genome-wide association studies (GWAS) point to complex phenotypes being determined by hundreds of loci that rarely encode transcription factors and which individually have small effects. Here, we use computer simulations and a simple fitting-free polymer model of chromosomes to show that spatial correlations arising from 3D genome organisation naturally lead to stochastic and bursty transcription as well as complex small-world regulatory networks (where the transcriptional activity of each genomic region subtly affects almost all others). These effects require factors to be present at sub-saturating levels; increasing levels dramatically simplifies networks as more transcription units are pressed into use. Consequently, results from GWAS can be reconciled with those involving overexpression. We apply this pan-genomic model to predict patterns of transcriptional activity in whole human chromosomes, and, as an example, the effects of the deletion causing the diGeorge syndrome.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - N Gilbert
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - D Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - A Papantonis
- Institute of Pathology, University Medical Center, Georg-August University of Göttingen, 37075, Göttingen, Germany
| | - M C F Pereira
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - P R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
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3
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Brackley CA. Polymer compaction and bridging-induced clustering of protein-inspired patchy particles. J Phys Condens Matter 2020; 32:314002. [PMID: 32175915 DOI: 10.1088/1361-648x/ab7f6c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to be able to compact DNA in vitro, and many others have been observed in foci or puncta when fluorescently labelled and imaged in vivo. In this work we study, using coarse-grained Langevin dynamics simulations, the compaction of polymers by simple model proteins and a phenomenon known as the 'bridging-induced attraction'. The latter is a mechanism observed in previous simulations [Brackley et al 2013 Proc. Natl Acad. Sci. USA 110 E3605], where proteins modelled as spheres form clusters via their multivalent interactions with a polymer, even in the absence of any explicit protein-protein attractive interactions. Here we extend this concept to consider more detailed model proteins, represented as simple 'patchy particles' interacting with a semi-flexible bead-and-spring polymer. We find that both the compacting ability and the effect of the bridging-induced attraction depend on the valence of the model proteins. These effects also depend on the shape of the protein, which determines its ability to form bridges.
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Bonato A, Brackley CA, Johnson J, Michieletto D, Marenduzzo D. Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins. Soft Matter 2020; 16:2406-2414. [PMID: 32067018 DOI: 10.1039/c9sm01875a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to explain the extrusion of chromatin loops of hundreds of kilo-base-pairs (kbp), which may then be stabilised by interactions between cohesin and CTCF proteins. Here we show that the flexibility of the chromatin fibre strongly affects this dynamical process, and find that diffusive loop extrusion is more efficient on stiffer chromatin regions. We also show that the dynamics of loop formation are faster in confined and collapsed chromatin conformations but that this enhancement is counteracted by the increased crowding. We provide a simple theoretical argument explaining why stiffness and collapsed conformations favour diffusive extrusion. In light of the heterogeneous physical and conformational properties of eukaryotic chromatin, we suggest that our results are relevant to understand the looping and organisation of interphase chromosomes in vivo.
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Affiliation(s)
- A Bonato
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Road, Edinburgh, EH9 3FD, UK.
| | - C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Road, Edinburgh, EH9 3FD, UK.
| | - J Johnson
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Road, Edinburgh, EH9 3FD, UK.
| | - D Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Road, Edinburgh, EH9 3FD, UK. and MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK and Department of Mathematical Sciences, University of Bath, North Rd, Bath BA2 7AY, UK
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Road, Edinburgh, EH9 3FD, UK.
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5
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Brackley CA, Marenduzzo D. Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions. Brief Funct Genomics 2020; 19:111-118. [DOI: 10.1093/bfgp/elz032] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/11/2023] Open
Abstract
Abstract
We review the mechanism and consequences of the ‘bridging-induced attraction’, a generic biophysical principle that underpins some existing models for chromosome organization in 3D. This attraction, which was revealed in polymer physics-inspired computer simulations, is a generic clustering tendency arising in multivalent chromatin-binding proteins, and it provides an explanation for the biogenesis of nuclear bodies and transcription factories via microphase separation. Including post-translational modification reactions involving these multivalent proteins can account for the fast dynamics of the ensuing clusters, as is observed via microscopy and photobleaching experiments. The clusters found in simulations also give rise to chromatin domains that conform well with the observation of A/B compartments in HiC experiments.
