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Dr Rosana Collepardo
Winton Advanced Research Fellow
Email: rc597 @ cam.ac.uk
Office: Maxwell building, room 274
TCM Group, Cavendish Laboratory
19 JJ Thomson Avenue,
Cambridge, CB3 0HE UK.
We develop and apply multi-scale computational models to investigate the structure of the genome at the nanoscale level, in conditions mimicking those inside cells. Our research aims to link epigenomes with the specific chromatin nanostructures they lead to, and also to elucidate the molecular-level mechanisms behind such link. Our multi-scale computational models are anchored in all-atom molecular dynamics simulations, coarse-graining techniques, theory, and experiments from collaborators.
In Plain English
Inside our cells, the DNA is not found free, it is wound around proteins, forming a remarkable structure know as chromatin. Through chromatin, the DNA compresses enormously to fit inside tiny (6 μm) nuclei, stores information at high densities and, moreover, maintains exquisite control over the accessibility of the data it carries. One way in which DNA access is controlled is through epigenetic marks: a pattern of chemical modificaitons that allow the same DNA sequences to be interpreted differently, generating diversity of cells. Indeed, epigenetics explain why the different cell types in our body (e.g. liver, skin, brain) have different behaviors despite having exactly the same DNA sequence. Our group develops computational approaches to investigate the physical principles that explain the storage and access of DNA inside cells, and the epigenetic control of chromatin structure . We also investigate the design principles of data storage in chromatin with the aim of translating them into design rules for novel sustainable data storage devices.
- Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study J Am Chem Soc, 137 10205 (2015)
- Chromatin fiber polymorphism triggered by variations of DNA linker lengths Proc Natl Acad Sci USA, 111 8061 (2014)
- Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins J Am Chem Soc, 136 18052 (2014)
- Crucial role of dynamic linker histone binding for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes Nucleic Acids Res 40 8803 (2012)
- The effect of linker histone’s nucleosome binding affinity on chromatin unfolding mechanisms Biophys J 101 1670 (2011)
- Biomolecular modelling and simulation: a field coming of age, Quart Rev Biophys 43 1 (2011)