A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling

Abstract

The ATPase ISWI is the molecular motor of several nucleosome remodeling complexes including ACF. We analyzed the ACF-nucleosome interactions and determined the characteristics of ACF-dependent nucleosome remodeling. In contrast to ISWI, ACF interacts symmetrically with DNA entry sites of the nucleosome. Two-color fluorescence cross-correlation spectroscopy measurements show that ACF can bind four DNA duplexes simultaneously in a complex that contains two Acf1 and ISWI molecules. Using bead-bound nucleosomal substrates, nucleosome movement by mechanisms involving DNA twisting was excluded. Furthermore, an ACF-dependent local detachment of DNA from the nucleosome was demonstrated in a novel assay based on the preferred intercalation of ethidium bromide to free DNA. The findings suggest a loop recapture mechanism in which ACF introduces a DNA loop at the nucleosomal entry site that propagates over the histone octamer surface and leads to nucleosome repositioning.

Chromatin remodeling: insights and intrigue from single-molecule studies

“…Thus, SWI/SNF and RSC translocate DNA loops onto nucleosomes, and they impart sufficient force to disrupt several histone-DNA contacts, but not a 'rip force' that can disrupt all the contacts at once (requiring >20 pN). This is consistent with most remodeling models 41,44,45,[54][55][56] , which propose that a DNA loop is created when an initial disruption of contacts on the outer wrap then propagates around the remaining portion of the nucleosome by diffusion. This requires only a small subset of histone-DNA contacts to be disrupted in propagation intermediates (see Fig.…”

“…As described above, RSC apparently imparts one helical twist for every ∼100 bp translocated 49 . Furthermore, biochemical data from Strohner et al 54 show that ISWI remodelers can slide a nucleosome 40-50 bp that has a bead tethered to a biotin group located on a DNA base near the nucleosomal dyad. As Strohner et al 54 suggest, this tethering to the bead should prevent a full DNA rotation during remodeling by ISWI.…”

“…Furthermore, biochemical data from Strohner et al 54 show that ISWI remodelers can slide a nucleosome 40-50 bp that has a bead tethered to a biotin group located on a DNA base near the nucleosomal dyad. As Strohner et al 54 suggest, this tethering to the bead should prevent a full DNA rotation during remodeling by ISWI. Furthermore, the ∼100-bp DNA loops formed on nucleosomes in the optical-tweezers experiments 50 would bear about ten full negative turns if they were formed by processive backbone tracking, a twist force that should cause either DNA melting or release of the DNA from the nucleosome.…”

“…The proposed models focus on the use of conformational changes to push a segment of DNA into the nucleosome 34,38,44,45,[54][55][56] . Above, I mentioned a model for remodeling by ISWI that combines DNA translocation occurring from an internal position with a conformational change to push DNA into the nucleosome 34,38,44,45,[54][55][56] (Fig. 3a).…”

Mechanisms of ATP dependent chromatin remodeling

“…Further evidence for the loop recapture model with bulge propagation comes from incorporation of ethidium bromide during nucleosome sliding by ACF [133]. Ethidium bromide intercalates into free DNA better than nucleosomal DNA and if nucleosomal DNA is made accessible during nucleosome mobilization, then site specific intercalation occurs followed by laser-induced crosslinking creating single-strand breaks at the intercalation sites [134,135].…”