Single cell analysis - the ultimate tool for finding the organization of chromatin in the nucleus

The DNA in a human cell, that is ~3 meters long, is packed in a ~10 μm nucleus. The DNA is immersed in a condensed soup of proteins, it is highly dynamic and takes part in a vast of processes such as protein expression and cell division. It must stay organized to prevent chromosome entanglement and its study is tedious.

Studying such a system faces a great challenge, and due to the statistical distributions of many parameters that are involved in the study, using single-cell studies is the only choice. The nature of the system requires to use both high spatial and temporal resolutions.

Accordingly, we adopted and further developed various methods for studying the organization of the genome in the nucleus on a single-cell basis. The methods include live-cell imaging, time-resolved spectroscopy, the use of fluorescence in situ hybridization (FISH), spectral karyotyping and time resolved intensity photobleaching (TRIP). The experimental results are processed by using biophysical modeling and allowed us to identify that lamin A as a major player for chromatin organization. It forms chromatin loops thereby restricting the chromatin dynamics in the whole nucleus volume. We also identified other relevant proteins.

Based on the results, we conclude that the organization of the DNA in the nucleus is based on a “chromatin matrix”, a structure that we describe here for the first time. I will describe the problem, the experimental and analysis methods and the conclusions.