Genome-wide detection of high abundance N⁶-methyladenosine sites by microarray

Abstract

N⁶-methyladenosine (m⁶A), the most abundant internal RNA modification, functions in diverse biological processes, including regulation of embryonic stem cell self-renewal and differentiation. As yet, methods to detect m⁶A in the transcriptome rely on the availability and quality of an m⁶A antibody and are often associated with a high rate of false positives. Here, based on our observation that m⁶A interferes with A–T/U pairing, we report a microarray-based technology to map m⁶A sites in mouse embryonic stem cells. We identified 72 unbiased sites exhibiting high m⁶A levels from 66 PolyA RNAs. Bioinformatics analyses suggest identified sites are enriched on developmental regulators and may in some contexts modulate microRNA/mRNA interactions. Overall, we have developed microarray-based technology to capture highly enriched m⁶A sites in the mammalian transcriptome. This method provides an alternative means to identify m⁶A sites for certain applications.