RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation

TLDR: The broad roles of m(6)A in regulating cell fates and embryonic development highlight the existence of another layer of epigenetic regulation at the RNA level, where mRNA is subjected to chemical modifications that affect protein expression.

Abstract: Both DNA and histone proteins undergo dynamic and reversible chemical modifications to control gene expression (Strahl and Allis 2000; Bird 2001; Suzuki and Bird 2008; Bhutani et al. 2011; Jones 2012; Kohli and Zhang 2013). Although post-transcriptional modifications are known to occur to RNAs, the impact of these modifications on gene expression regulation has only recently begun to be explored (He 2010). To date, more than a hundred structurally distinct chemical modifications have been found in eukaryotic RNAs (Cantara et al. 2011; Machnicka et al. 2013); however, the enzymes responsible for each modification and the biological consequences of these modified RNAs are largely unknown. RNA modifications were once considered to be static, but a flurry of recent discoveries has demonstrated that some chemical modifications can be dynamic and participate in the regulation of diverse physiological processes (Motorin and Helm 2011; Yi and Pan 2011; Chan et al. 2012; Fu et al. 2014; Meyer and Jaffrey 2014; Kirchner and Ignatova 2015). The presence of N6-methyladenosine (m6A) in polyadenylated mRNA was first discovered in the 1970s (Desrosiers et al. 1974; Perry and Kelley 1974; Lavi and Shatkin 1975; Wei et al. 1975; Schibler et al. 1977; Wei and Moss 1977) by researchers who were characterizing the 5′ cap structure of messenger RNA (mRNA) in mammalian cells. Since then, m6A has been identified as the most prevalent internal modification in mRNA and long noncoding RNA (lncRNA) in higher eukaryotes. It is widely conserved among eukaryotic species that range from yeast, plants, and flies to mammals as well as among viral mRNAs that replicate inside host nuclei (Krug et al. 1976; Beemon and Keith 1977; Horowitz et al. 1984; Bokar 2005). In addition to its occurrence in mRNA, m6A also exists in various classes of RNA in eukaryotes, bacteria, and archaea, including ribosomal RNAs, small nuclear RNAs, and transfer RNAs (Bjork et al. 1987; Maden 1990; Shimba et al. 1995; Gu et al. 1996; Agris et al. 2007; Piekna-Przybylska et al. 2008). Despite its widespread distribution in the mammalian transcriptome (on average, approximately three m6A sites per mRNA), functional insight has been lacking, possibly due to the low abundance of m6A mRNA and technical difficulties in global detection. Interest in the biological relevance of m6A in mRNA resurfaced after the discovery of two mammalian RNA demethylases, FTO (fat mass and obesity-associated protein) (Jia et al. 2011) and its homolog, ALKBH5 (Zheng et al. 2013), which selectively reverse m6A to adenosine in nuclear RNA. FTO is associated with human obesity (Dina et al. 2007; Frayling et al. 2007; Loos and Yeo 2014) and mental development (Hess et al. 2013), while ALKBH5 is shown to affect mouse spermatogenesis in a demethylation-dependent manner (Zheng et al. 2013), suggesting broad roles of m6A in various physiological processes. Shortly after these findings, YTHDF2 (YTH domain-containing family protein 2) was identified as the first m6A reader protein that preferentially recognizes m6A-containing mRNA (Dominissini et al. 2012; Wang et al. 2014a) and mediates mRNA decay (Wang et al. 2014a), thereby suggesting a role for m6A RNA as a negative regulator of gene expression. On the other hand, a transcriptome-wide m6A profiling method was developed to decipher the m6A RNA landscape (Dominissini et al. 2012; Meyer et al. 2012). Intriguingly, m6A sites in mammalian polyadenylated RNA are dominated by the conserved Pu[G > A]m6AC[A/C/U] motif that localizes near stop codons, in 3′ untranslated regions (UTRs), within long internal exons, and at 5′ UTRs (Dominissini et al. 2012; Meyer et al. 2012; Schwartz et al. 2013; Li et al. 2014; Luo et al. 2014), immediately raising the question of how this specificity is achieved. The m6A RNA landscape is initially sculptured by a methyltransferase complex, but for a long time, METTL3 (methyltransferase-like 3) was the only known SAM (S-adenosyl methionine)-binding subunit associated with mRNA methylation (Bokar et al. 1997). In 2014, a new mammalian methyltransferase, METTL14, was discovered to catalyze m6A methylation. Together with METTL3, these two proteins form a stable heterodimer complex that mediates cellular m6A deposition on mammalian mRNAs (Liu et al. 2014; Wang et al. 2014b). Recently, the mammalian splicing factor WTAP (Wilms’ tumor 1-associating protein) was identified as the third auxiliary factor of the core methyltransferase complex that affects cellular m6A methylation (Liu et al. 2014; Ping et al. 2014). The identification and characterization of the complete mammalian m6A methylation machinery are the first steps toward deciphering the selectivity and biological functions of m6A deposition in eukaryotic mRNAs. In this review, we mainly summarize recent progress in the study of m6A methylation in mRNA across different eukaryotes and discuss their newly discovered roles in post-transcriptional gene expression regulation. We first describe the features of m6A on a global scale and briefly introduce the mammalian m6A writers, erasers, and readers that specifically install, remove, or bind to m6A at defined sequence motifs (Fig. 1). We then discuss the evolutional conservation of the m6A methylation machinery across eukaryotic species that range from yeast, plants, and flies to mammals, highlighting the broad roles of methyltransferases and m6A in regulating cell status and embryonic development. Finally, we discuss the emerging functions of m6A in several mechanisms of post-transcriptional gene expression regulation with a special focus on the effects of m6A on differentiation and reprograming of stem cells. Figure 1. Illustration of the cellular pathways of m6A in nuclear RNAs. The m6A methyltransferases and demethylases dynamically control the m6A methylation landscape within the nucleus. The m6A reader proteins preferentially bind to the methylated RNA and mediate ...