Figure 2.

Examples of some known and potential artifacts associated with ribosome profiling. (A) Antibiotic pretreatments may cause increased initiation on upstream translation initiation sites (TISs) because arrested elongating ribosomes prevent scanning. (B) Antibiotics may not block elongation completely (on NNN codon in the A-site) but allow slow elongation (until preferred XYZ codon is in the A-site), which affects the estimation of local decoding rates. (C) Ribosome protected fragments shorter than 26 and longer than 34 nt may be excluded upon size selection. In contrast, mRNA protected by RNA binding proteins may be selected as RPFs.