The Biogenesis and Precise Control of RNA m6A Methylation

m6A is an abundant and conserved RNA modification in eukaryotic RNAs that affects RNA fate and is characterized by preferential deposition within the RRACH motif and enrichment in mRNA coding sequences and 3′-untranslated regions. The RNA methyltransferase complex, comprising of the methyltransferase-like 3 (METTL3)/METTL14 (methyltransferase-like 14) core subunit and other cofactors, is responsible for the deposition of m6A on mRNA, where METTL3 is the catalytic subunit and METTL14 is crucial for target recognition. Trimethylation of histone H3 at Lys36 emerges as a general determinant for m6A deposition by recruiting METTL14 and the associated RNA methyltransferase complex to guide m6A deposition cotranscriptionally. By recruiting or sequestering m6A methyltransferase components, transcription factors exhibit new roles in controlling m6A levels on specific transcripts in specific cellular contexts. 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. 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. an important methyl donor derived from ATP and methionine via the one-carbon metabolism. SAM is the main methyl donor in cellular methylation reactions, including DNA methylation, RNA methylation, and histone methylation. an antibody-based technique developed for studying RNA–protein interactions. Instead of using formaldehyde that is commonly used for DNA–protein crosslinking, CLIP uses UV light and the crosslinking is irreversible. a type of genetic engineering in which specific sites of the epigenome is modified without changing the actual DNA sequence. In addition to zinc-finger proteins and transcription activator-like effectors (TALEs), nuclease-deficient Cas9 fusions (dCas9 fusions) were recently developed in which the enzyme for specific epigenetic modification is fused to dCas9 and guided by gRNA (guide RNA) to the targeted DNA loci for editing. all the chemical modifications of DNA and histones. Such modifications regulate the expression of genes within the genome. the epitranscriptome includes all the chemical modifications of the transcriptome within a cell. Epitranscriptomics refers to the study of all functionally relevant changes to the transcriptome without alteration of the RNA sequence. a newly developed m6A profiling method that is independent of anti-m6A antibody and instead takes advantage of specific cleavage of unmethylated ACA motifs by the MazF endoribonuclease. The coverage of MAZTER-seq is therefore lower than the m6A antibody-based sequencing methods because it only detects m6A within the ACA motif. also known as m6A-seq, this technique utilizes the specific m6A antibody to immunoprecipitate fragmented RNA for subsequent deep sequencing. Although the resolution is not very high, MeRIP-seq provides a good way to reveal the m6A profile in the transcriptome. generated by methylation of adenosine at the N6 position. It is the most abundant internal modification in mRNA of most eukaryotes, and is also found in other types of RNAs, including tRNA, rRNA, small nuclear RNA (snRNA), and long noncoding RNA (lncRNA). m6A individual-nucleotide resolution crosslinking and immunoprecipitation, a method developed to increase the resolution of m6A-seq. In contrast to m6A-seq, UV-crosslinking is performed after the addition of anti-m6A antibodies. miCLIP-seq maps m6A locations in the transcriptome with single-nucleotide resolution. site-specific cleavage and radioactive-labeling followed by ligation-assisted extraction and thin-layer chromatography, a method to accurately determine m6A status at any site in mRNAs or lncRNAs.