Professor Yuval Garini, Physics Dept. and Institute of Nanotechnology, Bar Ilan University, Israel

Studying Chromatin Dynamics by Advanced Live Cell Imaging Methods

The DNA in a human cell (which is ~3 meters long) is packed in a tiny nucleus of ~10 μm radius. Although it is dynamic, it is well organized. By using advanced microscopy methods for live cell imaging, we study the mechanisms that organizes the chromatin in the nucleus. We identified a dynamic structure that was not known before that we call the ‘DNA matrix’.

These methods allowed us to identify that a protein, lamin A, forms chromatin loops thereby restricting the chromatin dynamics significantly in the whole nucleus volume. The methods we use are based on measuring the signal and fluctuations of fluorescent molecules and the use of biophysical models based on Smoluchowski equation and modified diffusion equations. It allowed us to identify not only the type of the protein, but also its bound and free fractions, concentration and diffusion properties.

The methods include single particle tracking, a new method that we have developed named time resolved intensity photobleaching (TRIP), as well as fluorescence correlation spectroscopy (FCS) and single particle tracking (SPT). We also use single-molecule methods for verifying the DNA-protein interaction, including tethered particle motion (TPM) and atomic force microscopy (AFM). The methods, their use, the biophysical modeling and the biological insight, will be described.