Evaluation ofN⁶-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes

Abstract

Low-level DNA N6-methyldeoxyadenosine (DNA-m6A) has recently been reported across various eukaryotes. Although anti-m6A antibody-based approaches are commonly used to measure DNA-m6A levels, this approach is known to be confounded by DNA secondary structures, RNA contamination, and bacterial contamination. To evaluate for these confounding features, we introduce an approach for systematically validating the selectivity of antibody-based DNA-m6A methods and use a highly selective anti-DNA-m6A antibody to reexamine patterns of DNA-m6A inC. reinhardtii,A. thaliana, andD. melanogaster. Our findings raise caution about the use of antibody-based methods for endogenous m6A quantification and mapping in eukaryotes.

DNA methylation in T cell leukaemia

“…Since expression of many genes is heavily dysregulated in cancers, we cannot exclude the possibility that 6mdA is present in cancer cells, but current analysis techniques are not sensitive enough to distinguish any true 6mdA events from false positives. More recent studies have confirmed our findings and the presence of 6mdA as a true epigenetic mark in mammals remains unresolved [89,446,450,451].…”

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools

“…2b, S8 ). Notably, given this FPR, fibertools is not suited for identifying non-specific genomic m6A events within species with low-level endogenous m6A (Kong et al ., 2022; Debo et al ., 2023).…”

The m6A reader YTHDC1-mediated lncRNA CTBP1-AS2 m6A modification accelerates cholangiocarcinoma progression

“…In addition to DNA and histones, intracellular RNAs (mRNA, lncRNA, snRNA, etc.) also have different types of post-transcriptional modifications, the most common of which is N6-adenosyl methylation (m6A) [ 33 , 34 ]. There is growing evidence that m6A modifications play important biological functions in mammals.…”