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Project ID: 648050
Funded under: H2020-EU.1.1.

Periodic Reporting for period 1 - THREEDCELLPHYSICS (The physics of three dimensional chromosome and protein organisation within the cell)

Reporting period: 2015-07-01 to 2016-12-31

Summary of the context and overall objectives of the project

"The 3D structure and organisation of chromosomes within mammalian cells are very important to determine gene regulation, and therefore they are crucial for cell development, and play important roles in aging and disease as well. For instance, a liver and a brain cell of our body share the same genetic material, yet the pattern of genes which they express is vastly different, as befits their completely different functionality and cellular environment. The way genes are switched on and off relies almost invariably on 3D structure: for instance, genes which are no longer needed after a cell has differentiated are turned off by methylation of the histone proteins which are wrapped around our DNA, and this triggers the formation of a compact 3D structure which cannot be easily scanned by a polymerase (the enzymes which allows DNA transcription, the first step towards protein production). Similarly, in a senescent cells (the microscopic hallmark of aging) the pattern of open and folded chromosome regions varies substantially, and microscopy shows that protein clusters arise concomitantly with particularly compact volumes (these are called "senescent associated foci"). Finally, diseases linked to abnormalities in 3D organisation of the chromosomes are frequent: examples are cancers and other genetic and/or developmental disorders, such as the Cornelia de Lange syndrome which is associated with loss of cohesins and CTCF, which are proteins involved in the formation of chromosome loops.
Therefore, there is a high potential dividend in understanding the way genomes are organised in 3D.

Very recently, there has been a dramatic rise in experimental studies of 3D DNA, chromosome and protein organisation. It is at least as important to parallel these with computational and theoretical work. Such work is needed for many reasons: (i) to interpret and analyse the experiments, (ii) to find the fundamental mechanisms underlying this organisation, and (iii) to design new experiments to test the predictions of theories such as ours. In this context, the primary goal of our work is to provide a major theoretical/modelling advance in our understanding of 3D chromosome/protein organisation. In our project, the modelling is done either in direct collaboration with experimentalists, or as a stand-alone study, to provide testable predictions which stimulate further work in the future. A unique feature of our work is that the scale of the simulations which we provide is much larger than previously achieved, as we rely on large computational resources which we have available in Edinburgh. A second unique aspect is that we simultaneously combine such large scale simulations both with large scale bioinformatic analyses, and with more fundamental theories involving concepts from various areas of physics, mostly statistical and soft matter physics.

More specifically, in this project we have the following main goals: (i) to provide a model to simulate the organisation of chromosomes in eukaryotic cells; (ii) to provide a model to understand DNA organisation in bacteria; (iii) to model realistic protein dynamics and structure formation, in both eukaryotes and bacteria."

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

"The work performed thus far is mostly relevant to project 1a (3D organisation of eukaryotic chromosomes); some of the results are also relevant to project 2b (intracellular protein clustering). We have also done work dealing with the bacterial nucleoid: part of it is published (this is the work on supercoiling), and part has been drafted for publication. Regarding the work finished and published thus far (see the 6 publications linked to the project), the main results can be grouped under three main headings.

1. Development, validation and application of a 3D "transcription factor" model for chromosome organisation (relevant papers: [1,2,6]).
By using molecular dynamics simulations coupled to bioinformatic data, we have proposed a model to study the organisation of mammalian (and in general eukaryotic) chromosomes at different scale. In particular, we have studied the organisation of a number of small loci in mammalian genomes, such as the globin loci within the mouse (see paper [2]) and the SAMD4A locus within the human genome (see paper [6]). The model we have proposed relies on readily available bioinformatic data (DNAse hypersensitive sites and a small number of histone modifications) which are available for a large number of organisms, and cell types. Importantly, there is no fitting in our model: we can predict the 3D structure of a region of interest simply starting from these datasets; in all cases we considered the predictions conform well to experimental data of our collaborators on the papers (which employ variants of the "chromosome conformation capture" technique). This approach is attracting interest already: for instance following the work presented in [2] we have been asked by a biology group to collaborate to model SAMD4A in humans, and this has led to the work presented in [6]. Other groups have also contacted us to help them model the 3D organisation of regions that they have been interested in.
The model is also applicable at a much larger scale, for instance to whole chromosomes, as we have done in [1], a work where we focussed on dissecting the polymer physics mechanisms behind the formation of topological domains in human chromosomes. The work in [1] constituted the first example of a fitting-free model being used to simulate domain formation in a whole chromosome.

2. Proposal of a new model for epigenetic dynamics coupled to chromosome folding (paper [4]).
In the work under heading 1., we used epigenetic data (e.g., histone modifications, DNase hypersensitivity) which was available for the cell line of interest. In other words, we considered a fixed epigenetic landscape. Some important questions, however, are how this epigenetic landscape is set up in the first place, when a cell differentiates, and how it can be re-established after each round of cell division. To begin to address this new question, we have proposed a model where the 1D epigenetic information (along the chromosome) is dynamic, and is coupled to the 3D chromosome folding dynamics. Our model is the first one which addresses the direct coupling between 1D epigenetic dynamics and 3D chromosome dynamics, and we have shown that this coupling provides a generic route towards a discontinuous transition between an epigenetically disordered and open chromosome to a folded and more compact chromosome where one of the epigenetic state dominates. Because the transition is discontinuous, there is hysteresis, equivalently memory, hence our model can begin to explain how cells can "remember" their epigenetic state from one generation to the next.

