Comparative analysis of the m6A epitranscriptome in HeLa-expressed HPV18 early transcripts reveals its potential impact on splicing

Abstract

Human papillomavirus (HPV)-driven cancers remain a major global health burden, and understanding how post-transcriptional regulation shapes viral gene expression may inform new therapeutic strategies. Here, we reanalysed independently generated public HeLa datasets to identify candidate RNA modification sites on integrated HPV18 transcripts expressed from the HeLa genome. Using Oxford Nanopore direct RNA sequencing of native RNAs and in vitro transcribed controls, together with GLORI, eTAM-seq and staged 4sU-GLORI datasets, we identified a set of candidate m6A sites on HPV18 early transcripts. m6A levels at a subset of these sites were reduced following perturbation of the m6A pathway, most clearly after METTL3 inhibition, WTAP knockdown or FTO overexpression. We further show that the E6*I-proximal m6A site at position 224 is enriched on unspliced transcripts in direct RNA sequencing, eTAM-seq and staged 4sU-GLORI data. In contrast, we find no convincing evidence for m5C or pseudouridine within the HPV18 regions covered by these datasets. Together, our analyses provide a prioritized candidate map of RNA modifications on HeLa-expressed HPV18 early transcripts.