The Biogenesis and Precise Control of RNA m6A Methylation

Abstract

N⁶-Methyladenosine (m⁶A) is the most prevalent internal RNA modification in mRNA, and has been found to be highly conserved and hard-coded in mammals and other eukaryotic species. The importance of m⁶A for gene expression regulation and cell fate decisions has been well acknowledged in the past few years. However, it was only until recently that the mechanisms underlying the biogenesis and specificity of m⁶A modification in cells were uncovered. We review up-to-date knowledge on the biogenesis of the RNA m⁶A modification, including the cis-regulatory elements and trans-acting factors that determine general de novo m⁶A deposition and modulate cell type-specific m⁶A patterns, and we discuss the biological significance of such regulation.

Keywords: H3K36me3; RNA modification; biogenesis; dynamic control; epitranscriptome; m(6)A deposition.

Figure 1.. The m⁶A methylation machinery and the biological functions of m⁶A.

The m⁶A modification is installed onto mRNA by the methyltransferase complex (Writers) comprising of the METTL3-METTL14 heterodimer core subunit and other cofactors, including WTAP, KIAA1429, ZC3H13, and RBM15/RBM15b. METTL16 alone can catalyze m⁶A formation in U6 snRNA and some structured RNAs, while ZCCHC4 is responsible for deposition of m6A on rRNA. The RNA m⁶A modification can be reversibly removed by RNA demethylases (Erasers) FTO and ALKBH5. The biological functions of m⁶A modification are achieved by specific recognition and binding by RNA binding proteins (Readers), which affects RNA fate by regulating RNA splicing, export, decay, stabilization, and translation.

Figure 2.. Key Figure: Regulation on m⁶A deposition.

H3K36me3 is installed onto histone tails by SETD2 co-transcriptionally. METTL14, acts as an H3K36me3 reader, binds directly to the H3K36me3 mark and recruits the m⁶A methyltransferase complex, which deposits m⁶A onto newly transcribed nascent RNAs. Given that H3K36me3 is enriched in 3’ end of gene bodies, such a mechanism allows for the shaping of the m⁶A landscape characterized by the enrichment of m⁶A in CDS and 3’ UTR, especially around stop codons. In addition to the H3K36me3 mediated global regulation, transcription factors act to fine tune m⁶A levels of specific transcripts under specific cell contexts. ZFP217 recruits METTL3 to the promoters of pluripotency transcripts, including Nanog, Sox2, Klf4 and Myc. Binding of METTL3 by ZFP217 prevents its binding to METTL14, leading to the hypomethylation and increasing stability of these target transcripts that are needed to maintain the pluripotent state of ESCs. During ESC differentiation, activated SMAD2/3 recruits the RNA methyltransferase complex to the promoter of Nanog, facilitating deposition of m⁶A and the rapid degradation of the Nanog transcripts. In leukemia cells, CEBPZ recruits METTL3 to deposit m⁶A on transcripts critical for leukemia maintenance and promote their translation.