Fig. 4: METTL3 regulates gene expression in hTSCs in both m⁶A-dependent and m⁶A-independent manners.

a RNA m⁶A modification distribution profiles in P0 hTSCs along the 5’UTR, CDS, 3’UTR, and non-coding regions. b Volcano plot showing differentially methylated mRNAs comparing P2 to P0 hTSCs. Blue and red points represent significantly hypo- and hyper-methylated transcripts, respectively. Wald test of Poisson GLM with p_cutoff =1E-10 was performed. c Distribution of peaks with decreased m⁶A modification in P2 versus P0 hTSCs along the 5’UTR, CDS, and 3’UTR regions. These peaks were mapped to the known consensus m⁶A motif. Motif enrichment p value was from hypergeometric test. d Scatter plot showing differential analysis combining RNA-seq and MeRIP-seq results comparing P2 to P0 hTSCs. Red dots represent transcripts with m⁶A modification, and gray dots represent transcripts without m⁶A modification. e IGV tracks showing MeRIP-seq results of trophoblast master regulator genes GATA2 and TFAP2C, and key imprinting genes PEG3 and PEG10 relative to the input in P0 and P2 hTSCs. f Scatter plot showing differential analysis combining RNA-seq and MeRIP-seq results comparing P2 to P0 hTSCs within three indicated gene sets. Red dots represent transcripts with m⁶A modification, and gray dots represent transcripts without m⁶A modification. g Bar chart showing the number of transcripts with and without m⁶A modification within three gene sets. h IGV tracks showing MeRIP-seq results of STB marker genes ERVW-1 and CGA, SASP gene GDF15, and inflammation-related gene IL4R relative to the input in P0 and P2 hTSCs.