Chromatin remodelling: it's a tracking business

Abstract

Chromatin is a dynamic material consisting of DNA wrapped around nucleosomes. Chromatin assembly is very important for many processes, such as DNA replication and repair, and it is necessary for the compaction of the eukaryotic genome. One of the complexes involved in chromatin assembly is the ATP-dependent chromatin-assembly factor (ACF), which assembles nucleosomes onto DNA. It consists of two subunits: ISWI, which contains the ATP hydrolysis activity, and Acf1. ISWI has motifs in common with DNA helicases, which unwind the DNA helix. However, it is not known how ACF works, as no helicase activity has been detected for chromatin remodelling complexes. Fyodorov and Kadonaga have provided insight into the mechanism of ACF by showing that it operates as a processive DNA-tracking motor to assemble nucleosomes on DNA [1xDynamics of ATP-dependent chromatin assembly by ACF. Fyodorov, D.V. and Kadonaga, J.T. Nature. 2002; 418: 896–900CrossrefSee all References][1].If ACF is a DNA-tracking enzyme, a proportion of the ACF complexes will be in the process of tracking along DNA and, therefore, unavailable to assemble chromatin on a new DNA substrate. Using an in vitro chromatin assembly assay with two sequentially added substrates, the authors show that once chromatin assembly is initiated on the first DNA substrate, it is not initiated as efficiently on the second. This implies that the complex is involved in tracking along the DNA. The authors saw a lag of ∼15–30 minutes before nucleosome assembly on the second substrate, suggesting that this is the length of time ACF tracks along DNA. When the authors used a single template assay and sub-stoichiometric levels of ACF, the products consisted of two populations. One population had partially assembled chromatin, with about seven nucleosomes, and the other had none. This suggests that the complex loads about seven nucleosomes before dissociation. When these complexes were digested with a nuclease, the nucleosomes were shown to be in tandem arrays. Together, these data imply that ACF assembles nucleosomes by tracking processively along the DNA.Several other enzymes that track along DNA are ATP dependent. For example, helicases hydrolyze ∼1–3 ATP molecules per base pair. Fyodorov and Kadonaga examined the ATP requirement for chromatin assembly by ACF and found that the complex hydrolyzed 2–4 ATP molecules per base pair, comparable to the ATP consumption of helicases. Therefore, ACF is a DNA-tracking motor that requires large amounts of energy. ACF could require more energy than helicases if other steps in nucleosome assembly are ATP-dependent, but this is a subject for future research. It is likely that the tracking mechanism of ACF also applies to other chromatin remodelling complexes.