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Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D. Extrusion without a motor: a new take on the loop extrusion model of genome organization. Nucleus 2019; 9:95-103. [PMID: 29300120 PMCID: PMC5973195 DOI: 10.1080/19491034.2017.1421825] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo “Non-equilibrium chromosome looping via molecular slip-links”, Physical Review Letters 119 138101 (2017)
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Affiliation(s)
- C A Brackley
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - J Johnson
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - D Michieletto
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - A N Morozov
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - M Nicodemi
- b Dipartimento di Fisica , Universita' di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo , Naples , Italy
| | - P R Cook
- c Sir William Dunn School of Pathology , University of Oxford , South Parks Road, Oxford , OX1 3RE , UK
| | - D Marenduzzo
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
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Foglino M, Locatelli E, Brackley CA, Michieletto D, Likos CN, Marenduzzo D. Non-equilibrium effects of molecular motors on polymers. Soft Matter 2019; 15:5995-6005. [PMID: 31292585 DOI: 10.1039/c9sm00273a] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are represented as freely diffusing beads which, upon encountering the substrate, bind to it through a short-ranged attractive potential. When bound, motors and polymer beads experience an equal and opposite active force, directed tangential to the polymer; this leads to motion of the motors along the polymer contour. The inclusion of explicit motors differentiates our model from other recent active polymer models. We study, by means of Langevin dynamics simulations, the effect of the motor activity on both the conformational and dynamical properties of the substrate. We find that activity leads, in addition to the expected enhancement of polymer diffusion, to an effective reduction of its persistence length. We discover that this effective "softening" is a consequence of the emergence of double-folded branches, or hairpins, and that it can be tuned by changing the number of motors or the force they generate. Finally, we investigate the effect of the motors on the probability of knot formation. Counter-intuitively our simulations reveal that, even though at equilibrium a more flexible substrate would show an increased knotting probability, motor activity leads to a marked decrease in the occurrence of knotted conformations with respect to equilibrium.
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Affiliation(s)
- M Foglino
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, UK
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8
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Pereira MCF, Brackley CA, Lintuvuori JS, Marenduzzo D, Orlandini E. Entropic elasticity and dynamics of the bacterial chromosome: A simulation study. J Chem Phys 2018; 147:044908. [PMID: 28764377 DOI: 10.1063/1.4995992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a "piston"-a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein sizes and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the "piston": while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they "pop-off" one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.
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Affiliation(s)
- M C F Pereira
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - J S Lintuvuori
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Universite Paris-Saclay, 91405 Orsay Cedex, France
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - E Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, Padova, 35131 PD, Italy
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9
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Bentivoglio A, Ancona M, Brackley CA, Gonnella G, Marenduzzo D. Non-equilibrium phase transition in a model for supercoiling-dependent DNA transcription. Soft Matter 2018; 14:3632-3639. [PMID: 29691522 DOI: 10.1039/c7sm02452e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We study a variant of a recently proposed non-equilibrium stochastic model for supercoiling-dependent transcription in DNA. In the case of a circular DNA molecule with overall positive supercoiling, we find a non-equilibrium phase transition between an absorbing phase, where all genes are switched off due to the supercoiling, and an active phase with a non-zero transcription rate. Mean field theory predicts that the transition should be continuous at a critical value of the background supercoiling, and we focus our analysis on this case. Our simulations suggest that the switch between the transcribed and silent phases may actually be a fluctuation-induced discontinuous transition, where the jump in the transcription rate decreases with the number of genes in the system.
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Affiliation(s)
- A Bentivoglio
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
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10
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Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D. Nonequilibrium Chromosome Looping via Molecular Slip Links. Phys Rev Lett 2017; 119:138101. [PMID: 29341686 DOI: 10.1103/physrevlett.119.138101] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Indexed: 06/07/2023]
Abstract
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - J Johnson
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - D Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - A N Morozov
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - M Nicodemi
- Dipartimento di Fisica, Universita' di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - P R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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11
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Brackley CA, Michieletto D, Mouvet F, Johnson J, Kelly S, Cook PR, Marenduzzo D. Simulating topological domains in human chromosomes with a fitting-free model. Nucleus 2017; 7:453-461. [PMID: 27841970 DOI: 10.1080/19491034.2016.1239684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC content). Individual spheres (representing bi- and multi-valent transcription factors) can bind reversibly and selectively to beads with the appropriate color. During molecular dynamics simulations, the factors bind, and the string spontaneously folds into loops, rosettes, and topologically-associating domains (TADs). This organization occurs in the absence of any specified interactions between distant DNA segments, or between transcription factors. A comparison with Hi-C data shows that simulations predict the location of most boundaries between TADs correctly. The model is "fitting-free" in the sense that it does not use Hi-C data as an input; consequently, one of its strengths is that it can - in principle - be used to predict the 3D organization of any region of interest, or whole chromosome, in a given organism, or cell line, in the absence of existing Hi-C data. We discuss how this simple model might be refined to include more transcription factors and binding sites, and to correctly predict contacts between convergent CTCF binding sites.
