Chromatin remodelling: the industrial revolution of DNA around histones

Abstract

Chromatin-remodelling machines (remodellers) are large, multi-protein complexes that use the energy of ATP hydrolysis to mobilize and restructure nucleosomes. Nucleosomes wrap 146 bp of DNA in ∼1.7 turns around a histone-octamer disk, and the DNA inside the nucleosome is generally inaccessible to DNA-binding factors. Remodellers provide access to the underlying DNA to enable transcription, chromatin assembly, DNA repair and other processes. Central questions in the chromatin field include how remodellers convert the energy of ATP hydrolysis into a mechanical force to mobilize the nucleosome, and how different remodeller complexes select which nucleosome to move and restructure. Remodellers are partitioned into five families with specialized biological roles. However, all remodellers contain a subunit with a conserved ATPase domain. As well as the conserved ATPase, each remodeller complex contains unique proteins that specialize each remodeller for these biological roles. However, as all remodellers move nucleosomes, and as all movement is ATP dependent, mobilization is probably a property of the conserved ATPase subunit. The ATPase domains of remodellers are similar in sequence and structure to known DNA-translocating proteins in viruses and bacteria. Recent evidence with the SWI/SNF and ISWI remodeller families has revealed that remodeller ATPases are directional DNA translocases that are capable of the directional pumping of DNA. This property is applied to nucleosomes in the following manner: the ATPase seems to bind ∼40 bp inside the nucleosome, from which location it pumps DNA around the histone-octamer surface. This enables the movement of the nucleosome along the DNA, allowing the exposure of DNA to regulatory factors. The additional domains and proteins that are attached to the ATPase are important for nucleosome selection, and additionally help to regulate the ATPase activity. These attendant proteins bind to histones and nucleosomal DNA, and their binding to these epitopes is affected by the histone-modification state. Therefore, the modification state of histones helps to determine whether the nucleosome is an appropriate substrate for a remodeller complex.