Base excision repair in chromatin: Insights from reconstituted systems

Abstract

The process of base excision repair has been completely reconstituted in vitro and structural and biochemical properties of the component enzymes thoroughly studied on naked DNA templates. More recent work in this field aims to understand how BER operates on the natural substrate, chromatin [1,2]. Toward this end, a number of researchers, including the Smerdon group, have focused attention to understand how individual enzymes and reconstituted BER operate on nucleosome substrates. While nucleosomes were once thought to completely restrict access of DNA-dependent factors, the surprising finding from these studies suggests that at least some BER components can utilize target DNA bound within nucleosomes as substrates for their enzymatic processes. This data correlates well with both structural studies of these enzymes and our developing understanding of nucleosome conformation and dynamics. While more needs to be learned, these studies highlight the utility of reconstituted BER and chromatin systems to inform our understanding of in vivo biological processes.

Keywords: Base excision repair; Chromatin; Histones; Long-patch (LP) BER; Nucleosomes; Short-patch (SP) BER.

Fig. 1. Schematic showing mechanisms by which BER enzymes access targets within nucleosomes

A. DNA damage sites (red star) on the surface of the nucleosome can be accessed by spontaneous unwrapping of DNA (blue line) from the core histone octamer surface (blue circle) for factors for which access is impeded by presence of the histones or that require DNA conformations not achievable within the nucleosome (green factors). Factors for which the DNA conformation and accessibilty found within the nucleosome are compatible with enzyme activity, can process targets without the requirement for DNA unwrapping (orange factor). B. For damage that is that is oriented toward the core histone octamer, or otherwise inaccessible, DNA unwrapping may be required to allow access to both types of factors. C. DNA motility within the nucleosome influences activity of BER enzymes. This schematic depicts a cut-away view down the helical axis of DNA (blue circle) on the surface of the core histone octamer (rectangle). Left: DNA damage is orientated away from the core histone octamer, and is nominally compatible with BER activities. In this case rotational excursions of the DNA may actually reduce activity of BER enzymes (red arrows). Middle: Damage is oriented directly toward the core histone octamer surface, maximally sub-optimal with respect to accessibility of BER factors. Rotational excursions will generally increase accessibilty (green arrows) Right: Rotational orientations in between maximally optimal and sub-optimal such that excursions may increase or decrease activity of factors.