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Affiliation(s)
- C A Brackley
- a SUPA, School of Physics & Astronomy , University of Edinburgh , Edinburgh , UK
| | - D Michieletto
- a SUPA, School of Physics & Astronomy , University of Edinburgh , Edinburgh , UK
| | - F Mouvet
- a SUPA, School of Physics & Astronomy , University of Edinburgh , Edinburgh , UK
| | - J Johnson
- a SUPA, School of Physics & Astronomy , University of Edinburgh , Edinburgh , UK
| | - S Kelly
- b Department of Plant Sciences , University of Oxford , Oxford , UK
| | - P R Cook
- c Sir William Dunn School of Pathology , University of Oxford , Oxford , UK
| | - D Marenduzzo
- a SUPA, School of Physics & Astronomy , University of Edinburgh , Edinburgh , UK
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12
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Fosado YAG, Michieletto D, Allan J, Brackley CA, Henrich O, Marenduzzo D. A single nucleotide resolution model for large-scale simulations of double stranded DNA. Soft Matter 2016; 12:9458-9470. [PMID: 27845464 DOI: 10.1039/c6sm01859a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The computational modelling of DNA is becoming crucial in light of new advances in DNA nano-technology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules - up to a million base pairs - for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. The model captures the main characteristics of DNA, such as the different persistence lengths for double and single strands, pitch, torsional rigidity and the presence of major and minor grooves. The model constitutes a starting point for the future implementation of further features, such as sequence specificity and electrostatic repulsion. We show that the behaviour of the presented model compares favourably with single molecule experiments where dsDNA is manipulated by external forces or torques. We finally present some results on the kinetics of denaturation of linear DNA and supercoiling of closed dsDNA molecules.
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Affiliation(s)
- Y A G Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
| | - D Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
| | - J Allan
- Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - C A Brackley
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
| | - O Henrich
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK and EPCC, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
| | - D Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
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Brackley CA, Johnson J, Bentivoglio A, Corless S, Gilbert N, Gonnella G, Marenduzzo D. Stochastic Model of Supercoiling-Dependent Transcription. Phys Rev Lett 2016; 117:018101. [PMID: 27419594 DOI: 10.1103/physrevlett.117.018101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 06/06/2023]
Abstract
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix and that these enzymes bind more favorably to regions where the genome is unwound. Within this model, we show that when the transcriptionally induced flux of supercoiling increases, there is a sharp crossover from a regime where torsional stresses relax quickly and gene transcription is random, to one where gene expression is highly correlated and tightly regulated by supercoiling. In the latter regime, the model displays transcriptional bursts, waves of supercoiling, and up regulation of divergent or bidirectional genes. It also predicts that topological enzymes which relax twist and writhe should provide a pathway to down regulate transcription.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - J Johnson
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - A Bentivoglio
- Dipartimento di Fisica, Università di Bari and INFN, Sezione di Bari, 70126 Bari, Italy
| | - S Corless
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - N Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - G Gonnella
- Dipartimento di Fisica, Università di Bari and INFN, Sezione di Bari, 70126 Bari, Italy
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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Johnson J, Brackley CA, Cook PR, Marenduzzo D. A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction. J Phys Condens Matter 2015; 27:064119. [PMID: 25563801 DOI: 10.1088/0953-8984/27/6/064119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present computer simulations of the phase behaviour of an ensemble of proteins interacting with a polymer, mimicking non-specific binding to a piece of bacterial DNA or eukaryotic chromatin. The proteins can simultaneously bind to the polymer in two or more places to create protein bridges. Despite the lack of any explicit interaction between the proteins or between DNA segments, our simulations confirm previous results showing that when the protein-polymer interaction is sufficiently strong, the proteins come together to form clusters. Furthermore, a sufficiently large concentration of bridging proteins leads to the compaction of the swollen polymer into a globular phase. Here we characterise both the formation of protein clusters and the polymer collapse as a function of protein concentration, protein-polymer affinity and fibre flexibility.
