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

Abstract

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 N(6)-methyladenosine (m(6)A) 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 m(6)A modification landscape in a transcriptome-wide manner, using a novel approach, m(6)A-seq, based on antibody-mediated capture and massively parallel sequencing. We identify over 12,000 m(6)A 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 m(6)A 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 m(6)A has a fundamental role in regulation of gene expression.

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

“…Consistent with this, buildup of m 6 A and H3K4me2 levels is correlated with infertility that emerges after several generations 53. The asymmetric DNA motifs of m 6 A in C. elegans are reminiscent of mRNA motifs of methylation catalyzed by enzymes of the related METTL3/METTL14 clades 126. Hence, it is possible that damt‐1 and other METTL4‐like enzymes act on ssDNA generated during transcription.…”

The dual role of N6‐methyladenosine modification of RNAs is involved in human cancers

“…And detecting the precise site of m 6 A in RNA is hindered by the following facts. M 6 A shares nearly identical chemical properties with adenine, and it is non‐stoichiometric 6. In addition, M 6 A could also reverse‐transcribe to a thymine and it would not alter the coding capacity of transcripts 6, 14.…”

“…In addition, M 6 A could also reverse‐transcribe to a thymine and it would not alter the coding capacity of transcripts 6, 14. In 2012, MeRIP‐seq (methylated RNA immunoprecipitation sequencing), also known as M 6 A‐seq (m 6 A‐specific methylated RNA immunoprecipitation with next‐generation sequencing), was developed for profiling the transcriptome‐wide m 6 A distribution 6, 35. In this method, mRNA was fragmented into 100‐nt‐sized oligonucleotides and immunoprecipitated with an m 6 A‐specific antibody.…”

“…They are N6‐methyladenosine (m 6 A), N7‐methylguanosine, 5‐methylcytosine and N1‐methyladenosine, etc . Recent studies have illustrated that m 6 A modification is a highly abundant and conservative RNA modification in eukaryotic cells 5, 6. In addition, changes in m 6 A modification are observed to be involved in multiple cellular processes, which may have impacts on several human diseases 7, 8.…”

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

“…m 6 A is found within a conserved consensus sequence (G/A)(G/A) A CU (with a preference for (G/A)G A CU) in different eukaryotes (Horowitz et al ., 1984; Narayan & Rottman, 1988; Dominissini et al ., 2012; Meyer et al ., 2012; Luo et al ., 2014; Wan et al ., 2015). However, only a subset of potential sites is actually modified and the mechanisms underlying the specificity of writing are not yet understood.…”