THREEDCELLPHYSICS SIGNED
The physics of three dimensional chromosome and protein organisation within the cell
Total Cost €
0EC-Contrib. €
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Project "THREEDCELLPHYSICS" data sheet
The following table provides information about the project.
| Coordinator |
THE UNIVERSITY OF EDINBURGH
Organization address contact info |
| 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.
| # | ||||
|---|---|---|---|---|
| 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 |
|---|---|---|---|
| 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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