For the first time, a group of scientists at the Centre for Genomic Regulation (CRG) and the Institute of Photonic Sciences (ICFO) in Barcelona have been able to visualize and even count the smallest units which, packaged together, form the genome. This study was possible due to the use of super-resolution microscopy, a cutting-edge optical technique that received the Nobel Prize in Chemistry in 2014. In combination with innovative quantitative approaches and numerical simulations, the scientists were also able to define the genome architecture at the nano scale. Most importantly, they found that the nucleosomes are assembled in irregular groups across the chromatin and nucleosome-free-DNA regions separate these groups.
"By using the STORM technique...we have been able to view and even count nucleosomes across the chromatin fibers and determine their organization. STORM overcomes the diffraction limit that normally restricts the spatial resolution of conventional microscopes and enables us to precisely define the chromatin fiber structure," stated Prof. Melike Lakadamyali, group leader at ICFO.
The technique allowed the researchers to go deeper and, by comparing stem cells to differentiated cells, they observed key differences in the chromatin fiber architectures of both cells. Pia Cosma, group leader and ICREA research professor at the CRG, explained, "We found that stem cells have a different chromatin structure than somatic (specialized) cells. At the same time, this difference correlates with the level of pluripotency. The more pluripotent a cell is, the less dense is its packaging. It gives us new clues to understand the stem cells functioning and their genomic structure, which will be helpful for example, in studying cell reprogramming."
What scientists have found is that DNA is not regularly packaged with nucleosomes; instead nucleosomes are assembled in groups of varying sizes, called "nucleosome clutches." They found that pluripotent stem cells have, on average, clutches with less density of nucleosomes. In addition, clutch size is related to the pluripotency potential of stem cells, meaning that the more pluripotent a cell is, the fewer nucleosomes are included in its clutches.
Even though all the cells in our body have the same genetic information, they are not expressing all the genes at the same time. So, when a cell specializes, some of the DNA regions are silenced or less accessible to the molecule that reads the genome: the RNA polymerase. Depending on the specialization of the cells, different levels of DNA packaging will occur. This work, published in the journal Cell, establishes a new understanding of how the chromatin fiber is assembled and packaged forming a specific DNA structure in every cell.