No evidence for DNA N ⁶ -methyladenine in mammals

Abstract

N 6 -methyladenine (6mdA) is a widespread DNA modification in bacteria. More recently, 6mdA has also been characterized in mammalian DNA. However, measurements of 6mdA abundance and profiles are often very dissimilar between studies, even when performed on DNA from identical mammalian cell types. Using comprehensive bioinformatics analyses of published data and novel experimental approaches, we reveal that efforts to assay 6mdA in mammals have been severely compromised by bacterial contamination, RNA contamination, technological limitations, and antibody nonspecificity. These complications render 6mdA an exceptionally problematic DNA modification to study and have resulted in erroneous detection of 6mdA in several mammalian systems. Together, our results strongly imply that the evidence published to date is not sufficient to support the presence of 6mdA in mammals.

Mapping the epigenetic modifications of DNA and RNA

“…The third generation sequencing methods are also used to identify 6mA in DNA, which are discussed in the third part. However, recent studies revealed that the sample contamination, RNA contamination, technological limitations, and antibody non-specificity may cause serious problems in quantification and sequencing of 6mA in mammalian genomic DNA, casting doubts on the significance of 6mA in the mammalian genome (O’Brown et al, 2019 ; Douvlataniotis et al, 2020 ; Musheev et al, 2020 ). However, 6mA could be a regulatory mark in mammalian mitochondrial DNA (mtDNA) (Hao et al, 2020 ).…”

Epigenetic Clock: DNA Methylation in Aging

“…To date, only a few enzymes involved in 6mA methylation, such as N6AMT1 and ALKBH1, have been identified in mammals [ 10 , 14 ]. However, a recent study challenged currently used 6mA detection techniques and suggested that more powerful evidence is needed to support the presence of 6mA [ 15 ]. DNA methylation modifications typically occur in promoter regions and then recruit classical readers of DNA methylation, methyl-CpG-binding proteins (MBDs).…”

Role of epigenetics and miRNAs in orofacial clefts

“…A‐methylation of DNA is observed in prokaryotes and some eukaryotes, including protists and Caenorhabditis elegans , where it is part of a transgeneration control mechanism over mitochondrial stress adaptation in the latter species (Ma et al, 2019). More recent studies have refuted claims of N 6 mA playing an epigenetic or functional role in mammalian DNA methylation; one study suggests sample contamination by RNA or bacteria along with technical limitations (Douvlataniotis, Bensberg, Lentini, Gylemo, & Nestor, 2020), whereas another provides evidence that N 6 mA is misincorporated into the genome by DNA polymerase following the processing of ribo‐N 6 mA by the nucleotide salvage pathway (Musheev, Baumgartner, Krebs, & Niehrs, 2020). Given these circumstances, A‐methylation in DNA is a difficult epigenetic mechanism to prove.…”