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.

A new layer of transcriptional control: N ⁶ -methyladenosine (m ⁶ A) is the most abundant messenger RNA modification in almost all eukaryotes. Liu et al. now show that m ⁶ A is also cotranscriptionally added onto various chromosome-associated regulatory RNAs (carRNAs) in mammalian cells. Disruption of m ⁶ A modification of these RNAs increases their abundance and promotes gene transcription by increasing the chromatin accessibility. Thus, m ⁶ A serves as a switch to regulate carRNA levels by tuning nearby chromatin state and downstream transcription. Science , this issue p. 580

Dynamic mRNA modification in the form of N⁶-methyladenosine (m⁶A) adds considerable richness and sophistication to gene regulation. The m⁶A mark is asymmetrically distributed along mature mRNAs, with approximately 35% of m⁶A residues located within the coding region (CDS). It has been suggested that methylation in CDS slows down translation elongation. However, neither the decoding feature of endogenous mRNAs nor the physiological significance of CDS m⁶A has been clearly defined. Here, we found that CDS m⁶A leads to ribosome pausing in a codon-specific manner. Unexpectedly, removing CDS m⁶A from these transcripts results in a further decrease of translation. A systemic analysis of RNA structural datasets revealed that CDS m⁶A positively regulates translation by resolving mRNA secondary structures. We further demonstrate that the elongation-promoting effect of CDS methylation requires the RNA helicase-containing m⁶A reader YTHDC2. Our findings established the physiological significance of CDS methylation and uncovered non-overlapping function of m⁶A reader proteins.

N⁶-methyladenosine (m⁶A) on chromosome-associated regulatory RNAs (carRNAs), including repeat RNAs, plays important roles in tuning the chromatin state and transcription, but the intrinsic mechanism remains unclear. Here, we report that YTHDC1 plays indispensable roles in the self-renewal and differentiation potency of mouse embryonic stem cells (ESCs), which highly depends on the m⁶A-binding ability. Ythdc1 is required for sufficient rRNA synthesis and repression of the 2-cell (2C) transcriptional program in ESCs, which recapitulates the transcriptome regulation by the LINE1 scaffold. Detailed analyses revealed that YTHDC1 recognizes m⁶A on LINE1 RNAs in the nucleus and regulates the formation of the LINE1-NCL partnership and the chromatin recruitment of KAP1. Moreover, the establishment of H3K9me3 on 2C-related retrotransposons is interrupted in Ythdc1-depleted ESCs and inner cell mass (ICM) cells, which consequently increases the transcriptional activities. Our study reveals a role of m⁶A in regulating the RNA scaffold, providing a new model for the RNA-chromatin cross-talk.