Nano-Positioning-System Provides Structural Insights into ATP-Dependent Nucleosome Remodeling

Abstract

The packaging of chromosomal DNA by nucleosomes condenses and organizes the genome, but occludes many regulatory DNA elements. In order to allow central nuclear processes such as DNA replication, recombination, repair and transcription, cells have evolved so-called chromatin remodeling complexes, which use the energy of ATP hydrolysis to move, destabilize, eject, or restructure nucleosomes.Chd1 (Chromodomain-helicase-DNA-binding protein 1) is a single-subunit chromatin remodeler consisting of three domains, namely the characteristic tandem-chromodomain, the helicase domain and the DNA-binding domain. It has been shown to assemble, slide and space nucleosomes in vitro and associate with actively transcribed regions of the genome in vivo, but the molecular mechanism of Chd1 remodeling is still not well understood.Single-molecule (sm) techniques such as sm-FRET allow the direct and real-time investigation of conformational changes within macromolecular complexes and hence are perfectly suited to study the mechanism of molecular processes such as chromatin remodeling.Here, we apply sm-FRET and the recently developed Nano-Positioning-System (NPS) [1] to determine the conformation of Chd1 bound to a mononucleosome. Briefly, we determine the distances between several known positions on the nucleosome to unknown positions on different domains of Chd1. The NPS computes the 3-dimensional position probability densities of the sites on Chd1 relative to the nucleosome. By combining our position probability densities with data from SAXS and x-ray crystallography on the structure of the different Chd1 domains, a structure of Chd1 bound to a mononucleosome can be modeled.[1] Muschielok et al., Nature Methods, 5, 965 (2008).