Extended Data Figure 3. Characterization of m⁶A modification and gene expression change in the early embryonic transcriptome of zebrafish.

a, Venn diagrams show the overlap of two replicates of m⁶A-modified transcripts determined by m⁶A-seq and m⁶A-CLIP-seq at five time points. b, Distribution of m⁶A-sites (number of m⁶A-seq peaks) in the six gene groups over time. c, Number of m⁶A-modified genes identified in both m⁶A-seq and m⁶A-CLIP-seq at five time points. d, Quantification of the m⁶A/(G+A+C+U) ratio of mRNAs purified from zebrafish embryos at various developmental time points by LC-MS/MS. The fluctuation observed may reflect the complex dynamics of the decay of the methylated maternal transcripts, the transcription and methylation of newly synthesized zygotic mRNAs, and their subsequent decay during early development. All time points were normalized to 0 h.p.f. value. Error bars, mean ±s.d., n = 3 (technical replicates). e, Consensus motif identified by HOMER with m⁶A-CLIP peaks at five time points. f, Metagene profiles depict the subtranscript distribution pattern of m⁶A-sites (from m⁶A-seq) within the zebrafish transcriptome. m⁶A-seq peak signals are enriched after the start codon and before the stop codon. g–h, Gene Ontology (GO) analysis of non-methylated maternal transcripts (g) and methylated ones (h). i, Table showing the number of genes downregulated and upregulated in maternal ythdf2^−/− mutants at 4 h.p.f. within the 6 gene expression clusters (top 20%).