Nucleosome Remodeling

The ordered arrangement of nucleosomes results in compact and protective chromatin organization, which may obstruct the access to genetic information in several ways. 

First, DNA binding proteins, such as RNA polymerase, cannot readily associate with the DNA bound to the histone surface. In addition, the DNA wound around the histone is highly bent, making it unrecognizable by the DNA binding proteins. Finally, non-histone chromatin proteins may get associated with nucleosomes causing further compaction. 

Therefore, eukaryotic cells have enzymes called ATP-dependent chromatin remodeling complexes that can temporarily and locally remodel the nucleosomes.

These complexes contain an ATP hydrolyzing subunit that binds both to the histone proteins and to the DNA wound around it. Hydrolysis of ATP provides the energy required to disrupt the interaction between the histone core and the DNA.

Energy obtained from multiple rounds of ATP hydrolysis allows the remodeling complexes to cause nucleosome sliding - a process where the histone is moved along the DNA without dissociating from it. 

Nucleosome sliding is best explained by the loop-bulge propagation model. Here, the DNA from the linker region is pushed to the histone core, forming a loop. 

This bulge then propagates around the histone core like a wave, breaking and reforming histone-DNA interactions. This process shifts the histone core along the DNA, exposing the hitherto inaccessible DNA sequences. 

Remodeling complexes, in association with histone chaperones, facilitate partial or complete replacement of nucleosome octamer cores, indirectly affecting the chromatin folding. For example, the replacement of histone H3 with centromere-specific H3 histones marks the location of centromere on the chromosome. 

Non-histone DNA binding proteins also influence the nucleosome position and stability. Some bound proteins may favor nucleosome formation, and other proteins may not allow nucleosomes to be formed in their vicinity. 

The exact location of nucleosomes therefore depends on the nature of non-histone DNA binding proteins; and due to the presence of the chromatin remodeling complexes the composition and arrangement of nucleosomes is highly dynamic.