DNA–Histone Cross-Link Formation via Hole Trapping in Nucleosome Core Particles

Abstract

Radical cations (holes) produced in DNA by ionizing radiation and other oxidants yield DNA−protein cross-links (DPCs). Detailed studies of DPC formation in chromatin via this process are lacking. We describe here a comprehensive examination of DPC formation within nucleosome core particles (NCPs), which are the monomeric component of chromatin. DNA holes are introduced at defined sites within NCPs that are constructed from the bottom-up. DPCs form at DNA holes in yields comparable to those of alkali-labile DNA lesions that result from water trapping. DPC-forming efficiency and site preference within the NCP are dependent on translational and rotational positioning. Mass spectrometry and the use of mutant histones reveal that lysine residues in histone Nterminal tails and amino termini are responsible for the DPC formation. These studies are corroborated by computational simulation at the microsecond time scale, showing a wide range of interactions that can precede DPC formation. Three consecutive dGs, which are pervasive in the human genome, including G-quadruplex-forming sequences, are sufficient to produce DPCs that could impact gene expression.

Key molecular DNA damage responses of human cells to radiation

“…Radiation can also cleave disulfide bonds and alter protein conformations, disrupting normal biological functions of proteins and affecting cellular activities ( Fitzner et al, 2023 ). On DNA, IR induces the generation of radical cations (holes), leading to DNA-protein crosslinks (DPCs) ( Wen et al, 2023 ). Additionally, IR causes significant amounts of single-strand and DSBs through the rapid decay of transient molecular resonances localized on fundamental DNA components ( Boudaïffa et al, 2000 ).…”