Genomic 8-oxoguanine is associated with transcriptionally active chromatin and elevated gene expression in Plasmodium falciparum

Abstract

Epigenetic regulation is central to the developmental progression and pathogenicity of the unicellular eukaryotic parasite Plasmodium falciparum; yet, the contribution of DNA base modifications remains poorly understood. One such modification, 8-oxoguanine (8-oxoG), which was initially identified as an oxidative lesion and a marker of DNA damage, has since emerged as a transcriptional regulator in advanced eukaryotes. Given that P. falciparum encounters a highly oxidative environment in human blood, we investigated the potential gene regulatory role of 8-oxoG during its intra-erythrocytic developmental cycle (IDC). Using immunodetection assays, we first confirmed the presence of 8-oxoG in P. falciparum genomic DNA and observed a gradual increase in 8-oxoG abundance from ring to schizont stages. We then optimized oxidative DNA immunoprecipitation sequencing (OxiDIP-seq) for the highly AT-rich parasite genome and generated genome-wide 8-oxoG profiles across four IDC timepoints, which revealed reproducible enrichment of 8-oxoG at discrete genomic loci, with more than 50% of the peaks stable across developmental stages. Notably, 8-oxoG accumulated at putative G-quadruplex-forming sequences in the parasite genome and preferentially localized within exonic regions of protein-coding genes, exhibiting a marked enrichment near STOP codons and within 3' untranslated regions. This in turn correlated with significantly higher steady-state transcript levels of 8-oxoG-marked genes, with stage-specific changes in 8-oxoG enrichment closely matching transcriptional activity. Furthermore, 8-oxoG-marked loci were preferentially associated with active and poised histone post-translational modifications, while showing no evidence of altered nucleosome occupancy. Collectively, these findings demonstrate that 8-oxoG is a widespread and non-random DNA modification in P. falciparum and suggest that it may function as an epigenetic mark associated with transcriptionally permissive chromatin and gene activation during parasite blood-stage development.