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Affiliation(s)
- J Johnson
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, UK
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Brackley CA, Allan J, Keszenman-Pereyra D, Marenduzzo D. Topological constraints strongly affect chromatin reconstitution in silico. Nucleic Acids Res 2015; 43:63-73. [PMID: 25432958 PMCID: PMC4288149 DOI: 10.1093/nar/gku1085] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 12/22/2022] Open
Abstract
The fundamental building block of chromatin, and of chromosomes, is the nucleosome, a composite material made up from DNA wrapped around a histone octamer. In this study we provide the first computer simulations of chromatin self-assembly, starting from DNA and histone proteins, and use these to understand the constraints which are imposed by the topology of DNA molecules on the creation of a polynucleosome chain. We take inspiration from the in vitro chromatin reconstitution protocols which are used in many experimental studies. Our simulations indicate that during self-assembly, nucleosomes can fall into a number of topological traps (or local folding defects), and this may eventually lead to the formation of disordered structures, characterised by nucleosome clustering. Remarkably though, by introducing the action of topological enzymes such as type I and II topoisomerase, most of these defects can be avoided and the result is an ordered 10-nm chromatin fibre. These findings provide new insight into the biophysics of chromatin formation, both in the context of reconstitution in vitro and in terms of the topological constraints which must be overcome during de novo nucleosome formation in vivo, e.g. following DNA replication or repair.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics & Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - J Allan
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - D Keszenman-Pereyra
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - D Marenduzzo
- SUPA, School of Physics & Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
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Brackley CA, Morozov AN, Marenduzzo D. Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS. J Chem Phys 2014; 140:135103. [DOI: 10.1063/1.4870088] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Abstract
In bacteria, regulatory proteins search for a specific DNA-binding target via "facilitated diffusion": a series of rounds of three-dimensional diffusion in the cytoplasm, and one-dimensional (1D) linear diffusion along the DNA contour. Using large scale Brownian dynamics simulations we find that each of these steps is affected differently by crowding proteins, which can either be bound to the DNA acting as a road block to the 1D diffusion, or freely diffusing in the cytoplasm. Macromolecular crowding can strongly affect mechanistic features such as the balance between three-dimensional and 1D diffusion, but leads to surprising robustness of the total search time.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - M E Cates
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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Brackley CA, Cates ME, Marenduzzo D. Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity. Phys Rev Lett 2012; 109:168103. [PMID: 23215135 DOI: 10.1103/physrevlett.109.168103] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Indexed: 06/01/2023]
Abstract
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modeled as a sphere with a binding site on its surface, along DNA, modeled as a semiflexible polymer. We consider both the effect of DNA organization in three dimensions and of sequence heterogeneity. We find that in a network of DNA loops, which are thought to be present in bacterial DNA, the search process is very sensitive to the spatial location of the target within such loops. Therefore, specific genes might be repressed or promoted by changing the local topology of the genome. On the other hand, sequence heterogeneity creates traps which normally slow down facilitated diffusion. When suitably positioned, though, these traps can, surprisingly, render the search process much more efficient.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, United Kingdom
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Brackley CA, Turner MS. Two-point heterogeneous connections in a continuum neural field model. Biol Cybern 2009; 100:371-383. [PMID: 19350264 DOI: 10.1007/s00422-009-0308-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 03/22/2009] [Indexed: 05/27/2023]
Abstract
We examine a novel heterogeneous connection scheme in a 1D continuum neural field model. Multiple two-point connections are added to a local connection function in order to model the "patchy" connections seen in, for example visual cortex. We use a numerical approach to solve the equations, choosing the locations of the two-point connections stochastically. We observe self-sustained persistent fluctuations of activity which can be classified into two types (one of which is similar to that seen in network models of discrete excitable neurons, the other being particular to this model). We study the effect of parameters such as system size and the range, number and strength of connections, on the probability that a particular realisation of the connections is able to exhibit persistent fluctuations.
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Affiliation(s)
- C A Brackley
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.
