RNA stability profiling in SETD2 and METTL14 knockdown HepG2 cells

To evaluate the effect of SETD2 and METTL14 on mRNA stability, we conducted RNA-seq in SETD2 or METTL14 knockdown HepG2 cells as well as control cells with or without actinomycin D treatment. Our RNA stability profiling revealed that depletion of SETD2 and METTL14 resulted in global reduction of RNA stability, and the changes were correlated between SETD2 and METTL14 knockdown cells. Overall design: HepG2 cells were infected with lentiviral shRNAs against SETD2, METTL14 and non-specific control (shCtrl), and selected by puromycin to generate stable knockdown lines. We treated HepG2 cells with actinomycin D to inhibit transcription and collected cells at indicated time points (i.e., 0h, 1h, 3h, 6h). The total RNA was extracted by miRNeasy Kit (Qiagen) and sequenced by Illumina. For RNA stability profiling, RNA half-life was calculated by comparing the gene expression at 1, 3, 6 hours with actinomycin treatment to that in un-treated samples, with two biological replicates for each group.