Topology of the human and mouse m⁶A RNA methylomes revealed by m⁶A-seq

An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. Although biochemical studies indicate that N⁶-methyladenosine (m⁶A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. Here we present the human and mouse m⁶A modification landscape in a transcriptome-wide manner, using a novel approach, m⁶A-seq, based on antibody-mediated capture and massively parallel sequencing. We identify over 12, 000 m⁶A sites characterized by a typical consensus in the transcripts of more than 7, 000 human genes. Sites preferentially appear in two distinct landmarks-around stop codons and within long internal exons-and are highly conserved between human and mouse. Although most sites are well preserved across normal and cancerous tissues and in response to various stimuli, a subset of stimulus-dependent, dynamically modulated sites is identified. Silencing the m⁶A methyltransferase significantly affects gene expression and alternative splicing patterns, resulting in modulation of the p53 (also known as TP53) signalling pathway and apoptosis. Our findings therefore suggest that RNA decoration by m⁶A has a fundamental role in regulation of gene expression.