Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

Genome Res. 2013 Oct;23(10):1636-50. doi: 10.1101/gr.157354.113. Epub 2013 Jun 13.


UPF1 is a DNA/RNA helicase with essential roles in nonsense-mediated mRNA decay (NMD) and embryonic development. How UPF1 regulates target abundance and the relationship between NMD and embryogenesis are not well understood. To explore how NMD shapes the embryonic transcriptome, we integrated genome-wide analyses of UPF1 binding locations, NMD-regulated gene expression, and translation in murine embryonic stem cells (mESCs). We identified over 200 direct UPF1 binding targets using crosslinking/immunoprecipitation-sequencing (CLIP-seq) and revealed a repression pathway that involves 3' UTR binding by UPF1 and translation but is independent of canonical targeting features involving 3' UTR length and stop codon placement. Interestingly, NMD targeting of this set of mRNAs occurs in other mouse tissues and is conserved in human. We also show, using ribosome footprint profiling, that actively translated upstream open reading frames (uORFs) are enriched in transcription factor mRNAs and predict mRNA repression by NMD, while poorly translated mRNAs escape repression. Together, our results identify novel NMD determinants and targets and provide context for understanding the impact of UPF1 and NMD on the mESC transcriptome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 3' Untranslated Regions*
  • Animals
  • Binding Sites / genetics
  • Codon, Terminator
  • Embryonic Stem Cells / metabolism*
  • Evolution, Molecular
  • Gene Expression Regulation*
  • Humans
  • Mice
  • Mice, Inbred C57BL
  • Nonsense Mediated mRNA Decay*
  • Open Reading Frames
  • Protein Biosynthesis
  • RNA Helicases
  • RNA, Messenger / metabolism*
  • Sequence Analysis, RNA
  • Trans-Activators / genetics
  • Trans-Activators / metabolism*
  • Transcription Factors / metabolism
  • Transcriptome*


  • 3' Untranslated Regions
  • Codon, Terminator
  • RNA, Messenger
  • Rent1 protein, mouse
  • Trans-Activators
  • Transcription Factors
  • RNA Helicases
  • UPF1 protein, human

Associated data

  • GEO/GSE41785