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  1. AU=Brackley Chris A.
  2. AU="Klünker, Wolf-Ulrich"
  3. AU="Cody N Heiser"
  4. AU="Xing-Ding Zhou"
  5. AU="Abdallah, Al-Ola"
  6. AU=Grimminck Koen
  7. AU="Roulston, T’ai H."
  8. AU="Morgan, Robert D"
  9. AU="Hayashida, Hirotoshi"
  10. AU=Kivisto Ilkka
  11. AU="Miller, Heinz"
  12. AU="Campbell, Joshua W"
  13. AU="Miller, David J"
  14. AU="Morales-Ledesma, Leticia"
  15. AU="Rongkard, Patpong"
  16. AU="Martínez Rolando, Lidia"
  17. AU="Dogra, Surabhi"
  18. AU="Liu, Xiaolei"
  19. AU=Machesky Laura
  20. AU="Schadrac C Agbla"

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  1. Artikel ; Online: Simulating the chromatin-mediated phase separation of model proteins with multiple domains.

    Ancona, Marco / Brackley, Chris A

    Biophysical journal

    2022  Band 121, Heft 13, Seite(n) 2600–2612

    Abstract: We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates that arise due to liquid-liquid ... ...

    Abstract We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates that arise due to liquid-liquid phase separation, or a via a "bridging-induced attraction" mechanism. For proteins that interact multivalently, we obtain a phase diagram which includes liquid-like droplets, droplets with absorbed polymer, and coated polymer regimes. Of particular interest is a regime where protein droplets only form due to interaction with the polymer; here, unlike a standard phase separating system, droplet density rather than size varies with the overall protein concentration. We also observe that protein dynamics within droplets slow down as chromatin is absorbed. If the protein-protein interactions have a strictly limited valence, fractal or gel-like condensates are instead observed. A specific example that inspired our model is heterochromatin protein 1, or HP1. Recent in vivo experiments have shown that HP1 exhibits similar droplet size buffering behavior as our simulations. Overall, our results provide biologically relevant insights into the general nature of protein-chromatin condensates in living cells.
    Mesh-Begriff(e) Chromatin ; Chromobox Protein Homolog 5 ; Polymers
    Chemische Substanzen Chromatin ; Polymers ; Chromobox Protein Homolog 5 (107283-02-3)
    Sprache Englisch
    Erscheinungsdatum 2022-05-28
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2022.05.039
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  2. Buch ; Online: Simulating the chromatin mediated phase separation of model proteins with multiple domains

    Ancona, Marco / Brackley, Chris A.

    2021  

    Abstract: We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to liquid-liquid ... ...

    Abstract We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to liquid-liquid phase separation, or a via a 'bridging-induced attraction' mechanism. For proteins which interact multivalently, we obtain a phase diagram which includes liquid-like droplets, droplets with absorbed polymer, and coated polymer regimes. Of particular interest is a regime where protein droplets only form due to interaction with the polymer; here, unlike a standard phase separating system, droplet density rather than size varies with the overall protein concentration. We also observe that protein dynamics within droplets slow down as chromatin is absorbed. If the protein-protein interactions have a strictly limited valence, fractal or gel-like condensates are instead observed. Together this provides biologically relevant insights into the nature of protein-chromatin condensates in living cells.

    Comment: Main article: 10 pages, 6 figures; Supplementary Material: 16 pages, 15 figures
    Schlagwörter Condensed Matter - Soft Condensed Matter ; Physics - Biological Physics ; Physics - Computational Physics
    Thema/Rubrik (Code) 612
    Erscheinungsdatum 2021-07-30
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Transcription modulates chromatin dynamics and locus configuration sampling.

