Mammalian UPF3A and UPF3B activate NMD independently of their EJC binding

Nonsense-mediated mRNA decay (NMD) can occur independently of some NMD factors such as UPF3B. We have performed total RNA-Seq in HCT116 cells under NMD factor knockout (with CRISPR-Cas9) and/or knockdown (with siRNA transfection) conditions to identify mRNA substrates regulated by different NMD factors. We have also performed RIPiT-Seq to identify the footprints of three compositionally distinct EJCs that contain the following pairs of proteins: MAGOH-EIF4A3, UPF3B-EIF4A3 or CASC3-EIF4A3 in WT HCT116 cells. Total RNA-Seq were performed in three different batches. Controls from the same batch are used for downstream analysis. For total RNA-Seq, three replicates of each condition are used and for RIPiT-Seq experiments, four replicates of each RIPiT are used.