The predominant view that chromatin remodellers work to unwind DNA from nucleosomes is derived from elegant but non-physiological in vitro studies. These experiments used cell-free extracts and artificial nucleosome templates that do not recapitulate the three-dimensional complexity of chromatin structure in vivo, such as its organization into heterochromatin or euchromatin and into chromosome territories. The evidence presented in this Review and elsewhere indicates that chromatin remodellers have an intricate role in determining the overall structure and long-range interactions of chromatin. It is also becoming clear that nuclear architecture and gene positioning contribute to gene regulation (see ref. 89 for a review), so new assays must be developed to examine the contribution of chromatin remodellers to the establishment and regulation of higher-order chromatin structure. Techniques such as chromosome conformation capture (3C)90 will be crucial, but other assays, for example using artificially reconstructed three-dimensional chromatin in vitro, will be needed to answer such questions.