3. Proposal of a model for supercoiling-dependent transcription (paper [5]).
In both bacterial and eukaryotic cells, DNA is "supercoiled": i.e., the DNA double helix is either underwound or overwound, and this is important to determine whether a gene is expressed (transcribed) or not, because the local DNA structure affects the likeliness with which a polymerase will bind to the promoter of a given gene. We have proposed a new 1D model which couples the dynamics of supercoiling to the stochastic dynamics of genetic transcription. This model leads to a set of surprising predictions: the coupling between supercoiling and polymerase binding naturally leads to bursty transcription, and to the upregulation of divergent genes: both facts are generically observed in transcription both in bacteria and in eukaryotes, such as yeast or the fly. We have also predicted a new phenomenon: supercoiling should trigger the setup of transcription waves in arrays of parallel genes, which can nowadays in principle be engineered in vitro or in vivo through gene editing.

Besides these main areas, we have also obtained preliminary results for a model for double-stranded DNA: here, we work at a much higher level of detail and model each base pair in the DNA double helix. The rationale for this higher resolution model is, among other things, that it allows to model DNA supercoiling in 3D more accurately. This model can also be of use for some aspects of DNA-protein interaction where this level of detail is of interest or importance.


[1] Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains.
Chris A. Brackley, James Johnson, Steven Kelly, Peter R. Cook, Davide Marenduzzo
Nucleic Acids Research 44, 3503-3512 (2016); doi: 10.1093/nar/gkw135.

[2] Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
Chris A. Brackley, Jill M. Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R. Hughes, Veronica J. Buckle, Davide Marenduzzo, Genome Biology 17, 59 (2016); doi: 10.1186/s13059-016-0909-0.

[3] A single nucleotide resolution model for large-scale simulations of double stranded DNA. Y. A. G. Fosado, D. Michieletto, J. Allan, C. A. Brackley, O. Henrich, D. Marenduzzo, Soft Matter, 12, 9458-9470 (2016); doi: 10.1039/C6SM01859A.

[4] Polymer model with Epigenetic Recoloring Reveals a Pathway for the de novo Establishment and 3D Organization of Chromatin Domains. D. Michieletto, E. Orlandini, D. Marenduzzo, Physical Review X 6, 041047 (2016); doi: 10.1103/PhysRevX.6.041047.

[5] Stochastic Model of Supercoiling-Dependent Transcription. C. A. Brackley, J. Johnson, A. Bentivoglio, S. Corless, N. Gilbert, G. Gonnella, D. Marenduzzo, Physical Review Letters 117, 018101 (2016); doi: 10.1103/PhysRevLett.117.018101.
[6] Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Lilija Brant, Theodore Georgomanolis, Milos Nikolic, Chris A Brackley, Petros Kolovos, Wilfred van Ijcken, Frank G Grosveld, Davide Marenduzzo, Argyris Papantonis, Molecular Systems Biology 12, 891 (2016), doi: 10.15252/msb.20167311."

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

"1. The fitting-free model for chromatin and chromosome organisation developed in papers [1,2,6] goes beyond the state of the art because it is the first fitting-free model used to model chromosome organisation within mammalian nuclei, including large scale simulations of a whole human chromosome.
This work has already had an impact within the biology community as well: following we list some activities which have been stimulated by our work.
(i) Following the work in [2] we have been asked by a number of biology lab to model chromosome regions of interest in their research. These labs include A. Papantonis's lab in Cologne, Nick Gilbert's and Bob Hill's labs in Edinburgh, Ajaz-ul-Wani's lab in Kashmere. The work with A. Papantonis has resulted in the work discussed in [6], where our model has been compared to a new experimental technique to assess chromosome conformation using native forces, or crosslinking. The work with ul-Wani is ongoing and focuses on another organism (Drosophila), highlighting the generality of our approach, which can be used genome-wide and for a variety of eukaryotes.
(ii) Following the work in [1] we have been asked to write an extra view in Nucleus: this is essentially an auto-commentary which increases the visibility of the original paper.
(iii) Due to the interest raised by our simulation work performed overall within the THREEDCELLPHYSICS project, I have been asked to coedit with Nick Gilbert (Edinburgh) a Special Issue in Chromosome Research on Genome Organisation. This Special Issue contains contributions by both experimentalists and theorists/simulators, and is going to be published in early 2017.

Regarding wider societal impact, it is expected that the conformation of chromatin in genomic loci associated with specific diseases may provide important clues to the understanding of the microscopic and molecular basis of such pathologies, and we plan to collaborate with Nick Gilbert in the Western General Hospital in Edinburgh to further pursue these possibilities in the future. This collaboration is likely to involve a PhD student, either in Physics or in Medicine (funded independently of the current ERC grant).

2. The work on epigenetic modelling goes beyond the state of the art as there was previously no model which directly addressed the coupling between 1D epigenetic dynamics and 3D chromatin/chromosome folding.
This work, published in Phys. Rev. X in December 2016, has already attracted attention among the community. It has been highlighted in Physics, via a Focus article written by Philip Ball and entitled "How cells remember who they are", see

3. The work on supercoiling-mediated transcription goes beyond the state of the art as it provides the first ever model which considers the coupling between transcription and supercoiling dynamics. The prediction of transcription waves (triggered by supercoiling) is particularly novel and we hope it will stimulate further experimental work to find these in the lab."
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