Participation of Histones in DNA Damage and Repair within Nucleosome Core Particles: Mechanism and Applications

Abstract

Conspectus DNA is damaged by various endogenous and exogenous sources, leading to a diverse group of reactive intermediates that yield a complex mixture of products. The initially formed products are often metastable and can react to yield lesions that are more biologically deleterious. Mechanistic studies are frequently carried out on free DNA as the substrate. The observations do not necessarily reflect the reaction environment inside human cells where genomic DNA is condensed as chromatin in the nucleus. Chromatin is made up of monomeric structural units called nucleosomes, which are comprised of DNA wrapped around an octameric core of histone proteins (two copies each of histones H2A, H2B, H3, and H4). This account presents a summary of our work in the past decade on the mechanistic studies of DNA damage and repair in reconstituted nucleosome core particles (NCPs). A series of metastable lesions and reactive intermediates, such as abasic sites (AP), N7-methyl-2′-deoxyguanosine (MdG), and 2′-deoxyadenosin-N6-yl radical (dA•), have been independently generated in a site-specific manner in bottom-up-synthesized NCPs. Detailed mechanistic studies on these NCPs revealed that histones actively participate in DNA damage and repair processes in diverse ways. For instance, nucleophilic residues in the flexible histone N-terminal tails, such as Lys and N-terminal α-amine, react with electrophilic DNA damage and reactive intermediates. In some cases, transient intermediates are produced, leading to the promotion or suppression of damage and repair processes. In other examples, reactions with histones yield reversible or stable DNA–protein cross-links (DPCs). Histones also utilize acidic and basic residues, such as histidine and aspartic acid, to catalyze DNA strand cleavage through general acid/base catalysis. Alternatively, a Tyr in histone plays a vital role in nucleosomal DNA damage and repair via radical transfer. Finally, the reactivity discovered during the mechanistic studies has facilitated the development of new reagents and methods with applications in biotechnology. This research has enriched our knowledge of the roles of histone proteins in DNA damage and repair and their contributions to epigenetics and may have significant biological implications. The residues in histone N-terminal tails that react with DNA lesions also play pivotal roles in regulating the structure and function of chromatin, indicating that there may be cross-talk between DNA damage and repair in eukaryotic cells and epigenetic regulation. Also, in view of the biased amino acid composition of histones, these results provide hints about how the proteins have evolved to minimize their deleterious effects but maximize beneficial ones for maintaining genome integrity. Finally, previously unreported DPCs and histone post-translational modifications have been discovered through this research. The effects of these newly identified lesions on the structure and function of chromatin and their fates inside cells remain to be elucidated.

Buffered Lugol's Iodine Preserves DNA Fragment Lengths

“…2016 ). These histones can catalyze DNA cleavage in nonphysiological, low-pH environments when protonated ( Ren et al. 2022 ).…”

Photo-caged 2-butene-1,4-dial as an efficient, target-specific photo-crosslinker for covalent trapping of DNA-binding proteins

“…3A, S8, and S9, Table S1 ‡). 28,39,43 PBDA-modied NCPs were irradiated for various durations, and the DNA-histone crosslink yields were quantied by SDS-PAGE (Fig. S10 ‡).…”

“…19,[21][22][23] We have previously demonstrated that a C4 ′oxidized abasic site (C4-AP) reacts with primary amines to form stable conjugates. [24][25][26][27][28] In the present study, we designed and synthesized an analogue of C4-AP, photo-caged 2-butene-1,4dial (PBDA, Fig. 1B), as a new photo-crosslinker for identifying DNA-binding proteins.…”

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

“…DNA–protein cross-links (DPCs) block transcription and replication and as such pose a significant biological threat. , The first known DNA-dependent proteases that are postulated to be constituents of a general DPC repair pathway have been discovered in the past decade. − DPC repair deficiency has already been associated with the Ruijs–Aalfs syndrome, which gives rise to premature aging and early onset liver cancer. ,, DPCs are produced by a variety of chemical agents, including aldehydes and chemotherapeutic agents. − Transient DPCs formed between histone proteins and the epigenetic base 5-formylcytosine (5fC) play a role in regulating transcription in cells. − DPCs also result from nucleobase oxidation, including ionization induced by a variety of UV-absorbing photochemical reagents and the direct effect of ionizing radiation, which is used to treat more than 50% of cancer patients. − Ionizing radiation produces DPCs in greater quantities than either DNA–DNA interstrand cross-links or double-strand breaks. , Despite the prevalence and biological significance of radiation-induced DPC formation within chromatin, there is a gap in our knowledge regarding their formation from nucleobase radical cations that are generated via direct ionization. We report our investigation of this chemistry in nucleosome core particles (NCPs), the monomeric component of chromatin.…”