Organisation of the Eukaryotic Nucleus
Genes are not located at random within the genome: even in the mostly operon-free eukaryotes, genes that are controlled by the same transcription factors are clustered together. This level of organisation is very poorly understood and we are investigating the funtional significance of this arrangement in Saccharomyces cerevisiae. Using particle-based simulations and experimental techniques such as Chromosome Conformation Capture (3C), we are investigating the effects gene clustering has on gene expression, and how different modes of motion of DNA binding proteins lead to advantages of certain genomic architectures.
We are also adapting the concept of chromatin types to S. cerevisiae by combining genome-wide data of chromatin binding proteins and analysing them by Hidden Markov Models to determine these types.
Chromatin types are biologically distinct subsets of chromatin proteins that represent the genomic context in which gene regulation occurs.
We are extending the current understanding of chromatin types by determining their co-localisation in 3D.
Finally, we are interested in DNA transposition. Collaborating with biochemists who study the human mariner transposon, we propose a new and comprehensive model on how details of the molecular mechanism enable a successful invasion strategy by these molecular parasites.