Fig. 2

Increased P-body formation accounts for the global RNA stabilization after YTHDF1-3 triple knockdown. a Boxplots showing changes in RNA abundance after single knockdown or triple knockdown of YTHDFs in HeLa cells. Gray boxes, non-targets (NT) in each analysis (for siDF1, non-DF1 bound transcripts; for siDF2, non-DF2 bound transcripts; for siDF3, non-DF3 bound transcripts; for siDF1-3, non-methylated transcripts). Colored boxes, YTHDF1 targets (brown), YTHDF2 targets (red), YTHDF3 targets (blue), and m⁶A modified transcripts (purple). b Fluorescence microscopy analysis of P-body numbers after single knockdown or triple knockdown of YTHDFs in HeLa cells. Numbers of DCP1A foci per cell were quantified with CellProfiler 3.0. Number of cells analyzed: siCtrl (32), siMETTL3 (49), siDF1 (57), siDF2 (56), siDF3 (46), siDF1/2/3 (41). c Boxplots showing changes in RNA abundance after triple knockdown of YTHDFs, grouped by both m⁶A modification status and P-body enrichment (depleted: “Depl”, enriched: “Enr”).Red boxes denote m⁶A methylated transcripts and gray boxes denote unmethylated transcripts. d Scatter plots showing enrichment of m⁶A-modified transcripts in the P-body enriched pool. Top: EDC3 dataset, bottom: EDC4 dataset. Red dots denote m⁶A methylated transcripts and gray dots denote unmethylated transcripts. e Boxplots showing changes in RNA abundance after DDX6 knockdown in control (left) or YTHDF1-3 (right) knockdown HeLa cells grouped by both m⁶A modification status and P-body enrichment in WT cells (depleted: “Depl”, enriched: “Enr”). Red boxes denote m⁶A methylated transcripts and gray boxes denote unmethylated transcripts. f Boxplots showing changes in RNA abundance after DDX6 overexpression in control (left) or YTHDF1-3 (right) knockdown HeLa cells grouped by both m⁶A modification status and P-body enrichment in WT cells (depleted: “Depl”, enriched: “Enr”). Red boxes denote m⁶A methylated transcripts and gray boxes denote unmethylated transcripts. For boxplots, the center line represents the median, the box limits show the upper and lower quartiles, and whiskers represent 1.5 × interquartile range. P values were determined by a Mann-Whitney-Wilcoxon test