Atypically large footprints are attributable to a 5′ extension of the mRNA region protected by the ribosome. Mapping of the 5′ and 3′ ends of footprint lengths 25–45 nt relative to the start and stop codons (red dashed lines) from IP libraries of FLAG-UPF1, UPF1-FLAG, and UPF1-FLAG/upf2Δ (+CHX). For each footprint length, footprint count at each nucleotide position relative to the start or stop reference codons were normalized to the total footprint count in the library, and these normalized counts from biological replicates were averaged. Different footprint lengths align at the 3′ ends but diverge at the 5′ ends. L and M fragment size classes are as indicated for each sample. Lines at the bottom of the figure indicate the approximate 5′ and 3′ limits of the L and M fragments over the start and stop reference codons.
