Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition

Abstract

How DNA lesions in nucleosomes are recognized for global genome nucleotide excision repair (GG-NER) remains poorly understood, and the roles that histone tails may play remains to be established. Histone H3 and H4 N-terminal tails are of particular interest as their acetylation states are important in regulating nucleosomal functions in transcription, replication and repair. In particular the H3 tail has been the focus of recent attention as a site for the interaction with XPC, the GG-NER lesion recognition factor. Here we have investigated how the structure and dynamics of the DNA lesion cis-B[a]P-dG, derived from the environmental carcinogen benzo[a]pyrene (B[a]P), is impacted by the presence of flanking H3 and H4 tails. This lesion is well-repaired by GG-NER, and adopts a base-displaced/intercalated conformation in which the lesion partner C is displaced into the major groove. We used molecular dynamics simulations to obtain structural and dynamic characterizations for this lesion positioned in nucleosomal DNA so that it is bracketed by the H3 and H4 tails. The H4 tail was studied in unacetylated and acetylated states, while the H3 tail was unacetylated, its state when it binds XPC (Kakumu, Nakanishi et al., 2017). Our results reveal that upon acetylation, the H4 tail is released from the DNA surface; the H3 tail then forms a pocket that induces flipping and capture of the displaced lesion partner base C. This reveals synergistic effects of the behavior of the two tails. We hypothesize that the dual capability of the H3 tail to sense the displaced lesion partner base and to bind XPC could foster recognition of this lesion by XPC for initiation of GG-NER in nucleosomes.

Comparison of the Base Excision and Direct Reversal Repair Pathways for Correcting 1,N6-Ethenoadenine in Strongly Positioned Nucleosome Core Particles

“…Notably, this modeling does not account for the dynamic histone tails that could also modulate binding of repair enzymes. It is intriguing to consider that the H2B and H4 tails near site 97 may contribute to the unexpectedly low amount of excision by AAG at this location, as histone tails have been shown to alter the structure and dynamics of damaged DNA. , The H2B tail is also in close proximity to site 102 and may account for the unexpected lower levels of εA excision by AAG. However, the unexpectedly high excision at site 105 indicates that the microenvironment generated by the H2B tail may have more complex and nuanced effects that include local structural changes, sterics, and electrostatics.…”

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

“…These potential synergistic tail−tail interactions are not unexpected as computational studies have shown that the acetylation of the H4 tail impacts the ability of the H3 tail to interact with other proteins. 55 Similarly, the maximum shift from position 65 to position 64, making it a more OUT lesion, in the gH3 NCP does not confer enhanced εA excision. In contrast, the gH2B NCPs show a small enhancement of activity while retaining the same maximum at position 65 seen in native NCPs.…”

“…The H4 tail, important for internucleosomal interactions, in this region may undergo a conformational change in the absence of the H3 tail that inhibits AAG binding or excision activity. These potential synergistic tail–tail interactions are not unexpected as computational studies have shown that the acetylation of the H4 tail impacts the ability of the H3 tail to interact with other proteins . Similarly, the maximum shift from position 65 to position 64, making it a more OUT lesion, in the gH3 NCP does not confer enhanced εA excision.…”

A dynamic view of histone tails interaction with clustered abasic sites in a nucleosome core particle

“…This work constitutes a proof of concept for studying DNA-protein interactions within a nucleosome core particle harboring multiple sites damage, and our protocol sets the grounds for further studies of Ap reactivity upon histone post-translational modifications 31 and the role of histone tail in DNA repair proteins recruitment. 32…”