Contributions of DNA, histone chaperones and chromatin remodeling enzymes to nucleosome positioning.
The eukaryotic genome is packaged by wrapping ~147 bp units of DNA around histone octamers to form chains of nucleosomes. The packaging of the DNA within a nucleosome reduces access of the DNA to most transcription factors and polymerases. In between nucleosomes, there are regions of more accessible DNA, called linker regions that vary from a few base pairs to several hundred base pairs. Thus within any given cell type, the precise partitioning of the genome into nucleosome-bound and nucleosome-free DNA regions can have large consequences on gene regulation and help define a particular cellular state. Recent studies suggest that the genome plays a large role in encoding its own packaging through differences in affinity of the underlying sequence for the histone octamer. Nucleosome locations are also regulated by several different ATP-dependent chromatin remodeling enzymes, which enable rapid rearrangements in chromatin structure in response to developmental cues. Thirdly, the in vivo nucleosome assembly process involves proteins called histone chaperones. No individual factor is capable of playing a dominant role in generating the immense specificity required to regulate transcription in eukaryotes. This gives rise to the question of what are the relative contributions to nucleosome positions due to each of these factors. This question has been investigated with biochemical reconstitutions and activity assays, which tracked nucleosome position distributions and kinetics in the presence of various factors. Our data support a model in which remodeling enzymes move nucleosomes to new locations by a general sequence-independent mechanism. However, consequent to the rate-limiting remodeling step, the local DNA sequence promotes a collapse of remodeling intermediates into highly resolved positions that are dictated by thermodynamic differences between adjacent positions. Analogously, histone chaperones have been found to reduce thermodynamic equilibration among all available nucleosome positions, but leads to local equilibration after a rapid histone deposition step. Future understanding of how these factors coordinate their activities in vivo and in the presence of transcription factors, will hopefully lead to better predictive models of gene regulation.