    Forte, Giada / Buckle, Adam / Boyle, Shelagh / Marenduzzo, Davide / Gilbert, Nick / Brackley, Chris A

    Nature structural & molecular biology

    2023  Band 30, Heft 9, Seite(n) 1275–1285

    Abstract: In living cells, the 3D structure of gene loci is dynamic, but this is not revealed by 3C and FISH experiments in fixed samples, leaving a notable gap in our understanding. To overcome these limitations, we applied the highly predictive heteromorphic ... ...

    Abstract In living cells, the 3D structure of gene loci is dynamic, but this is not revealed by 3C and FISH experiments in fixed samples, leaving a notable gap in our understanding. To overcome these limitations, we applied the highly predictive heteromorphic polymer (HiP-HoP) model to determine chromatin fiber mobility at the Pax6 locus in three mouse cell lines with different transcription states. While transcriptional activity minimally affects movement of 40-kbp regions, we observed that motion of smaller 1-kbp regions depends strongly on local disruption to chromatin fiber structure marked by H3K27 acetylation. This also substantially influenced locus configuration dynamics by modulating protein-mediated promoter-enhancer loops. Importantly, these simulations indicate that chromatin dynamics are sufficiently fast to sample all possible locus conformations within minutes, generating wide dynamic variability within single cells. This combination of simulation and experimental validation provides insight into how transcriptional activity influences chromatin structure and gene dynamics.
    Mesh-Begriff(e) Mice ; Animals ; Chromatin ; Chromosomes ; Regulatory Sequences, Nucleic Acid ; Promoter Regions, Genetic ; Molecular Conformation
    Chemische Substanzen Chromatin
    Sprache Englisch
    Erscheinungsdatum 2023-08-03
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-023-01059-8
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  4. Artikel ; Online: Model for Quorum-Sensing Mediated Stochastic Biofilm Nucleation.

    Sinclair, Patrick / Brackley, Chris A / Carballo-Pacheco, Martín / Allen, Rosalind J

    Physical review letters

    2022  Band 129, Heft 19, Seite(n) 198102

    Abstract: Surface-attached bacterial biofilms cause disease and industrial biofouling, as well as being widespread in the natural environment. Density-dependent quorum sensing is one of the mechanisms implicated in biofilm initiation. Here we present and analyze a ...

    Abstract Surface-attached bacterial biofilms cause disease and industrial biofouling, as well as being widespread in the natural environment. Density-dependent quorum sensing is one of the mechanisms implicated in biofilm initiation. Here we present and analyze a model for quorum-sensing triggered biofilm initiation. In our model, individual, planktonic bacteria adhere to a surface, proliferate, and undergo a collective transition to a biofilm phenotype. This model predicts a stochastic transition between a loosely attached, finite layer of bacteria near the surface and a growing biofilm. The transition is governed by two key parameters: the collective transition density relative to the carrying capacity and the immigration rate relative to the detachment rate. Biofilm initiation is complex, but our model suggests that stochastic nucleation phenomena may be relevant.
    Mesh-Begriff(e) Quorum Sensing ; Biofilms ; Bacteria
    Sprache Englisch
    Erscheinungsdatum 2022-11-18
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.129.198102
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  5. Artikel: A computational model for microbial colonization of an antifouling surface.

    Sinclair, Patrick / Longyear, Jennifer / Reynolds, Kevin / Finnie, Alistair A / Brackley, Chris A / Carballo-Pacheco, Martín / Allen, Rosalind J

    Frontiers in microbiology

    2022  Band 13, Seite(n) 920014

    Abstract: Biofouling of marine surfaces such as ship hulls is a major industrial problem. Antifouling (AF) paints delay the onset of biofouling by releasing biocidal chemicals. We present a computational model for microbial colonization of a biocide-releasing AF ... ...

