PhD defence J. (Jente) van Staalduinen

Below is a brief summary of the dissertation:

The human body consists of several hundreds of unique cell types. Although individual cells contain the same genetic material in their core, cells acquire unique morphologies and characteristics by selectively switching on and off subsets of genes. Which genes are turned on depends on the action of distal elements called enhancers. How enhancers and gene find each other in 3D space is a central question in biology. Currently, we do not understand which chromatin-related processes affect the individual motion of enhancers and genes. In this thesis, I investigated whether we can use live locus labeling techniques to answer these questions. We recorded the movement of different locations throughout a genomic region and found that local gene activity is not associated with changes in motion, a relationship that had been previously demonstrated for other genes. This study therefore demonstrates that the effect of gene activity on movement of enhancers and genes is context dependent. While recording the motion of DNA, we realized that these measurements can be affected by rotations of the nucleus and movement of the cell. We compared various methods from the literature in their ability to accurately correct for this confounding factor. We found that recording of a handful of alternatively labeled points in the nucleus can provide enough information to separate the motion of DNA from the cell. In short, the application of locus labeling techniques in living cells, as presented in this dissertation, offers unique opportunities to investigate new aspects of enhancer biology.