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THREEDCELLPHYSICS SIGNED

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

Total Cost €

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EC-Contrib. €

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Partnership

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Project "THREEDCELLPHYSICS" data sheet

The following table provides information about the project.

Coordinator
THE UNIVERSITY OF EDINBURGH 

Organization address
address: OLD COLLEGE, SOUTH BRIDGE
city: EDINBURGH
postcode: EH8 9YL
website: www.ed.ac.uk

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country United Kingdom [UK]
 Project website http://www2.ph.ed.ac.uk/
 Total cost 1˙499˙236 €
 EC max contribution 1˙499˙236 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-CoG
 Funding Scheme ERC-COG
 Starting year 2015
 Duration (year-month-day) from 2015-07-01   to  2020-06-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    THE UNIVERSITY OF EDINBURGH UK (EDINBURGH) coordinator 1˙499˙236.00

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 Project objective

Understanding the fundamental mechanisms behind the functioning of cells and their interior has long been a biology-only enterprise. This view has radically changed in the last decade or so, culminating in the invention of a whole new field, named 'cell physics', which uses the tools of physics to gain a more quantitative and deeper understanding of the inner working of a cell. The aim of my research fits broadly in this new field, although the scale of the computational studies which I plan are thus far unprecedented. I will focus my programme on the spatial organisation of DNA and chromosomes, proteins, and DNA-protein networks within the intracellular environment. I will therefore aim to answer questions such as: How is DNA organised in living cells, such as bacteria and eukaryotic nuclei? What is the role of proteins in DNA and chromosome folding in vivo? How does genome organisation differ in healthy and sick nuclei? How do proteins and RNA move around and self-organise into supramolecular structures in the crowded intracellular environment? I propose to work on the simulation and theoretical side of these problems, while maintaining very close collaborations with key experimental players in these fields who will provide me with a large number of experimental data (obtained by more sophisticated version of the original well-known 'chromosome conformation capture' technique) to maximise the impact and output of the modelling work.

