<i>N</i> <sup>6</sup> -methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcriptionA 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
FTO mediates LINE1 m <sup>6</sup> A demethylation and chromatin regulation in mESCs and mouse developmentN 6 -methyladenosine (m 6 A) is the most abundant internal modification on mammalian messenger RNA. It is installed by a writer complex and can be reversed by erasers such as the fat mass and obesity-associated protein FTO. Despite extensive research, the primary physiological substrates of FTO in mammalian tissues and development remain elusive. Here, we show that FTO mediates m 6 A demethylation of long-interspersed element-1 (LINE1) RNA in mouse embryonic stem cells (mESCs), regulating LINE1 RNA abundance and the local chromatin state, which in turn modulates the transcription of LINE1-containing genes. FTO-mediated LINE1 RNA m 6 A demethylation also plays regulatory roles in shaping chromatin state and gene expression during mouse oocyte and embryonic development. Our results suggest broad effects of LINE1 RNA m 6 A demethylation by FTO in mammals.
N6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNAZiyang Hao, Tong Wu, Xiaolong Cui et al.|Molecular Cell|2020 Exon architecture controls mRNA m <sup>6</sup> A suppression and gene expressionN 6 -methyladenosine (m 6 A) is the most abundant messenger RNA (mRNA) modification and plays crucial roles in diverse physiological processes. Using a massively parallel assay for m 6 A (MPm 6 A), we discover that m 6 A specificity is globally regulated by suppressors that prevent m 6 A deposition in unmethylated transcriptome regions. We identify exon junction complexes (EJCs) as m 6 A suppressors that protect exon junction–proximal RNA within coding sequences from methylation and regulate mRNA stability through m 6 A suppression. EJC suppression of m 6 A underlies multiple global characteristics of mRNA m 6 A specificity, with the local range of EJC protection sufficient to suppress m 6 A deposition in average-length internal exons but not in long internal and terminal exons. EJC-suppressed methylation sites colocalize with EJC-suppressed splice sites, which suggests that exon architecture broadly determines local mRNA accessibility to regulatory complexes.
Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolutionQing Dai, Lisheng Zhang, Hui‐Lung Sun et al.|Nature Biotechnology|2022 Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq), which uses a bisulfite-mediated reaction to convert pseudouridine stoichiometrically into deletion upon reverse transcription without cytosine deamination. BID-seq enables detection of abundant Ψ sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10-20 ng input RNA. We uncover consensus sequences for Ψ in mammalian mRNA and assign different 'writer' proteins to individual Ψ deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detect the presence of Ψ within stop codons of mammalian mRNA and confirm the role of Ψ in promoting stop codon readthrough in vivo. BID-seq will enable future investigations of the roles of Ψ in diverse biological processes.