Flexibility of DNA within transcriptionally active nucleosomes: analysis by circular dichroism measurements

On the role of inter-nucleosomal interactions and intrinsic nucleosome dynamics in chromatin function

Evidence is emerging that many diseases result from defects in gene functions, which, in turn, depend on the local chromatin environment of a gene. However, it still remains not fully clear how chromatin activity code is 'translated' to the particular 'activating' or 'repressing' chromatin structural transition. Commonly, chromatin remodeling in vitro was studied using mononucleosomes as a model. However, recent data suggest that structural reorganization of a single mononucleosome is not equal to remodeling of a nucleosome particle under multinucleosomal content - such as, interaction of nucleosomes via flexible histone termini could significantly alter the mode (and the resulting products) of nucleosome structural transitions. It is becoming evident that a nucleosome array does not constitute just a 'polymer' of individual 'canonical' nucleosomes due to multiple inter-nucleosomal interactions which affect nucleosome dynamics and structure. It could be hypothesized, that inter-nucleosomal interactions could act in cooperation with nucleosome inherent dynamics to orchestrate DNA-based processes and promote formation and stabilization of highly-dynamic, accessible structure of a nucleosome array. In the proposed paper we would like to discuss the nucleosome dynamics within the chromatin fiber mainly as it pertains to the roles of the structural changes mediated by inter-nucleosomal interactions.

Chromatin structural transitions in Drosophila embryo cell-free extract result in a high conformational flexibility of nucleosomal DNA

DNA within chromatin has considerably more restricted flexibility in comparison with naked DNA. This raises the main question of how the functioning multi-enzyme complexes overcome the nucleosomal level of DNA packaging. We studied the DNA conformational flexibility of reconstituted chromatin in a cell-free system derived from Drosophila embryo extracts. Using this system, we have found evidence for a energy-independent chromatin remodelling process that efficiently destabilizes the nucleosome structure resulting in a high conformational flexibility of nucleosomal DNA. The described chromatin remodelling process may lay on the basis of defined molecular principles governing the molecular heterogeneity of chromatin structures in vivo.