Krzysztof Banecki
supervisor: Dariusz Plewczyński
Chromatin models have proven to be powerful tools in studying spatial genome organization in cell nucleus. Since both microscopy and 3C-based methods do not allow to directly infer the underlying structure of the genome physical models are necessary. Moreover, such models provide a quantitative framework for testing the hypotheses regarding molecular mechanisms that take place in the nucleus. Over the last 20 years a variety of algorithms have been presented to solve the problem of 3-dimentional genome organisation. However, the task that those algorithms are seeking to achieve is plagued with problems. Starting from the biases that naturally occur in Hi-C contact matrices together with inability of this kind of data to grasp the nature of the complex processes of chromatin folding leave the goal of thorough understanding those processes elusive.
Here we present some of the recent advancements in the field of 3-dimentional chromatin modelling based on Hi-C data together with some of our own results. Example 3D genome reconstruction algorithms are going to be discussed. Our consensus method for chromatin folding reconstruction is presented and our image-driven model of the cell nuclei of Arabidopsis Thaliana is going to be shown.