Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin

Abstract

Human genome stability requires efficient repair of oxidized bases, which is initiated via damage recognition and excision by NEIL1 and other base excision repair (BER) pathway DNA glycosylases (DGs). However, the biological mechanisms underlying detection of damaged bases among the million-fold excess of undamaged bases remain enigmatic. Indeed, mutation rates vary greatly within individual genomes, and lesion recognition by purified DGs in the chromatin context is inefficient. Employing super-resolution microscopy and co-immunoprecipitation assays, we find that acetylated NEIL1 (AcNEIL1), but not its non-acetylated form, is predominantly localized in the nucleus in association with epigenetic marks of uncondensed chromatin. Furthermore, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) revealed non-random AcNEIL1 binding near transcription start sites of weakly transcribed genes and along highly transcribed chromatin domains. Bioinformatic analyses revealed a striking correspondence between AcNEIL1 occupancy along the genome and mutation rates, with AcNEIL1-occupied sites exhibiting fewer mutations compared to AcNEIL1-free domains, both in cancer genomes and in population variation. Intriguingly, from the evolutionarily conserved unstructured domain that targets NEIL1 to open chromatin, its damage surveillance of highly oxidation-susceptible sites to preserve essential gene function and to limit instability and cancer likely originated ∼500 million years ago during the buildup of free atmospheric oxygen.

GRB2 enforces homology-directed repair initiation by MRE11

“…As RPA70 binds to a conserved OB1 fold in the nSH3 domain of GRB2, which occurs in many DNA repair proteins [e.g., BRCA2, BLM-complex proteins, and ligase-1 ( 41 )], further studies may test and uncover GRB2 as an adapter for recruitment of other DNA repair proteins. Currently, GRB2 targeting of MRE11 and RPA to γH2AX for efficient HDR has apparent analogies to recruitment of NEIL1 glycosylase to oxidation-susceptible open chromatin sites for efficient BER, as revealed by the notable correspondence between NEIL1 occupancy and mutation rates along the genome ( 42 ).…”

An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2

“…Indeed, we also know from biology that catalytically inactive proteins that bind and hold damaged DNA can control damage outcomes, as seen for ATL that forms a complex with alkylated base damage and thereby alters repair pathway outcome from base repair to the nucleotide excision repair pathway ( Tubbs et al, 2009 ). Analogously, XPG impacts multiple repair pathways by binding and sculpting DNA junctions and protein partners in addition to its nuclease activity ( Tsutakawa et al, 2020 ), FEN1 sculpts 5’ flaps to avoid template switching at replication forks ( Perry et al, 2006 , Trego et al, 2011 , Tsutakawa et al, 2017 ), GRB2 adaptor protein efficiently brings MRE11 nuclease to DNA breaks ( Ye et al, 2021 ), XRCC1 links MRE11 and PolQ to promote alternative end joining of DNA breaks ( Eckelmann et al, 2020 ), SLX4IP binds and maintains SLX4-XPF-ERCC1 complex for inter-strand crosslink repair ( Zhang et al, 2019 ), and acetylation targets oxidative base repair initiation to open chromatin ( Bacolla et al, 2021 ). In extreme examples, transient polyvalent binding by flexible proteins and RNA can create phase separated condensates of functional proteins for processes such as repair, as seen for DNA break repair protein KU and its complex with long non-coding RNA ( Thapar et al, 2021 ).…”

NEIL1 and NEIL2 Are Recruited as Potential Backup for OGG1 upon OGG1 Depletion or Inhibition by TH5487

“…In addition, highly transcribed genomic regions are enriched in acetylated NEIL1. This preferential binding of acetylated NEIL1 correlates with low mutation frequencies, implying that NEIL1 protects transcription start sites from oxidative DNA damage [ 32 ]. Importantly, NEIL1 and NEIL2 share common substrates including FapyG, and FapyA, thymine glycol and 5-hydroxyuracil present in single-stranded, duplex and bubble-structure oligonucleotides [ 33 ].…”