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. Author manuscript; available in PMC: 2020 Mar 7.
Published in final edited form as: Mol Cell. 2019 Jan 24;73(5):959–970.e5. doi: 10.1016/j.molcel.2018.12.009

Figure 1. Assigning ribosome functional states to distinct footprint sizes (21 and 28 nt RPFs) from ribosome profiling samples.

Figure 1.

(A) Schematic representation of the eukaryotic elongation cycle. PreAcc: pre-accommodation; PrePT: Pre-peptide bond formation; PreTrans: Pre-translocation. (B and C) Scatter plots showing mutation rates of 25S rRNA (a function of DMS reactivity) comparing CHX-pretreated (B) or ANS-pretreated (C) relative to mock pretreatment. Nucleotides protected by CHX or ANS are color-coded and labeled. (D) Fold change in mutation rates of nucleotides A1755 and A1756 for CHX-pretreatment with in vivo DMS modification (CHX in vivo), ANS-pretreatment with in vivo DMS modification (ANS in vivo), ANS-pretreatment with DMS modification in lysate (ANS lysate), and TIG with DMS modification in lysate (TIG lysate) (n=2, ±SD). (E) Average ribosome occupancies aligned at stop codons using 21 nt RPFs (top), 28 nt RPFs (middle) and both RPFs (bottom) for WT and eRF1-depleted (eRF1d) cells. (F) Scatter plot comparing 64 codon-specific ribosome occupancies (pause scores) for 21 nt RPFs in WT and eRF1d cells.