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

Publicaciones

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

Autores: Marco Ancona, Davide Michieletto, Davide Marenduzzo
Publicado en: Physical Review E, Edición 101/4, 2020, ISSN 2470-0045
Editor: American Physical Society
DOI: 10.1103/physreve.101.042408

Mechanistic modeling of chromatin folding to understand function

Autores: Chris A. Brackey, Davide Marenduzzo, Nick Gilbert
Publicado en: Nature Methods, Edición 17/8, 2020, Página(s) 767-775, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-020-0852-6

Nonequilibrium Strategy for Fast Target Search on the Genome

Autores: F. Cagnetta, D. Michieletto, D. Marenduzzo
Publicado en: Physical Review Letters, Edición 124/19, 2020, ISSN 0031-9007
Editor: American Physical Society
DOI: 10.1103/physrevlett.124.198101

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

Autores: Adam Buckle, Nick Gilbert, Davide Marenduzzo, Chris A Brackley
Publicado en: Bioinformatics, Edición 35/22, 2019, Página(s) 4773-4775, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz480

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

Autores: C A Brackley, D Marenduzzo
Publicado en: Briefings in Functional Genomics, Edición 19/2, 2020, Página(s) 111-118, ISSN 2041-2657
Editor: Oxford University Press
DOI: 10.1093/bfgp/elz032

Dynamical Scaling and Phase Coexistence in Topologically Constrained DNA Melting

Autores: Y. A. G. Fosado, D. Michieletto, D. Marenduzzo
Publicado en: Physical Review Letters, Edición 119/11, 2017, ISSN 0031-9007
Editor: American Physical Society
DOI: 10.1103/physrevlett.119.118002

Genome organization: experiments and modeling

Autores: Nick Gilbert, Davide Marenduzzo
Publicado en: Chromosome Research, Edición 25/1, 2017, Página(s) 1-4, ISSN 0967-3849
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10577-017-9551-2

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

Autores: M. C. F. Pereira, C. A. Brackley, J. S. Lintuvuori, D. Marenduzzo, E. Orlandini
Publicado en: The Journal of Chemical Physics, Edición 147/4, 2017, Página(s) 044908, ISSN 0021-9606
Editor: American Institute of Physics
DOI: 10.1063/1.4995992

Nonequilibrium Chromosome Looping via Molecular Slip Links

Autores: C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, D. Marenduzzo
Publicado en: Physical Review Letters, Edición 119/13, 2017, ISSN 0031-9007
Editor: American Physical Society
DOI: 10.1103/physrevlett.119.138101

Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses

Autores: Davide Michieletto, Davide Marenduzzo, Enzo Orlandini, Matthew Turner
Publicado en: Polymers, Edición 9/12, 2017, Página(s) 349, ISSN 2073-4360
Editor: MDPI AG
DOI: 10.3390/polym9080349

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

Autores: C. A. Brackley, D. Michieletto, F. Mouvet, J. Johnson, S. Kelly, P. R. Cook, D. Marenduzzo
Publicado en: Nucleus, Edición 7/5, 2016, Página(s) 453-461, ISSN 1949-1034
Editor: Landes Bioscience
DOI: 10.1080/19491034.2016.1239684

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

Autores: D. Michieletto, E. Orlandini, D. Marenduzzo
Publicado en: Scientific Reports, Edición 7/1, 2017, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-017-13916-w

Shaping epigenetic memory via genomic bookmarking

Autores: Michieletto, Davide; Chiang, Michael; Colì, Davide; Papantonis, Argyris; Orlandini, Enzo; Cook, Peter R; Marenduzzo, Davide
Publicado en: Nucleic Acids Research, Edición 6, 2018, ISSN 1362-4962
Editor: Oxford University Press
DOI: 10.1101/184598

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

Autores: Chris A. Brackley, Benno Liebchen, Davide Michieletto, Francois Mouvet, Peter R. Cook, Davide Marenduzzo
Publicado en: Biophysical Journal, Edición 112/6, 2017, Página(s) 1085-1093, ISSN 0006-3495
Editor: 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

Autores: C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, D. Marenduzzo
Publicado en: Nucleus, Edición 9/1, 2018, Página(s) 95-103, ISSN 1949-1034
Editor: 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

Autores: Chris A. Brackley, James Johnson, Steven Kelly, Peter R. Cook, Davide Marenduzzo
Publicado en: Nucleic Acids Research, Edición 44/8, 2016, Página(s) 3503-3512, ISSN 0305-1048
Editor: 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

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

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

Autores: Y. A. G. Fosado, D. Michieletto, J. Allan, C. A. Brackley, O. Henrich, D. Marenduzzo
Publicado en: Soft Matter, Edición 12/47, 2016, Página(s) 9458-9470, ISSN 1744-683X
Editor: 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

