Author response: Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway

Abstract

The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing long 3'UTRs to perform dual roles in mRNA quality control and gene expression regulation. However, expansion of vertebrate 3'UTR functions has required a physical expansion of 3'UTR lengths, complicating the process of detecting nonsense mutations. We show that the polypyrimidine tract binding protein 1 (PTBP1) shields specific retroviral and cellular transcripts from NMD. When bound near a stop codon, PTBP1 blocks the NMD protein UPF1 from binding 3'UTRs. PTBP1 can thus mark specific stop codons as genuine, preserving both the ability of NMD to accurately detect aberrant mRNAs and the capacity of long 3'UTRs to regulate gene expression. Illustrating the wide scope of this mechanism, we use RNA-seq and transcriptome-wide analysis of PTBP1 binding sites to show that many human mRNAs are protected by PTBP1 and that PTBP1 enrichment near stop codons correlates with 3'UTR length and resistance to NMD.

An alternative UPF1 isoform drives conditional remodeling of nonsense‐mediated mRNA decay

“…If UPF1 LL can more efficiently associate with mRNAs normally shielded from NMD by the protective RBPs, then we would expect a correlation between the transcripts affected by protective protein depletion and those enriched for UPF1 LL binding. Indeed, mRNAs preferentially recovered by CLIP‐UPF1 LL were significantly down‐regulated in response to PTBP1 depletion in HEK‐293 cells from our previous work (Ge et al , 2016; Data ref: Ge et al , 2016), a result expected for NMD substrates normally shielded by the protective RBP (Appendix Fig S2D). We observed a similar downregulation of mRNAs enriched for CLIP‐UPF1 LL binding in a publicly available RNA‐seq dataset of mouse neuronal progenitor cells depleted of PTBP1 and its brain‐specific paralogue PTBP2 (Appendix Fig S2E; Linares et al , 2015; Data ref: Linares et al , 2015).…”