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

Project Information

THREEDCELLPHYSICS

Grant agreement ID: 648050

DOI 10.3030/648050

Project closed

EC signature date 16 June 2015

Start date 1 July 2015

End date 30 June 2020

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 499 236,00

EU contribution € 1 499 236,00

Coordinated by

THE UNIVERSITY OF EDINBURGH
United Kingdom

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (34)

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 16/9, 2020, Page(s) 2406-2414, ISSN 1744-683X
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sm01875a