How do we know that the high-occupancy footprints correspond to ribosomes that are decoding the stop codon vs. stalled with eRF1 bound?
As in Figure 4, log2 relative occupancy, log2 large footprint abundance, and log2 small footprint abundance in comparisons of three untreated replicates and two 3-AT treated samples.
Of these four, three were previously processed by a de novo footprinting algorithm that searches DHSs for locations with high footprint occupancy scores, and genome coordinates of the footprints were made openly available [ 24].
In a system undergoing less rapid apoptosis, such as those explored at the single cell level (Cohen et al., 2008; Geva-Zatorsky et al., 2010), there may be greater opportunity for proteins to accumulate and reveal relationships between ribosome footprint occupancy and protein production.
Here, we observe a consistent increase in A-site occupancy among the footprints matching the Dnmt2 down-regulated proteins (Figs 6C and EV5C).
Five transcripts have particularly intriguing ribosomal traces, with locations along the transcript having peak occupancy of 10 or more footprints in at least one of the four replicates.
As with overall occupancy, the relative abundances of small footprints and the relative abundance of large footprints were both highly correlated between replicates.
London buses, based on average occupancy of 15 people, have a footprint of 80g of CO2 per kilometer, double the Tube.
In principle, using the ribosome footprint data to establish occupancy as a function of position might seem easy: align the reads to the reference genome to identify the 10 or so codons under each read, and tabulate the frequency of each codon observed in each position.
We can no longer conclude that the variation in small footprints (post-decoding) drives total occupancy, because those correlations are necessarily dependent on the overall ratio of small to large footprints.
Our nucleotide-resolution protein occupancy profiles resolved a precise ORC-dependent footprint at 269 origins in G2.
