However, if site-specific footprint length variations occur in eukaryotes on specific sequences, it would affect ribosome profiles of individual mRNAs.
Instead, we now include much stronger evidence that both small and large footprints show variation between codons that is very consistent between replicates, and that these two values (abundance of large and small footprints per codon) are independent of each other.
Nevertheless, much past and recent work has focused on domestic national averages, neglecting both the growing importance of international trade on household carbon footprint and the variation between households of different income levels and demographics.
This is likely to be the footprint of allelic variation at this position.
As ribosome pausing typically increases the likelihood of capturing a footprint by sequencing, variations in codon-specific ribosome occupancy can be used to infer changes in translation rates (Ingolia et al., 2011; Li et al., 2012; Stadler and Fire, 2011).
DOI: http://dx.doi.org/10.7554/eLife.01257.011 Codon-specific differences in ribosome occupancy could have been driven by variation in small footprint counts, variation in large footprint counts, or both, potentially revealing the variability of each stage of elongation.
Calculation from Eq. 1 provides the variations of footprint areas for the flat-footed and the high-arched groups respectively while walking: 0.147±0.041, 0.084±0.034 (p<0.084±0.034
The RRT analysis of E. coli footprints also showed interesting variation at positions 2, 3, and 4, which we will consider elsewhere.> Lareau et al. (2014) starved Saccharomyces cerevisiae for histidine using the His3 inhibitor 3-aminotriazole.
As more germplasm resequencing data become available, meaningful comparative analysis of upstream regulatory sequence variation by phylogenetic footprinting must be pursued towards the discovery of novel alleles and associated networks with potential applications in rice breeding.
Nonetheless, although the overall ratio of small to large footprints varied, the codon-specific variation in this ratio was robust.
