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The physics of three dimensional chromosome and protein organisation within the cell

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Publications

Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability

Author(s): Marco Ancona, Davide Michieletto, Davide Marenduzzo
Published in: Physical Review E, 101/4, 2020, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/physreve.101.042408

Mechanistic modeling of chromatin folding to understand function

Author(s): Chris A. Brackey, Davide Marenduzzo, Nick Gilbert
Published in: Nature Methods, 17/8, 2020, Page(s) 767-775, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-020-0852-6

Nonequilibrium Strategy for Fast Target Search on the Genome

Author(s): F. Cagnetta, D. Michieletto, D. Marenduzzo
Published in: Physical Review Letters, 124/19, 2020, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.124.198101

capC-MAP: software for analysis of Capture-C data

Author(s): Adam Buckle, Nick Gilbert, Davide Marenduzzo, Chris A Brackley
Published in: Bioinformatics, 35/22, 2019, Page(s) 4773-4775, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz480

Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions

Author(s): C A Brackley, D Marenduzzo
Published in: Briefings in Functional Genomics, 19/2, 2020, Page(s) 111-118, ISSN 2041-2657
Publisher: Oxford University Press
DOI: 10.1093/bfgp/elz032

Dynamical Scaling and Phase Coexistence in Topologically Constrained DNA Melting

Author(s): Y. A. G. Fosado, D. Michieletto, D. Marenduzzo
Published in: Physical Review Letters, 119/11, 2017, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.119.118002

Genome organization: experiments and modeling

Author(s): Nick Gilbert, Davide Marenduzzo
Published in: Chromosome Research, 25/1, 2017, Page(s) 1-4, ISSN 0967-3849
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10577-017-9551-2

Entropic elasticity and dynamics of the bacterial chromosome: A simulation study

Author(s): M. C. F. Pereira, C. A. Brackley, J. S. Lintuvuori, D. Marenduzzo, E. Orlandini
Published in: The Journal of Chemical Physics, 147/4, 2017, Page(s) 044908, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.4995992

Nonequilibrium Chromosome Looping via Molecular Slip Links

Author(s): C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, D. Marenduzzo
Published in: Physical Review Letters, 119/13, 2017, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.119.138101

Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses

Author(s): Davide Michieletto, Davide Marenduzzo, Enzo Orlandini, Matthew Turner
Published in: Polymers, 9/12, 2017, Page(s) 349, ISSN 2073-4360
Publisher: MDPI AG
DOI: 10.3390/polym9080349

Simulating topological domains in human chromosomes with a fitting-free model

Author(s): C. A. Brackley, D. Michieletto, F. Mouvet, J. Johnson, S. Kelly, P. R. Cook, D. Marenduzzo
Published in: Nucleus, 7/5, 2016, Page(s) 453-461, ISSN 1949-1034
Publisher: Landes Bioscience
DOI: 10.1080/19491034.2016.1239684

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

Author(s): D. Michieletto, E. Orlandini, D. Marenduzzo
Published in: Scientific Reports, 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-13916-w

Shaping epigenetic memory via genomic bookmarking

Author(s): Michieletto, Davide; Chiang, Michael; Colì, Davide; Papantonis, Argyris; Orlandini, Enzo; Cook, Peter R; Marenduzzo, Davide
Published in: Nucleic Acids Research, 6, 2018, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1101/184598

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains

Author(s): Chris A. Brackley, Benno Liebchen, Davide Michieletto, Francois Mouvet, Peter R. Cook, Davide Marenduzzo
Published in: Biophysical Journal, 112/6, 2017, Page(s) 1085-1093, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2017.01.025

Extrusion without a motor: a new take on the loop extrusion model of genome organization

Author(s): C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, D. Marenduzzo
Published in: Nucleus, 9/1, 2018, Page(s) 95-103, ISSN 1949-1034
Publisher: Landes Bioscience
DOI: 10.1080/19491034.2017.1421825

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

Author(s): Chris A. Brackley, James Johnson, Steven Kelly, Peter R. Cook, Davide Marenduzzo
Published in: Nucleic Acids Research, 44/8, 2016, Page(s) 3503-3512, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkw135

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

Author(s): Chris A. Brackley, Jill M. Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R. Hughes, Veronica J. Buckle, Davide Marenduzzo
Published in: Genome Biology, 17/1, 2016, Page(s) 59, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-016-0909-0

A single nucleotide resolution model for large-scale simulations of double stranded DNA

