Extended Data Fig. 5: Capturing Mettl3-dependent changes in RNA stability in paused ESCs.
From: m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency
a. Strategy for RNA stability analysis based on intronic and exonic reads. b-c. Examples of genes with different (Slc16a1, Six4) and similar (Mtor, Gapdh) intronic and exonic mRNA fold-changes between Mettl3−/− and Mettl3+/+ ESCs based on RNA-seq data (b) and validation of stability changes by actinomycin D stability assay (c). N = 3 biological replicates, t1/2: half-life. d. Linear regression of log2 total conversion counts (relative to time 0 h), as measured by SLAM-seq, showing an increase in transcriptome stability in paused Mettl3−/− ESCs. e. Changes in RNA expression in paused Mettl3−/− ESCs based on RNA-seq data (fold-change > 1.5) are associated with changes in RNA half-life in paused Mettl3−/− ESCs. Data are mean ± SD (b) or mean ± SEM (c). P-values (as indicated on figure) by two-tailed paired Student’s t-tests (b), linear regression test with interaction (c) and one-way ANOVA (e). Boxes in the box plots define the interquartile range (IQR) split by the median, with whiskers extending to the most extreme values within 1.5 × IQR beyond the box.
