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

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 N-terminal 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.