 Publications

year authors and title journal last update
List of publications.
2019 Giada Forte, Michele Caraglio, Davide Marenduzzo, Enzo Orlandini
Plectoneme dynamics and statistics in braided polymers
published pages: , ISSN: 2470-0045, DOI: 10.1103/physreve.99.052503
Physical Review E 99/5 2020-03-05
2018 Adam Buckle, Chris A. Brackley, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert
Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci
published pages: 786-797.e11, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2018.09.016
Molecular Cell 72/4 2020-02-27
2019 M. Foglino, E. Locatelli, C. A. Brackley, D. Michieletto, C. N. Likos, D. Marenduzzo
Non-equilibrium effects of molecular motors on polymers
published pages: 5995-6005, ISSN: 1744-683X, DOI: 10.1039/c9sm00273a
Soft Matter 15/29 2020-02-27
2019 Davide Michieletto, Davide Colì, Davide Marenduzzo, Enzo Orlandini
Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus
published pages: , ISSN: 0031-9007, DOI: 10.1103/physrevlett.123.228101
Physical Review Letters 123/22 2020-02-27
2018 Peter R Cook, Davide Marenduzzo
Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations
published pages: 9895-9906, ISSN: 0305-1048, DOI: 10.1093/nar/gky763
Nucleic Acids Research 46/19 2020-02-27
2019 D. Michieletto, M. Lusic, D. Marenduzzo, E. Orlandini
Physical principles of retroviral integration in the human genome
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-019-08333-8
Nature Communications 10/1 2020-02-27
2019 Enzo Orlandini, Davide Marenduzzo, Davide Michieletto
Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology
published pages: 8149-8154, ISSN: 0027-8424, DOI: 10.1073/pnas.1815394116
Proceedings of the National Academy of Sciences 116/17 2020-02-27
2019 Michael Chiang, Davide Michieletto, Chris A. Brackley, Nattaphong Rattanavirotkul, Hisham Mohammed, Davide Marenduzzo, Tamir Chandra
Polymer Modeling Predicts Chromosome Reorganization in Senescence
published pages: 3212-3223.e6, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2019.08.045
Cell Reports 28/12 2020-02-27
2019 Davide Colì, Enzo Orlandini, Davide Michieletto, Davide Marenduzzo
Magnetic polymer models for epigenetics-driven chromosome folding
published pages: , ISSN: 2470-0045, DOI: 10.1103/physreve.100.052410
Physical Review E 100/5 2020-02-27
2019 Marco Ancona, Alessandro Bentivoglio, Chris A. Brackley, Giuseppe Gonnella, Davide Marenduzzo
Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling
published pages: 369-376, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2019.04.023
Biophysical Journal 117/2 2020-02-27
2019 Oliver Wiese, Davide Marenduzzo, Chris A. Brackley
Nucleosome positions alone can be used to predict domains in yeast chromosomes
published pages: 17307-17315, ISSN: 0027-8424, DOI: 10.1073/pnas.1817829116
Proceedings of the National Academy of Sciences 116/35 2020-02-27
2019 Ivan Maryshev, Andrew B. Goryachev, Davide Marenduzzo, Alexander Morozov
Dry active turbulence in a model for microtubule–motor mixtures
published pages: 6038-6043, ISSN: 1744-683X, DOI: 10.1039/c9sm00558g
Soft Matter 15/30 2020-02-27
2016 C. A. Brackley, J. Johnson, A. Bentivoglio, S. Corless, N. Gilbert, G. Gonnella, D. Marenduzzo
Stochastic Model of Supercoiling-Dependent Transcription
published pages: 018101 (article , ISSN: 0031-9007, DOI: 10.1103/PhysRevLett.117.018101
Physical Review Letters 117/1 2020-01-24
2017 C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, D. Marenduzzo
Nonequilibrium Chromosome Looping via Molecular Slip Links
published pages: , ISSN: 0031-9007, DOI: 10.1103/physrevlett.119.138101
Physical Review Letters 119/13 2020-01-24
2017 Davide Michieletto, Davide Marenduzzo, Enzo Orlandini, Matthew Turner
Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses
published pages: 349, ISSN: 2073-4360, DOI: 10.3390/polym9080349
Polymers 9/12 2020-01-24
2017 M. C. F. Pereira, C. A. Brackley, J. S. Lintuvuori, D. Marenduzzo, E. Orlandini
Entropic elasticity and dynamics of the bacterial chromosome: A simulation study
published pages: 44908, ISSN: 0021-9606, DOI: 10.1063/1.4995992
The Journal of Chemical Physics 147/4 2020-01-24
2016 Chris A. Brackley, Jill M. Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R. Hughes, Veronica J. Buckle, Davide Marenduzzo
Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
published pages: 59, ISSN: 1474-760X, DOI: 10.1186/s13059-016-0909-0
Genome Biology 17/1 2020-01-24
2017 Y. A. G. Fosado, D. Michieletto, D. Marenduzzo
Dynamical Scaling and Phase Coexistence in Topologically Constrained DNA Melting
published pages: , ISSN: 0031-9007, DOI: 10.1103/physrevlett.119.118002
Physical Review Letters 119/11 2020-01-24
2016 Chris A. Brackley, James Johnson, Steven Kelly, Peter R. Cook, Davide Marenduzzo
Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains
published pages: 3503-3512, ISSN: 0305-1048, DOI: 10.1093/nar/gkw135
Nucleic Acids Research 44/8 2020-01-24
2017 Chris A. Brackley, Benno Liebchen, Davide Michieletto, Francois Mouvet, Peter R. Cook, Davide Marenduzzo
Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains
published pages: 1085-1093, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2017.01.025
Biophysical Journal 112/6 2020-01-24
2016 D. Michieletto, E. Orlandini, D. Marenduzzo
Polymer model with Epigenetic Recoloring Reveals a Pathway for the de novo Establishment and 3D Organization of Chromatin Domains
published pages: , ISSN: 2160-3308, DOI: 10.1103/PhysRevX.6.041047
Physical Review X 6/4 2020-01-24
2016 C. A. Brackley, D. Michieletto, F. Mouvet, J. Johnson, S. Kelly, P. R. Cook, D. Marenduzzo
Simulating topological domains in human chromosomes with a fitting-free model
published pages: 453-461, ISSN: 1949-1034, DOI: 10.1080/19491034.2016.1239684
Nucleus 7/5 2020-01-24
2016 Y. A. G. Fosado, D. Michieletto, J. Allan, C. A. Brackley, O. Henrich, D. Marenduzzo
A single nucleotide resolution model for large-scale simulations of double stranded DNA
published pages: 9458-9470, ISSN: 1744-683X, DOI: 10.1039/C6SM01859A
Soft Matter 12/47 2020-01-24
2017 Nick Gilbert, Davide Marenduzzo
Genome organization: experiments and modeling
published pages: 1-4, ISSN: 0967-3849, DOI: 10.1007/s10577-017-9551-2
Chromosome Research 25/1 2020-01-24
2018 Michieletto, Davide; Chiang, Michael; Colì, Davide; Papantonis, Argyris; Orlandini, Enzo; Cook, Peter R; Marenduzzo, Davide
Shaping epigenetic memory via genomic bookmarking
published pages: , ISSN: 1362-4962, DOI: 10.1101/184598
Nucleic Acids Research 6 2020-01-24
2016 Lilija Brant, Theodore Georgomanolis, Milos Nikolic, Chris A Brackley, Petros Kolovos, Wilfred van Ijcken, Frank G Grosveld, Davide Marenduzzo, Argyris Papantonis
Exploiting native forces to capture chromosome conformation in mammalian cell nuclei
published pages: 891, ISSN: 1744-4292, DOI: 10.15252/msb.20167311
Molecular Systems Biology 12/12 2020-01-24
2018 C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, D. Marenduzzo
Extrusion without a motor: a new take on the loop extrusion model of genome organization
published pages: 95-103, ISSN: 1949-1034, DOI: 10.1080/19491034.2017.1421825
Nucleus 9/1 2020-01-24

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