Fig. 2

Disome-seq detects the translational pauses missed in monosome-seq. a The schematic of disome-seq for yeast cells cultivated in the rich medium. b The length distribution of disome footprints obtained from yeast cells cultivated in the rich medium. Similar to Fig. 1d. c Widespread ribosome collisions were detected in the yeast genome. Numbers of translated genes (genes with at least one monosome footprint) with and without disome footprints are shown in orange and gray, respectively. Footprints in two biological replicates were combined. 589,461 monosome footprints were used to define translated genes, and the disome-seq footprints were down-sampled to 18,082 footprints in order to match the population ratio between monosomes and disomes (32.6:1). d More frequent ribosome collision was observed in the gene with higher monosome density. e The translational pauses detected from monosome footprints (blue) and disome footprints (orange) rarely overlapped. Only the codon site with the footprint abundance greater than the mean of the corresponding gene was considered as a translational pause. If the A-site of a monosome footprint overlaps the A-site of the leading ribosome of a disome footprint, the translational pause is considered as “shared.” The disome-seq reads were down-sampled as in Fig. 2c. f Two genes exemplify the unique information of translational pauses obtained by disome-seq. The A-site of a monosome footprint (blue) or that of the leading ribosome of a disome footprint (orange) is shown along the coding sequence (CDS) of CYC8 and TEF4. g The schematic of estimating the distance (d) to the closest human pause for a yeast pause. h The distribution of d between yeast and humans. The P value was given by the permutation test