Extended Data Fig. 8: METTL3 depletion leads to an increase in the m⁶A DIP peaks in hPSCs.

METTL3 depletion leads to an increase in the m⁶A DIP peaks in hPSCs. (a) SID-UPLC-MS/MS quantification of m⁶A in the total nucleic acids (left panel), and in ultrafiltrate fractions released upon RNase H treatment of siCTL and siMETTL3 hPSCs (right panel). The data are means of 2 independent experiments. (b) The total numbers of consensus m⁶A peaks in WT and siMETTL3 hiPSCs. (c) Heatmaps showing the distribution of density of indicated reads across peak-containing genomic regions (3 kb around peak center) for S9.6 DRIP in WT and m⁶A DIP in WT and siMETTL3 hPSCs. The colour of each line represents the density of reads for a given peak. The width of the heatmaps is normalized by peak length. (d) Pie chart showing the percentages of transcripts differentially expressed between siCTL and siMETTL3 hPSCs (p < 0.01) and without significant changes in expression amongst genes containing siMETTL3-specific m⁶A peaks. P values were calculated using the Standard ballgown parametric F-test. (e) Pie chart demonstrating the percentages of genes differentially expressed between siCTL and siMETTL3 hPSCs containing siMETTL3-specific m⁶A peaks (diff peaks) and without such peaks (No diff peaks). (f) Average profile of m⁶A peak densities for all genes sorted based on levels of their expression in siMETTL3 hPSCs. The colour gradient represents log₁₀ of mean RPKM per bin. (g) Average profile of m⁶A peak densities for all genes sorted based on the fold change of their expression between siCTL and siMETTL3 hPSCs. The colour gradient represents log₁₀ of mean fold change (FC) per bin.