Author(s): Y. A. G. Fosado, D. Michieletto, J. Allan, C. A. Brackley, O. Henrich, D. Marenduzzo
Published in: Soft Matter, 12/47, 2016, Page(s) 9458-9470, ISSN 1744-683X
Publisher: Royal Society of Chemistry
DOI: 10.1039/C6SM01859A

Polymer model with Epigenetic Recoloring Reveals a Pathway for the de novo Establishment and 3D Organization of Chromatin Domains

Author(s): D. Michieletto, E. Orlandini, D. Marenduzzo
Published in: Physical Review X, 6/4, 2016, ISSN 2160-3308
Publisher: American Physical Society
DOI: 10.1103/PhysRevX.6.041047

Stochastic Model of Supercoiling-Dependent Transcription

Author(s): C. A. Brackley, J. Johnson, A. Bentivoglio, S. Corless, N. Gilbert, G. Gonnella, D. Marenduzzo
Published in: Physical Review Letters, 117/1, 2016, Page(s) 018101 (article number), ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.117.018101

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

Author(s): Lilija Brant, Theodore Georgomanolis, Milos Nikolic, Chris A Brackley, Petros Kolovos, Wilfred van Ijcken, Frank G Grosveld, Davide Marenduzzo, Argyris Papantonis
Published in: Molecular Systems Biology, 12/12, 2016, Page(s) 891, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20167311

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology

Author(s): Enzo Orlandini, Davide Marenduzzo, Davide Michieletto
Published in: Proceedings of the National Academy of Sciences, 116/17, 2019, Page(s) 8149-8154, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1815394116

Physical principles of retroviral integration in the human genome

Author(s): D. Michieletto, M. Lusic, D. Marenduzzo, E. Orlandini
Published in: Nature Communications, 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-08333-8

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

Author(s): Adam Buckle, Chris A. Brackley, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert
Published in: Molecular Cell, 72/4, 2018, Page(s) 786-797.e11, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2018.09.016

Dry active turbulence in a model for microtubule–motor mixtures

Author(s): Ivan Maryshev, Andrew B. Goryachev, Davide Marenduzzo, Alexander Morozov
Published in: Soft Matter, 15/30, 2019, Page(s) 6038-6043, ISSN 1744-683X
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sm00558g

Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus

Author(s): Davide Michieletto, Davide Colì, Davide Marenduzzo, Enzo Orlandini
Published in: Physical Review Letters, 123/22, 2019, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.123.228101

Magnetic polymer models for epigenetics-driven chromosome folding

Author(s): Davide Colì, Enzo Orlandini, Davide Michieletto, Davide Marenduzzo
Published in: Physical Review E, 100/5, 2019, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/physreve.100.052410

Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling

Author(s): Marco Ancona, Alessandro Bentivoglio, Chris A. Brackley, Giuseppe Gonnella, Davide Marenduzzo
Published in: Biophysical Journal, 117/2, 2019, Page(s) 369-376, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2019.04.023

Polymer Modeling Predicts Chromosome Reorganization in Senescence

Author(s): Michael Chiang, Davide Michieletto, Chris A. Brackley, Nattaphong Rattanavirotkul, Hisham Mohammed, Davide Marenduzzo, Tamir Chandra
Published in: Cell Reports, 28/12, 2019, Page(s) 3212-3223.e6, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2019.08.045

Nucleosome positions alone can be used to predict domains in yeast chromosomes

Author(s): Oliver Wiese, Davide Marenduzzo, Chris A. Brackley
Published in: Proceedings of the National Academy of Sciences, 116/35, 2019, Page(s) 17307-17315, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1817829116

Non-equilibrium effects of molecular motors on polymers

Author(s): M. Foglino, E. Locatelli, C. A. Brackley, D. Michieletto, C. N. Likos, D. Marenduzzo
Published in: Soft Matter, 15/29, 2019, Page(s) 5995-6005, ISSN 1744-683X
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sm00273a

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations

Author(s): Peter R Cook, Davide Marenduzzo
Published in: Nucleic Acids Research, 46/19, 2018, Page(s) 9895-9906, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky763

Plectoneme dynamics and statistics in braided polymers

Author(s): Giada Forte, Michele Caraglio, Davide Marenduzzo, Enzo Orlandini
Published in: Physical Review E, 99/5, 2019, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/physreve.99.052503

Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins

Author(s): A. Bonato, C. A. Brackley, J. Johnson, D. Michieletto, D. Marenduzzo
Published in: Soft Matter, 16/9, 2020, Page(s) 2406-2414, ISSN 1744-683X
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sm01875a