Nucleosome Core Particles Lacking H2B or H3 Tails Are Altered Structurally and Have Differential Base Excision Repair Fingerprints

Abstract

A recently discovered post-translational modification of histone proteins is the irreversible proteolytic clipping of the histone N-terminal tail domains. This modification is involved in the regulation of various biological processes, including the DNA damage response. In this work, we used chemical footprinting to characterize the structural alterations to nucleosome core particles (NCPs) that result from a lack of a histone H2B or H3 tail. We also examine the influence of these histone tails on excision of the mutagenic lesion 1,N 6-ethenoadenine (εA) by the repair enzyme alkyladenine DNA glycosylase. We found that the absence of the H2B or H3 tail results in altered DNA periodicity relative to that of native NCPs. We correlated these structural alterations to εA excision by utilizing a global analysis of 21 εA sites in NCPs and unincorporated duplex DNA. In comparison to native NCPs, there is enhanced excision of εA in tailless H2B NCPs in regions that undergo DNA unwrapping. This enhanced excision is not observed for tailless H3 NCPs; rather, excision is inhibited in more static areas of the NCP not prone to unwrapping. Our results support in vivo observations of alkylation damage profiles and the potential role of tail clipping as a mechanism for overcoming physical obstructions caused by packaging in NCPs but also reveal the potential inhibition of repair by tail clipping in some locations. Taken together, these results further our understanding of how base excision repair can be facilitated or diminished by histone tail removal and contribute to our understanding of the underlying mechanism that leads to mutational hot spots.

High-Speed Atomic Force Microscopy Reveals the Nucleosome Sliding and DNA Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes

“…Well-studied PTMs include acetylation, methylation, phosphorylation, ubiquitylation, and ADP ribosylation . Several biochemical experiments on histone tail-less nucleosomes have revealed that histone tails play important roles in the formation of higher-order chromatin structures, − as well as in nucleosome structure and stability. − These findings strongly suggest that the histone tails themselves play a regulatory role in nucleosome stability, dynamics, and, ultimately, gene expression.…”

Recent Advances in DNA Lesion Mapping and Repair Mechanisms

“…Globular H2B histones missing the N-terminal tail enhanced excision of εA lesions by DNA-3-methyladenine glycosylase (AAG) due to unwrapping of the DNA in the DNA entry/exit region of the NCP, while globular H3 histones inhibited εA excision by altering DNA periodicity. 3 Taken together, the repair of damaged DNA on NCPs is influenced by the structural and dynamic constraints of DNA–histone interactions and any factor that causes disruption to these interactions.…”

“…For example, NCPs composed of macroH2A histone variants formed a mixture of octasomes and hexasomes, the latter facilitating the efficient removal of uracil by uracil-DNA glycosylase (UDG) and single-strand-selective monofunctional uracil-DNA glycosylase (SMUG1) in intermediate and low solvent-accessible regions and the dyad axis. Globular H2B histones missing the N-terminal tail enhanced excision of εA lesions by DNA-3-methyladenine glycosylase (AAG) due to unwrapping of the DNA in the DNA entry/exit region of the NCP, while globular H3 histones inhibited εA excision by altering DNA periodicity . Taken together, the repair of damaged DNA on NCPs is influenced by the structural and dynamic constraints of DNA–histone interactions and any factor that causes disruption to these interactions.…”