Divergent effects of eRF3 and Upf1 on the expression of uORF carrying mRNAs and ribosome protein genes

In addition to its role in translation termination, eRF3 has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with Upf1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbor upstream open reading frames in their 5' leader sequence and long 3' UTR. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3 or Upf1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3 and Upf1 and to compare the effect of each of these factors on gene expression. We show that eRF3 and Upf1 have very different impact on the human transcriptome, only ~250 transcripts being targeted by both factors. We also show that in contrast to Upf1, eRF3a depletion globally derepressed the expression of mRNAs containing translated uORFs. Finally, we find that eRF3a and Upf1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation. Overall design: Examination of the translational consequences of the inactivation of the eRF3 and Upf1 in HCT-116