Bioinformatics: Model the 3D genome of your favorite organism
Eukaryotic DNA is folded into a three-dimensional (3D) structure inside the nucleus of the cell. Newly developed technologies, such as the Hi-C method , have made it possible to probe this 3D structure, giving rise to large amounts of data concerning the spatial arrangement of DNA. In order to get a rendering of the shape and positions of all the chromosomes, bioinformatics algorithms are used.
The figure below shows an example of a 3D model of the human genome, generated from a bioinformatics software called Chrom3D, developed by the supervisor of the project .
In the figure, each human chromosome is shown in a separate color. Each “bead” corresponds to a small part (or domain) on the chromosome. The nucleus model is cut in half to be able to visualize the interior. Similar models can, in principle, be generated for any organism for which Hi-C data is available.
In this bioinformatics project, the student (together with the supervisor) will select an organism for which Hi-C data is already available. A non-exhaustive list of possible organisms is: Human (various tissues, celltypes), mouse, chimpanzee, bonobo, gorilla, Rhesus macaque, marmoset, drosophila, C. elegans, yeast, arabidopsis, rice, maize, foxtail millet and many others. The student will apply available computational tools to reconstruct the 3D genome structure of the selected organism from the data. The resulting 3D genome model will then be further annotated and analyzed. For example, the 3D positions of all annotated genes, including distances between them, can be predicted.
 Belton, J. M., McCord, R. P., Gibcus, J. H., Naumova, N., Zhan, Y., & Dekker, J. (2012). Hi–C: a comprehensive technique to capture the conformation of genomes. Methods, 58(3), 268-276.
 Paulsen, J., Ali, T. M. L., & Collas, P. (2018). Computational 3D genome modeling using Chrom3D. Nature protocols, 13(5), 1137.