Integrative Modelling for the Study of Genomic Structure and Function

Speaker: Giovanni Brandani, PhD.
Lecturer, Theoretical Biophysics lab,
Dept. of Biophysics, Graduate Sch. of Science,
Kyoto University

Eukaryotic genomes are tightly packed into the nucleus in the form of chromatin: a complex of DNA and proteins hierarchically organized starting from the basic unit of the nucleosome, up to loops linking together gene promoters to distant enhancers. This 3d organization supports the regulation of genes, but we still lack a clear understanding of this process at the molecular level.

Current computational and in vitro approaches are limited to simple model systems, while the interpretation of in vivo experiments remains a challenge. To move beyond such limitations, I will illustrate a Bayesian integrative approach to create a comprehensive near-atomic-level model of genes based on experimental data.

The model can be a starting point for molecular dynamics simulations exploring the physical principles governing the structure and function of genes, from the organization of chromatin fibers to the communication of enhancers and promoters through transcription factor condensation.