Ομιλητής: Γκουνταρούλης Δήμος
Μέρος, ώρα : Παρασκευή, 10 Ιανουαρίου 2020, 13:35, Αίθουσα Σεμιναρίων, Τομέα Μαθηματικών, ΣΕΜΦΕ (Κτίριο Ε, 2ος Όροφος)
Τίτλος : Topological Aspects of the Human Genome
Περίληψη : The 3D organization of the genome plays an important role in controlling gene expression. Very recently a new method of Oligopaint labeling and optical imaging permitted to determine positions of subsequent 30kb-large portions of chromatin fibers with 50 nm accuracy (B. Bintu et al. Science 362, 2018). We analysed the topology of deposited chromatin tracings. To simulate the effect of a limited precision of the determination of the centroid position of sequential 30kb-long chromatin blocks, we introduced method-specific tracing errors to positions of every vertex and we produced 10 independent tracings. All individual polygonal curves determined by cartesian coordinates of individual tracings were closed using the stochastic closure method and were analysed using knot invariants.We analysed 4727 deposited tracings of the same 2Mb-large chromosome regions of chromosome 21 of Oligopaint-stained IMR90 cells. The tracings behaved similarly to random walks with a moderate size. Nearly 50% of tracings were knotted and the frequency of forming a given knot was inversely correlated with its complexity.It is far from certain that the corresponding, traced 2Mb long chromatin fibres were indeed knotted. The reason of this uncertainty lies in the 50nm large errors in the determination of spatial positions of centroids of sequential 30 kb- large chromatin portions. However, when we applied error-mimicking perturbations applied to unknotted polygonal chains, we observed that several of deposited tracings that were robustly unknotted. It still unclear whether chromatin can be knotted. However, in all these cases where tracing errors were unable to change the topology of analysed tracings, we could conclude that traced 2MB long chromatin fibers were unknotted.
Affiliations:
- Center for Integrative Genomics , University of Lausanne, Switzerland
- SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Baylor College of Medicine, Houston Texas, USA
- Rice University, Houston Texas, USA