    Abstract Biofouling of marine surfaces such as ship hulls is a major industrial problem. Antifouling (AF) paints delay the onset of biofouling by releasing biocidal chemicals. We present a computational model for microbial colonization of a biocide-releasing AF surface. Our model accounts for random arrival from the ocean of microorganisms with different biocide resistance levels, biocide-dependent proliferation or killing, and a transition to a biofilm state. Our computer simulations support a picture in which biocide-resistant microorganisms initially form a loosely attached layer that eventually transitions to a growing biofilm. Once the growing biofilm is established, immigrating microorganisms are shielded from the biocide, allowing more biocide-susceptible strains to proliferate. In our model, colonization of the AF surface is highly stochastic. The waiting time before the biofilm establishes is exponentially distributed, suggesting a Poisson process. The waiting time depends exponentially on both the concentration of biocide at the surface and the rate of arrival of resistant microorganisms from the ocean. Taken together our results suggest that biofouling of AF surfaces may be intrinsically stochastic and hence unpredictable, but immigration of more biocide-resistant species, as well as the biological transition to biofilm physiology, may be important factors controlling the time to biofilm establishment.
    Sprache Englisch
    Erscheinungsdatum 2022-09-27
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.920014
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  6. Buch ; Online: Bridging-induced microphase separation

    Brackley, Chris A. / Marenduzzo, Davide

    photobleaching experiments, chromatin domains, and the need for active reactions

    2020  

    Abstract: We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer physics-inspired ... ...

    Abstract We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. 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 which conform well with the observation of A/B compartments in HiC experiments.

    Comment: 7 pages, 3 figures
    Schlagwörter Condensed Matter - Soft Condensed Matter ; Physics - Biological Physics ; Quantitative Biology - Subcellular Processes
    Thema/Rubrik (Code) 540
    Erscheinungsdatum 2020-10-12
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling.

    Fosado, Yair A G / Michieletto, Davide / Brackley, Chris A / Marenduzzo, Davide

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Band 118, Heft 10

    Abstract: We study the effect of transcription on the kinetics of DNA supercoiling in three dimensions by means of Brownian dynamics simulations of a single-nucleotide-resolution coarse-grained model for double-stranded DNA. By explicitly accounting for the action ...

    Abstract We study the effect of transcription on the kinetics of DNA supercoiling in three dimensions by means of Brownian dynamics simulations of a single-nucleotide-resolution coarse-grained model for double-stranded DNA. By explicitly accounting for the action of a transcribing RNA polymerase (RNAP), we characterize the geometry and nonequilibrium dynamics of the ensuing twin supercoiling domains. Contrary to the typical textbook picture, we find that the generation of twist by RNAP results in the formation of plectonemes (writhed DNA) some distance away. We further demonstrate that this translates into an "action at a distance" on DNA-binding proteins; for instance, positive supercoils downstream of an elongating RNAP destabilize nucleosomes long before the transcriptional machinery reaches the histone octamer. We also analyze the relaxation dynamics of supercoiled double-stranded DNA, and characterize the widely different timescales of twist diffusion, which is a simple and fast process, and writhe relaxation, which is much slower and entails multiple steps.
    Mesh-Begriff(e) Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; DNA, Bacterial/chemistry ; DNA, Bacterial/metabolism ; DNA, Superhelical/chemistry ; DNA, Superhelical/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/metabolism ; Molecular Dynamics Simulation ; Transcription, Genetic
    Chemische Substanzen Bacterial Proteins ; DNA, Bacterial ; DNA, Superhelical ; DNA-Binding Proteins ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Sprache Englisch
    Erscheinungsdatum 2021-02-05
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1905215118
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  8. Artikel: Predicting genome organisation and function with mechanistic modelling.

    Chiang, Michael / Brackley, Chris A / Marenduzzo, Davide / Gilbert, Nick

    Trends in genetics : TIG

    2021  Band 38, Heft 4, Seite(n) 364–378

    Abstract: Fitting-free mechanistic models based on polymer simulations predict chromatin folding in 3D by focussing on the underlying biophysical mechanisms. This class of models has been increasingly used in conjunction with experiments to study the spatial ... ...

