Settling the m⁶A debate: methylation of mature mRNA is not dynamic but accelerates turnover

Abstract

Post-transcriptional modification of RNA nucleosides has been implicated as a pivotal regulator of mRNA biology. In this issue of Genes & Development, Ke and colleagues (pp. 990-1006) provide insights into the temporal and spatial distribution of N 6 -methyladenosine (m 6 A) in RNA transcripts by analyzing different subcellular fractions. Using a recently developed biochemical approach for detecting m 6 A, the researchers show that m 6 A methylations are enriched in exons and are added to transcripts prior to splicing. Although m 6 A addition is widely thought to be readily reversible, they demonstrate in HeLa cells that once RNA is released from chromatin, the modifications are surprisingly static. This study integrates data from previous publications to clarify conflicting conclusions regarding the role of m 6 A in mRNA biogenesis and function. Ke and colleagues found that m 6 A methylation levels negatively correlate with transcript half-life but are not required for most pre-mRNA splicing events.Although N 6 -methyladenosine (m 6 A) modification of RNA was discovered in the 1970s, the prevalence of this modification in mammalian mRNAs has become evident only recently, with the advent of transcriptome-wide m 6 A detection. Advances in the field have shown that m 6 A methylations are introduced into mRNA by METTL3 in complex with METTL14 and WTAP (Liu et al. 2014). Experiments manipulating the levels of these proteins and other proteins that interact with m 6 A have suggested that this modification negatively affects mRNA stability and alters splicing patterns (Dominissini et al. 2012;Wang et al. 2014). These findings motivated researchers to investigate further the importance of this modification to mRNA biology. However, the mechanisms modulating m 6 A modification and its precise role in mRNA biogenesis and regulation have remained debatable. In this issue of Genes & Development, Ke et al. (2017) 6 A in chromatin-associated, nucleoplasmic, and cytoplasmic RNA fractions obtained from HeLa cells. They found that even for incompletely spliced chromatin-associated premRNA, the majority of m 6 A modifications is in exonic sequences. Additionally, the number and location of m 6 As do not change between nucleoplasmic and cytoplasmic RNAs (Fig. 1). Prior studies suggested that this modification is dynamic based on the presence of m 6 A demethylases in the nucleus (Jia et al. 2011); however, the findings of Ke et al. (2017) show that changes in the methylation state are minimal and occur at the pre-mRNA level prior to release from chromatin.After demonstrating that m 6 A methylation occurs before splicing is complete, the researchers assessed the number of m 6 A modifications in relation to splice sites. Although chromatin-associated RNA contains slightly more m Cold Spring Harbor Laboratory Press on May 11, 2018 -Published by genesdev.cshlp.org Downloaded from the same regions in nucleoplasmic or cytoplasmic transcripts, a reduction in the density of methylation marks was observed within 50 nucleotides of spl...

RNAs, Phase Separation, and Membrane‐Less Organelles: Are Post‐Transcriptional Modifications Modulating Organelle Dynamics?

“…Approaching sub‐cellular organelle resolution (beyond separating cytoplasm from nuclei and mitochondria) has not yet been achieved in RNA modification research. Addressing RNA content, structure and modification status in individual BioMCs using improved biochemical and structural methodology might be an interesting path forward, especially for an emerging field called “epitranscriptomics” that is presently trying to reconcile the low stoichiometry of detectable RNA modifications, specifically in mRNAs, with the reported adverse effects of RNA modification system mutations on cellular and organismal physiology …”

Occurrence and Functions of m6A and Other Covalent Modifications in Plant mRNA

“…Writing m 6 A mRNA-modifying enzymes are often referred to as writers, by analogy with signal transduction systems in which writers catalyze the formation of a regulatory posttranslational modification, readers act as effectors by binding to the modified amino acid, and erasers remove the modification to reset signaling (Lim and Pawson, 2010). We adopt this nomenclature here but note that its appropriateness is intensely debated, because it is difficult to obtain direct proof that the same mRNA molecules undergo reversible cycles of methylation and demethylation Mauer et al, 2017Mauer et al, , 2019Meyer and Jaffrey, 2017;Rosa-Mercado et al, 2017;Darnell et al, 2018;Wei et al, 2018a;Shi et al, 2019). Despite the simple biochemistry of the m 6 A writer reaction, nucleophilic substitution resulting in transfer of the methyl group from S-adenosylmethionine (SAM) to the N 6 -amine of adenosine, the major eukaryotic mRNA adenosine methyltransferase turns out to be extraordinarily complicated.…”

Emerging Roles of N6-Methyladenosine on HIV-1 RNA Metabolism and Viral Replication

“…Still, it is also possible that depletion of these RNA demethylases results in an indirect effect in the HIV-1 replication cycle. In this regard and considering that the reversibility of adenosine methylation was recently challenged ( Darnell et al, 2017 ; Ke et al, 2017 ; Rosa-Mercado et al, 2017 ), it is very important to determine whether HIV-1 transcripts are indeed hypermethylated in ALKBH5 and FTO knockdown cells.…”

“…Despite FTO has been shown to demethylate the body of certain mRNAs ( Zhao et al, 2014 ), it was recently reported that the N 6 ,2′- O -dimethyladenosine (m 6 Am) modification adjacent to the 7-methylguanosine cap structure rather than m 6 A is the main substrate of this demethylase ( Mauer et al, 2016 ). Moreover, although ALKBH5 is now considered as the major m 6 A eraser of mRNA, the reversibility of the methylation process in cells has been recently challenged ( Darnell et al, 2017 ; Ke et al, 2017 ; Rosa-Mercado et al, 2017 ).…”