Genome-wide identification of endogenous NMD-targeted RNAs in human stem cells [UPF2_NPCs]

Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that influences several biological processes. Specific features in messenger RNAs (mRNAs) have been found to trigger decay by NMD, leading to the assumption that NMD sensitivity is an intrinsic quality of a given transcript. Here, we provide evidence that, instead, an overriding factor dictating NMD sensitivity is the cell environment. Using several genome-wide techniques to detect NMD-target mRNAs, we find that hundreds of mRNAs are sensitized to NMD as human embryonic stem cells progress to form neural progenitor cells. Another class of mRNAs escape from NMD during this developmental progression. We show that the differential sensitivity to NMD extends to in vivo scenarios, and that the RNA-binding protein, HNRNPL, has a role in cell type-specific NMD. We also addressed another issue in the field-whether NMD factors are core or branch-specific in their action. Surprisingly, we found that UPF3B, an NMD factor critical for the nervous system, shares only 30% of NMD-target transcripts with the core NMD factor UPF2. Together, our findings have implications for how NMD is defined and measured, how NMD acts in different biological contexts, and how different NMD branches influence human diseases. To identify UPF2-target RNAs in NPCs, we performed bulk RNA sequencing (RNAseq) analysis of NPCs differentiated from hESCs from four groups: UPF2fl/fl-scramble siRNA (“Ctrl”), UPF2fl/fl-siUPF2 (“UPF2-KD”), UPF2-iKO-scramble siRNA (“UPF2-iKO”), and UPF2-iKO-siUPF2 (“UPF2-iKO & KD”).