Nucleosome positioning and chromatin organization

DNA is a very long polymer that contains the genetic code. Even though different cell types in our body (skin, muscle cells etc)  have exactly the same DNA code, these cells function very differently. This functional diversity is thought to be achieved through realizations of different "chromatin states". We now know that the fate of a cell is not just decided by the sequence of its DNA but also by the “state” of its chromatin. Chromatin is a 3-dimensional active  assembly of DNA bound by many proteins. Chromatin can be assembled/organized in multiple ways and that eventually results in different function. In other words, regulating 

its organization, different parts of the DNA (genes) are made inaccessible (off) and accessible (on) leading to different cell types and functions. 

 

In this talk, I will discuss some physical models we developed that is useful to understand different aspects of chromatin assembly, information storage at different layers, and copying of this information. First, we will discuss results from simulations of our physical models on how nucleosome organization---spatial positioning of certain proteins along DNA--- is crucial for gene regulation and how cells might maintain and inherit this nucleosome 

positioning information from parent to daughter cells.  In the second part, I will discuss how nucleosome positioning can affect the 3D organization of chromatin in the length scale of a gene.