    Abstract Fitting-free mechanistic models based on polymer simulations predict chromatin folding in 3D by focussing on the underlying biophysical mechanisms. This class of models has been increasingly used in conjunction with experiments to study the spatial organisation of eukaryotic chromosomes. Feedback from experiments to models leads to successive model refinement and has previously led to the discovery of new principles for genome organisation. Here, we review the basis of mechanistic polymer simulations, explain some of the more recent approaches and the contexts in which they have been useful to explain chromosome biology, and speculate on how they might be used in the future.
    Mesh-Begriff(e) Chromatin/genetics ; Chromosomes/genetics ; Eukaryota/genetics ; Genome/genetics ; Polymers
    Chemische Substanzen Chromatin ; Polymers
    Sprache Englisch
    Erscheinungsdatum 2021-11-29
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2021.11.001
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  9. Artikel ; Online: Nucleosome positions alone can be used to predict domains in yeast chromosomes.

    Wiese, Oliver / Marenduzzo, Davide / Brackley, Chris A

    Proceedings of the National Academy of Sciences of the United States of America

    2019  Band 116, Heft 35, Seite(n) 17307–17315

    Abstract: We use molecular dynamics simulations based on publicly available micrococcal nuclease sequencing data for nucleosome positions to predict the 3D structure of chromatin in the yeast genome. Our main aim is to shed light on the mechanism underlying the ... ...

    Abstract We use molecular dynamics simulations based on publicly available micrococcal nuclease sequencing data for nucleosome positions to predict the 3D structure of chromatin in the yeast genome. Our main aim is to shed light on the mechanism underlying the formation of chromosomal interaction domains, chromosome regions of around 0.5 to 10 kbp which show enriched self-interactions, which were experimentally observed in recent MicroC experiments (importantly these are at a different length scale from the 100- to 1,000-kbp-sized domains observed in higher eukaryotes). We show that the sole input of nucleosome positioning data is already sufficient to determine the patterns of chromatin interactions and domain boundaries seen experimentally to a high degree of accuracy. Since the nucleosome spacing so strongly affects the larger-scale domain structure, we next examine the genome-wide linker-length distribution in more detail, finding that it is highly irregular and varies in different genomic regions such as gene bodies, promoters, and active and inactive genes. Finally we use our simple simulation model to characterize in more detail how irregular nucleosome spacing may affect local chromatin structure.
    Mesh-Begriff(e) Chromatin Assembly and Disassembly ; Chromosomes, Fungal/chemistry ; Chromosomes, Fungal/metabolism ; Nucleosomes/chemistry ; Nucleosomes/metabolism ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/metabolism
    Chemische Substanzen Nucleosomes
    Sprache Englisch
    Erscheinungsdatum 2019-08-15
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1817829116
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  10. Artikel ; Online: Predictive Polymer Models for 3D Chromosome Organization.

    Chiang, Michael / Forte, Giada / Gilbert, Nick / Marenduzzo, Davide / Brackley, Chris A

    Methods in molecular biology (Clifton, N.J.)

    2021  Band 2301, Seite(n) 267–291

    Abstract: Polymer simulations and predictive mechanistic modelling are increasingly used in conjunction with experiments to study the organization of eukaryotic chromosomes. Here we review some of the most prevalent models for mechanisms which drive different ... ...

    Abstract Polymer simulations and predictive mechanistic modelling are increasingly used in conjunction with experiments to study the organization of eukaryotic chromosomes. Here we review some of the most prevalent models for mechanisms which drive different aspects of chromosome organization, as well as a recent simulation scheme which combines several of these mechanisms into a single predictive model. We give some practical details of the modelling approach, as well as review some of the key results obtained by these and similar models in the last few years.
    Mesh-Begriff(e) Chromosomes/genetics ; Computer Simulation ; Eukaryota ; Polymers
    Chemische Substanzen Polymers
    Sprache Englisch
    Erscheinungsdatum 2021-08-20
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1390-0_14
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