To study the function of Rli1/ABCE1 in vivo, we used ribosome profiling and 
biochemistry to characterize its contribution to ribosome recycling. When Rli1 
levels were diminished, 80S ribosomes accumulated both at stop codons and in the 
adjoining 3'UTRs of most mRNAs. Frequently, these ribosomes reinitiated 
translation without the need for a canonical start codon, as small peptide 
products predicted by 3'UTR ribosome occupancy in all three reading frames were 
confirmed by western analysis and mass spectrometry. Eliminating the 
ribosome-rescue factor Dom34 dramatically increased 3'UTR ribosome occupancy in 
Rli1 depleted cells, indicating that Dom34 clears the bulk of unrecycled 
ribosomes. Thus, Rli1 is crucial for ribosome recycling in vivo and controls 
ribosome homeostasis. 3'UTR translation occurs in wild-type cells as well, and 
observations of elevated 3'UTR ribosomes during stress suggest that modulating 
recycling and reinitiation is involved in responding to environmental changes.