Autores: D. Michieletto, E. Orlandini, D. Marenduzzo
Publicado en: Physical Review X, Edición 6/4, 2016, ISSN 2160-3308
Editor: American Physical Society
DOI: 10.1103/PhysRevX.6.041047

Stochastic Model of Supercoiling-Dependent Transcription

Autores: C. A. Brackley, J. Johnson, A. Bentivoglio, S. Corless, N. Gilbert, G. Gonnella, D. Marenduzzo
Publicado en: Physical Review Letters, Edición 117/1, 2016, Página(s) 018101 (article number), ISSN 0031-9007
Editor: American Physical Society
DOI: 10.1103/PhysRevLett.117.018101

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

Autores: Lilija Brant, Theodore Georgomanolis, Milos Nikolic, Chris A Brackley, Petros Kolovos, Wilfred van Ijcken, Frank G Grosveld, Davide Marenduzzo, Argyris Papantonis
Publicado en: Molecular Systems Biology, Edición 12/12, 2016, Página(s) 891, ISSN 1744-4292
Editor: 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

Autores: Enzo Orlandini, Davide Marenduzzo, Davide Michieletto
Publicado en: Proceedings of the National Academy of Sciences, Edición 116/17, 2019, Página(s) 8149-8154, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1815394116

Physical principles of retroviral integration in the human genome

Autores: D. Michieletto, M. Lusic, D. Marenduzzo, E. Orlandini
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-08333-8

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

Autores: Adam Buckle, Chris A. Brackley, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert
Publicado en: Molecular Cell, Edición 72/4, 2018, Página(s) 786-797.e11, ISSN 1097-2765
Editor: Cell Press
DOI: 10.1016/j.molcel.2018.09.016

Dry active turbulence in a model for microtubule–motor mixtures

Autores: Ivan Maryshev, Andrew B. Goryachev, Davide Marenduzzo, Alexander Morozov
Publicado en: Soft Matter, Edición 15/30, 2019, Página(s) 6038-6043, ISSN 1744-683X
Editor: Royal Society of Chemistry
DOI: 10.1039/c9sm00558g

Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus

Autores: Davide Michieletto, Davide Colì, Davide Marenduzzo, Enzo Orlandini
Publicado en: Physical Review Letters, Edición 123/22, 2019, ISSN 0031-9007
Editor: American Physical Society
DOI: 10.1103/physrevlett.123.228101

Magnetic polymer models for epigenetics-driven chromosome folding

Autores: Davide Colì, Enzo Orlandini, Davide Michieletto, Davide Marenduzzo
Publicado en: Physical Review E, Edición 100/5, 2019, ISSN 2470-0045
Editor: American Physical Society
DOI: 10.1103/physreve.100.052410

Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling

Autores: Marco Ancona, Alessandro Bentivoglio, Chris A. Brackley, Giuseppe Gonnella, Davide Marenduzzo
Publicado en: Biophysical Journal, Edición 117/2, 2019, Página(s) 369-376, ISSN 0006-3495
Editor: Biophysical Society
DOI: 10.1016/j.bpj.2019.04.023

Polymer Modeling Predicts Chromosome Reorganization in Senescence

Autores: Michael Chiang, Davide Michieletto, Chris A. Brackley, Nattaphong Rattanavirotkul, Hisham Mohammed, Davide Marenduzzo, Tamir Chandra
Publicado en: Cell Reports, Edición 28/12, 2019, Página(s) 3212-3223.e6, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2019.08.045

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

Autores: Oliver Wiese, Davide Marenduzzo, Chris A. Brackley
Publicado en: Proceedings of the National Academy of Sciences, Edición 116/35, 2019, Página(s) 17307-17315, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1817829116

Non-equilibrium effects of molecular motors on polymers

Autores: M. Foglino, E. Locatelli, C. A. Brackley, D. Michieletto, C. N. Likos, D. Marenduzzo
Publicado en: Soft Matter, Edición 15/29, 2019, Página(s) 5995-6005, ISSN 1744-683X
Editor: 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

Autores: Peter R Cook, Davide Marenduzzo
Publicado en: Nucleic Acids Research, Edición 46/19, 2018, Página(s) 9895-9906, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gky763

Plectoneme dynamics and statistics in braided polymers

Autores: Giada Forte, Michele Caraglio, Davide Marenduzzo, Enzo Orlandini
Publicado en: Physical Review E, Edición 99/5, 2019, ISSN 2470-0045
Editor: American Physical Society
DOI: 10.1103/physreve.99.052503

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

Autores: A. Bonato, C. A. Brackley, J. Johnson, D. Michieletto, D. Marenduzzo
Publicado en: Soft Matter, Edición 16/9, 2020, Página(s) 2406-2414, ISSN 1744-683X
Editor: Royal Society of Chemistry
DOI: 10.1039/c9sm01875a

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