Physical Modelling of Chromatin at Individual Nucleosome Scale

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In eukaryotic cells, genetic information is stored in chromosomes, each made from a complex called chromatin comprising of DNA and various structural proteins. The first level of this packaging is the nucleosome, which consists of eight histone octamers around which around 147 base pairs of DNA are wrapped, roughly arranged as a disk of about 10nm in diameter. Between these nucleosomes are sections of free linker DNA, usually varying between 20 and 90 base pairs in length, resulting in a structure analogous to beads on a string. However, less is known about the next level of packaging; the canonical picture is the 30nm fibre, where these beads on a string are folded into either a solenoidal or a zigzagged form, but there are issues with these geometrical models, since linker length is not uniform, so such regularly ordered arrangements may be an oversimplification. Indeed, although this structure has been demonstrated in laboratories under controlled conditions, it is debated whether the 30nm fibre even exists in vivo where cell conditions are much more complex, with physical and thermodynamic stresses from cell machinery and biochemical modifications of the histone proteins both leading to disruption of these fibres.One of the biggest implications of how DNA is packaged is the effect it has on gene expression. Since eukaryotic cells become highly specialised, only making use of a small fraction of the genetic information contained in their DNA, they require a mechanism to control which sections are transcribed and which are not. Sections of DNA wrapped up into nucleosomes are shielded from transcription machinery, whilst free sections are exposed so easily accessible. Adding to this, some transcription factors bind more readily to negatively supercoiled (under-wound) than to positively supercoiled (over-wound) DNA, so topological constraints enforced by nucleosome and protein locations may also have importance. Further, the exact mechanisms of promoter and enhancer interactions with genes are not well understood. Whilst recent models have been developed for DNA at the nucleotide scale (resolving the double helix) and for chromosomes at the scale of chromatin folding (resolving chromatin loops and domains) an intermediate model that is applicable to the sizes of promoters and enhancers is needed.Hence, the aim of this project is to develop a new coarse grained model for chromatin fibres at the resolution of individual nucleosomes, and to use molecular dynamics simulations to understand how varying the positions of these nucleosomes along the DNA changes the structure at higher levels. This will follow from previous, less realistic, beads-on-a-string models of chromatin at this scale, but increase the complexity whilst still keeping the computational efficiency high enough to simulate long enough sections of the genome to be biologically relevant. The model will consider natural nucleosome entry and exit angles, account for rotational forces along the contour of the polymer chain, and include phenomenological representations of the nucleosome potentials based on results from existing higher resolution models. Collaboration with biologists and the use of their experimentally obtained data on nucleosome positions is intended to allow for more accurate predictions of the geometry and behaviour of these chromatin fibres in vivo, and therefore should enable greater understanding of how gene expression is affected by changes to the underlying packaging of DNA at enhancer and promoter regions.