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Brackley CA, Turner MS. Persistent fluctuations of activity in undriven continuum neural field models with power-law connections. Phys Rev E Stat Nonlin Soft Matter Phys 2009; 79:011918. [PMID: 19257080 DOI: 10.1103/physreve.79.011918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 10/30/2008] [Indexed: 05/27/2023]
Abstract
We study the effect of random inhomogeneous connections on a continuous field description of neural tissue. We focus on a regime in which persistent random fluctuations in activity arise spontaneously in the absence of either time-varying or spatially inhomogeneous input. While present in real tissue and network models of discrete neurons, such behavior has not been reported in continuum models of this type. The activity contains frequencies similar to those seen experimentally. We consider a power-law envelope r(-alpha) for the inhomogeneity and present evidence that the statistical coherence (a measure of two-point correlation) rapidly percolates across the system as alpha is reduced below alphac approximately 1,2 in one and two dimensions, respectively.
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Affiliation(s)
- C A Brackley
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
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Brackley CA, Turner MS. Random fluctuations of the firing rate function in a continuum neural field model. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 75:041913. [PMID: 17500927 DOI: 10.1103/physreve.75.041913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 01/16/2007] [Indexed: 05/15/2023]
Abstract
We incorporate a source of noise into a continuum neural field model by allowing the firing threshold to fluctuate noisily about a mean value, and examine traveling wave front solutions. Under certain conditions we are able to calculate the first and second moments of the distributions of the resulting time varying front speed and shape. This is then compared with more complete numerical solutions. Fluctuations in the wave front speed and in the shape (i.e., fluctuations in activity at particular coordinate positions across the wave front) were found to increase as the magnitude of the fluctuations in firing threshold increased. The mean speed was found to increase as the magnitude of the fluctuations increases. The role of the correlation time for the threshold variation is also investigated. We also study the role of threshold fluctuations in the failure of front propagation, both in the fast and slow varying noise limits.
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Affiliation(s)
- C A Brackley
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
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Abstract
OBJECTIVES A survey of general dental practitioners and dental surgery assistants was carried out to ascertain their preferences and opinions on powder-free hydrogel-coated gloves compared with starch-powdered gloves. The aim was to relate the survey findings to laboratory measurements of the frictional characteristics of glove inner surfaces and their water absorptive capability. METHODS The survey was carried out using a questionnaire given to local dental practitioners. Glove friction and water absorption measurements were made using specially designed equipment. RESULTS The survey showed that a selected group of dentist and dental surgery assistants preferred hydrogel-coated gloves, particularly for damp donning, durability and long-term wear comfort. Laboratory measurements showed that the hydrogel coating gave a low friction coefficient against damp skin. The coating was durable, and absorbed water more readily than other treatments. CONCLUSION A survey of dental practitioners and dental surgery assistants and laboratory measurements indicates that hydrogel-coated gloves have superior properties, and are preferred to other non-sterile glove types.
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Affiliation(s)
- A D Roberts
- Malaysian Rubber Producers' Research Association, Hertford, UK
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Abstract
Abstract
The frictional properties of rubber surfaces modified by various treatments have been investigated in order to understand the factors which reduce the friction and give the surface appropriate qualities for practical use. The study was in two stages. Initial measurements were made on thin sheets of hot-vulcanized natural rubber; then followed tests on latex glove material to see how the initial results and understanding related to the application. Measurements of friction coefficient were made against a wavy glass plate, giving reproducible results, and against finger skin. Supplementary measurements were made of surface roughness and hardness, liquid contact angle, and water absorption. Factors of importance in the reduction of dry friction were found to be an increased surface roughness and hardness. In practice, difficulties may be experienced under slightly wet or damp conditions, which can increase the friction above the dry value. Here it was found to help if the surface treatment could absorb water. For surgeons' gloves in contact with moist skin, one particular treatment, a hydrogel polymer coating, gave the necessary surface roughness, hardness, and water absorptivity, making the gloves easy to don and pleasant to wear.
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Affiliation(s)
- A. D. Roberts
- 1Malaysian Rubber Producers' Research Association, Tun Abdul Razak Laboratory, Brickendonbury, Hertford SG13 8NL, United Kingdom
| | - C. A. Brackley
- 1Malaysian Rubber Producers' Research Association, Tun Abdul Razak Laboratory, Brickendonbury, Hertford SG13 8NL, United Kingdom
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