Ian A. Roundtree

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

N(6)-methyladenosine (m(6)A) is the most abundant internal modification in mammalian mRNA. This modification is reversible and non-stoichiometric and adds another layer to the dynamic control of mRNA metabolism. The stability of m(6)A-modified mRNA is regulated by an m(6)A reader protein, human YTHDF2, which recognizes m(6)A and reduces the stability of target transcripts. Looking at additional functional roles for the modification, we find that another m(6)A reader protein, human YTHDF1, actively promotes protein synthesis by interacting with translation machinery. In a unified mechanism of m(6)A-based regulation in the cytoplasm, YTHDF2-mediated degradation controls the lifetime of target transcripts, whereas YTHDF1-mediated translation promotion increases translation efficiency, ensuring effective protein production from dynamic transcripts that are marked by m(6)A. Therefore, the m(6)A modification in mRNA endows gene expression with fast responses and controllable protein production through these mechanisms.

Post-transcriptional gene regulation by mRNA modifications

The recent discovery of reversible mRNA methylation has opened a new realm of post-transcriptional gene regulation in eukaryotes. The identification and functional characterization of proteins that specifically recognize RNA N6-methyladenosine (m6A) unveiled it as a modification that cells utilize to accelerate mRNA metabolism and translation. N6-adenosine methylation directs mRNAs to distinct fates by grouping them for differential processing, translation and decay in processes such as cell differentiation, embryonic development and stress responses. Other mRNA modifications, including N1-methyladenosine (m1A), 5-methylcytosine (m5C) and pseudouridine, together with m6A form the epitranscriptome and collectively code a new layer of information that controls protein synthesis.

Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain

N(6)-methyladenosine (m(6)A) is the most abundant internal modification of nearly all eukaryotic mRNAs and has recently been reported to be recognized by the YTH domain family proteins. Here we present the crystal structures of the YTH domain of YTHDC1, a member of the YTH domain family, and its complex with an m(6)A-containing RNA. Our structural studies, together with transcriptome-wide identification of YTHDC1-binding sites and biochemical experiments, not only reveal the specific mode of m(6)A-YTH binding but also explain the preferential recognition of the GG(m(6)A)C sequences by YTHDC1.

Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine

Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine

YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic messenger RNA (mRNA) and plays critical roles in RNA biology. The function of this modification is mediated by m6A-selective ‘reader’ proteins of the YTH family, which incorporate m6A-modified mRNAs into pathways of RNA metabolism. Here, we show that the m6A-binding protein YTHDC1 mediates export of methylated mRNA from the nucleus to the cytoplasm in HeLa cells. Knockdown of YTHDC1 results in an extended residence time for nuclear m6A-containing mRNA, with an accumulation of transcripts in the nucleus and accompanying depletion within the cytoplasm. YTHDC1 interacts with the splicing factor and nuclear export adaptor protein SRSF3, and facilitates RNA binding to both SRSF3 and NXF1. This role for YTHDC1 expands the potential utility of chemical modification of mRNA, and supports an emerging paradigm of m6A as a distinct biochemical entity for selective processing and metabolism of mammalian mRNAs.

Nuclear m6A Reader YTHDC1 Regulates mRNA Splicing

N(6)-Methyladenosine (m(6)A) is emerging as a chemical mark that broadly affects the flow of genetic information in various biological processes in eukaryotes. Recently, Xiao et al. reported that the nuclear m(6)A reader protein YTHDC1 impacts mRNA splicing, providing a transcriptome-wide glance of splicing changes affected by this mRNA methylation reader protein.

Our views of dynamic N6-methyladenosine RNA methylation

We thank Darnell and coworkers in their Divergent Views article for noting our contributions to recent progress in the field of RNA modifications (Darnell et al. 2018). We agree with many of the viewpoints expressed: that a majority of messenger RNAN-methyladenosine (mA) methylation occurs cotranscriptionally, that one of the main functions of mA methylation on mRNA is to mark sets of transcripts for expedited turnover, and that this methylation may not dramatically affect splicing in HeLa cells. However, although the impact of mA methylation on splicing appears to be modest in many cell lines, we suggest caution because mA methylation is enriched in long exons and overrepresented in transcripts with alternative splicing variants (Dominissini et al. 2012). Several recent examples have revealed methylation-dependent changes in splicing: One demonstrated mA-modulated sex determination in Drosophila melanogaster (Haussmann et al. 2016; Lence et al. 2016), another found enhanced SAM synthetase expression mediated by a specific mA site installed by METTL16 (Pendleton et al. 2017), and recent reports uncovered extensive mA-dependent splicing changes mediated by ALKBH5 in male germ lines (Tang et al. 2017), as well as FTO-involved premRNA splicing changes (Bartosovic et al. 2017). The potential effects of RNA methylation on constitutive and alternative splicing in additional physiological contexts need to be further evaluated.

Publisher Correction: Post-transcriptional gene regulation by mRNA modifications

In Figure 5, translation initiation is promoted not by the indicated protein, but by YTHDF1 (see below).

Corrigendum: Structural basis for selective binding of m 6 A RNA by the YTHDC1 YTH domain

Nat. Chem. Biol. 10, 927–929 (2014); published online 21 September 2014; corrected after print 19 August 2015 In the version of this Brief Communication initially published, the email address for corresponding author, Chao Xu, was incorrect. It should be listed as chaor.xu@utoronto.edu. This error has been corrected in the PDF and HTML versions of the article.