Next-Generation Sequencing-Based Analysis of the Effects of N¹- and N⁶-Methyldeoxyadenosine Adducts on DNA Transcription

Abstract

DNA methylation can occur naturally or be induced by various environmental and chemotherapeutic agents. The regioisomeric N 1- and N 6-methyldeoxyadenosine (1mdA and 6mdA, respectively) represent an important class of methylated DNA adducts. In this study, we developed a shuttle vector- and next-generation sequencing-based assay to quantitatively assess the effects of 1mdA and 6mdA on the accuracy and efficiency of DNA transcription. Our results revealed that 1mdA can induce multiple types of mutant transcripts and strongly inhibit DNA transcription, whereas 6mdA is a nonmutagenic DNA adduct that can exhibit a subtle but significant inhibitory effect on DNA transcription in vitro and in human cells. Moreover, our results demonstrated that the transcription-coupled nucleotide excision repair pathway is dispensable for the removal of 1mdA and 6mdA from the template DNA strand in human cells. These findings provided new important insights into the functional interplay between DNA methylation modifications and transcription in mammalian cells.

Telomere maintenance genes-derived prognosis signature characterizes immune landscape and predicts prognosis of head and neck squamous cell carcinoma

“…[29] DNA adduct formation may cause damage to DNA, affecting cell function and health, [30,31] while also impacting transcription accuracy and efficiency, thus regulating cell function. [32] Phagosomes participate in immune responses, [33] play an important role in epigenetic regulation, [34] and are involved in the formation and regulation of the tumor microenvironment. [35]…”

“…[29] DNA adduct formation may cause damage to DNA, affecting cell function and health, [30,31] while also impacting transcription accuracy and efficiency, thus regulating cell function. [32] Phagosomes participate in immune responses, [33] play an important role in epigenetic regulation, [34] and are involved in the formation and regulation of the tumor microenvironment. [35] The GSEA analysis further elucidated the underlying mechanisms of heterogeneity between molecular subtypes derived from TMG and highlighted the crucial roles of certain key biological processes and cellular pathways in heterogeneity formation and prognosis, including immunoglobulin production, ROS, DNA adducts, and phagosome.…”