In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

A system for the expression of recombinant histone proteins has been developed and it provides the possibility of manipulating the histone proteins by site-directed mutagenesis. This can be used to study the roles of specific regions of the histone proteins in chromatin function and to introduce amino acids at specific sites within nucleosomes for the attachment of reporter compounds. This chapter describes the use of this approach to attach compounds that facilitate the study of the dynamic properties of chromatin. Recombinant histone technology can also be used to provide a means of attaching fluorescent dyes. Techniques for the detection of fluorescent dyes have increased, enabling detection down to the level of single molecules. To date, the major use of fluorescent technology to study chromatin structure has stemmed from the expression of green or yellow fluorescent protein (GFP or YFP, respectively) histone fusions in vivo. These have provided a powerful system for the study of the dynamic properties of chromatin in vivo.

The genome is divided into areas of condensed chromatin (heterochromatin) where genes are transcriptionally silent and regions of accessible chromatin where the majority of actively expressed genes reside. In their Perspective, Owen-Hughes and Bruno discuss new work ( Mizugu-chi et al .) that pinpoints the Swr1 ATPase as a crucial player in preventing the spread of silencing. The Swr1 adenosine triphosphatase (ATPase) catalyzes the exchange of H2A/H2B histone dimers in nucleosomes for H2A.Z/H2B dimers. The H2A.Z histone variant incorporated into nucleosomes then acts as a buffer against the spread of silencing.

ATP-dependent chromatin remodeling activities function to manipulate chromatin structure during gene regulation. One of the ways in which they do this is by altering the positions of nucleosomes along DNA. Here we provide support for the ability of these complexes to move nucleosomes into positions in which DNA is unraveled from one edge. This is expected to result in the loss of histone-DNA contacts that are important for retention of one H2A/H2B dimer within the nucleosome. Consistent with this we find that several chromatin remodeling complexes are capable of catalyzing the exchange of H2A/H2B dimers between chromatin fragments in an ATP-dependent reaction. This provides eukaryotes with additional means by which they may manipulate chromatin structure.