The presence of m 6A modifications can directly influence cellular RNAs by altering their secondary structure and/or interactions with RNA-binding proteins ( Liu et al. Furthermore, alterations in the levels and sites of m 6A modification are implicated in modulating gene expression during development ( Lence et al. 2017) as well as in stress responses ( Schwartz et al. Such regulation of m 6A modifications in mRNAs has been suggested to play important roles in regulating alternative splicing and 3′ end mRNA processing ( Bartosovic et al. 2017), and upon release of nascent RNA transcripts from chromatin, m 6As were found to be relatively stable ( Ke et al. More recently however, FTO was suggested to preferentially demethylate m 6Am modifications present at the cap+1 and cap+2 positions of many mRNAs ( Mauer et al.
2013), implying that m 6A modifications are reversible. The concept of dynamic m 6A modification was expanded by the discovery that ALKBH5 and FTO can act as demethylases ( Jia et al. Interestingly, many m 6A modifications have been reported to be sub-stoichiometric, suggesting that they are installed dynamically ( Dominissini et al. Recently, METTL16 was identified as a second active m 6A methyltransferase in human cells that is responsible for N 6-methylation of the U6 snRNA and the MAT2A mRNA, which both contain m 6A modifications in non-DRACH sequence contexts ( Pendleton et al. WTAP is suggested to serve as a structural scaffold that regulates the localization and catalytic activity of the complex ( Ping et al. Structural and functional studies have shown that METT元 is an active, S-adenosylmethionine-dependent m 6A methyltransferase while METTL14 acts as an RNA-binding platform that, together with RBM15/RBM15B, plays an important role in substrate recognition and binding ( Patil et al. The majority of m 6A modifications lie within a DRACH motif (D = A, G or U R = A or G H = A, C or U) and are thought to be introduced cotranscriptionally by a methyltransferase complex composed of METT元, METTL14, WTAP, RBM15/RBM15B, and KIAA1429 ( Liu et al. While m 6A modifications have been detected in both 5′ and 3′ untranslated regions (UTRs) as well as introns and exons, they are typically enriched in 3′ UTRs in close proximity to stop codons and have often been observed to form clusters ( Meyer et al. So far, in excess of 10,000 m 6A sites have been reported and approximately one in four mRNAs are suggested to carry such modifications ( Xuan et al. However, the recent development of approaches for the transcriptome-wide mapping of m 6A sites has enabled the functional importance of these modifications to be explored as they have provided inventories of m 6A-modified transcripts and defined the positions of m 6A modifications within these RNAs ( Dominissini et al. 1974 Adams and Cory 1975 Dubin and Taylor 1975). The presence of N 6-methyladenosine (m 6A) in mRNAs was first detected several decades ago (see for example, Desrosiers et al. RNA modifications in diverse cellular RNAs, often collectively termed the “epitranscriptome,” have emerged as important regulators of most aspects of gene expression ( Roundtree et al. YTHDC2 was recently found to promote a “fast-track” expression program for specific mRNAs, and our data suggest that YTHDC2 accomplishes this by recruitment of the RNA degradation machinery to regulate the stability of m 6A-containing mRNAs and by utilizing its distinct RNA-binding domains to bridge interactions between m 6A-containing mRNAs and the ribosomes to facilitate their efficient translation. We show that the YTH and R3H domains contribute to the binding of YTHDC2 to cellular RNAs, and using crosslinking and analysis of cDNA (CRAC), we reveal that YTHDC2 interacts with the small ribosomal subunit in close proximity to the mRNA entry/exit sites. The YTH domain of YTHDC2 preferentially binds m 6A-containing RNAs via a conserved hydrophobic pocket, whereas the ankyrin repeats mediate an RNA-independent interaction with the 5′–3′ exoribonuclease XRN1. In contrast to the other YTH domain-containing proteins, YTHDC2 has several defined domains and here, we have analyzed the contribution of these domains to the RNA and protein interactions of YTHDC2.
Several YTH domain-containing proteins have been identified as m 6A readers that regulate the splicing, translation, or stability of specific mRNAs. While m 6As can have direct effects on the structure, maturation, or translation of mRNAs, such modifications can also influence the fate of RNAs via proteins termed “readers” that specifically recognize and bind modified nucleotides. N 6-methyladenosine (m 6A) modifications in RNAs play important roles in regulating many different aspects of gene expression.
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