Chromatin Remodelling

The overall chromatin remodelling is not only carried out by histone modifications, but is also affected by ATP-dependent chromatin remodelling complexes (Dinant, Houtsmuller et al., 2008). The importance of these chromatin remodelling complexes is apparent, considering that 80% of the nuclear DNA is packaged by nucleosomes. For all cell processes involving DNA, like transcription, recombination, replication and repair mechanisms, the chromatin needs to be dynamic in order to give access to the genes. Chromatin remodelling therefore plays a crucial role in regulation of gene expression and misregulations.

 DNA interacts with the histones in the nucleosome by forming hydrogen bonds and salt links. ATP-dependent chromatin remodelling complexes are able to either break or reform these interactions (Kundu, Dasgupta, 2007). These complexes use the energy from ATP-hydrolysis to change either the structure or the position of the nucleosomes. These ATP-dependent changes in the chromatin structure, can help transcription factors and other regulatory proteins, which normally would be occluded by the histone proteins, to gain access to DNA sequences (Allis, 2007). The alterations of chromatin by remodelling complexes can be done in four different ways, see Figure.

Fig. Mechanisms for ATP-dependent remodelling. The change in position or composition of the nucleosomes is relative to the DNA wrapped around it. a) Nucleosome sliding to expose a region that was previously hidden. b) Histone exchange where a histone variant is transferred in to the octamer, instead of a standard histone. c) Nucleosome eviction exposes an even larger region of the DNA, with the removal of an octamer. d) Altered nucleosome structure where the path of DNA is creating a loop on the surface on the nucleosome. Modified after (Allis 2007).

                                    

The first one is sliding of the nucleosome (a), meaning that they are moved along the DNA strand (Kundu, Dasgupta, 2007). The second way is the exchange of histones within the histone octamer (b), so the nucleosome is changed to another variant. The third way, which is called nucleosome eviction (c) (Allis, 2007), is the transfer of an octamer from one part of the DNA to another part (Kundu, Dasgupta, 2007). The fourth one alters the path of how the DNA is wrapped around the nucleosome, leading to a gap between the surface of the nuclesome and the DNA strand (d) (Allis, 2007).