Extended Data Figure 5. Overlap between methylated genes and upregulated genes in maternal ythdf2^−/− embryos.

a, Quantification of the m⁶A/A ratio of the total mRNA purified from maternal ythdf2^−/− and wild-type embryos by LC-MS/MS. P values were determined using two-sided Student’s t-test for paired samples. Error bars, mean ± s.d. of two technical replicates (data points with same colour) from two biological experiments. b, Composition of upregulated, methylated genes in maternal ythdf2^−/− samples at 4 h.p.f. A total of 3,292 genes are both methylated and upregulated upon ythdf2 LOF, over 60% of which are maternal genes. c, Venn diagram depicts the overlapping of m⁶A-modified transcripts determined by m⁶A-seq, m⁶A-CLIP-seq, and differentially expressed transcripts between ythdf2 LOF samples and controls at 4 h.p.f. The 135 intersected genes were defined as the most stringent Ythdf2 RNA targets. Without including the MO-treated result (but with ythdf2^−/− result), we can estimate about 383 Ythdf2 target mRNAs. d, GO analysis of the most stringent Ythdf2 target genes.