Nucleosome Sliding by ACF is Processive and Bidirectional

Abstract

The packaging of DNA into chromatin presents significant challenges to essential nucleic acid transactions such as transcription, replication, and repair. This challenge is overcome by a variety of chromatin remodeling enzymes, which couple the energy of ATP hydrolysis to the assembly and mobilization of nucleosomes, thereby modulating the accessibility of DNA. It is generally accepted that most chromatin remodeling complexes employ a nucleosome ‘sliding’ mechanism, wherein a histone octamer is translated along DNA without trans-displacement. However, it has been difficult to directly characterize structural dynamics and kinetic intermediates during the remodeling process. Here we report a single-molecule Forster resonance energy transfer (FRET) based assay to monitor in real time the remodeling of individual nucleosomes by the human ATP-utilizing chromatin assembly and remodeling factor (ACF). We demonstrate that ACF can processively slide histone octamers along the DNA in an ATP dependent manner, exhibiting multiple kinetic pauses during translocation. A predominant pause was observed after ∼7 base pairs of DNA translocation, independent of the DNA sequence. Surprisingly, ACF exhibits bidirectional translocation activity and rapid switching of directionality: a single ACF functional unit can dynamically translate the histone octamer back and forth many times along the DNA prior to dissociation, suggesting that the functional unit of ACF is a dimer. These previously unknown remodeling intermediates and dynamics have significant implications on the mechanistic understanding of chromatin remodeling enzymes.