Table 1.
Novel translated ORFs identified by ribosome profiling compared to characterized translated ORFs by diverse metrics.
| Table 1 | Characterized noncoding RNAs (snoRNAs, tRNAs, Xist, HOTAIR, etc) | Characterized protein coding sequences | sORFs* identified as translated by ribosome profiling | uORFs* identified as translated by ribosome profiling |
|---|---|---|---|---|
| Association between footprint arrangement and putative start codons7,11,12,* | No general association | Footprint-covered regions usually start precisely at AUG codons, occasionally near-cognate codons | Footprint-covered regions usually start precisely at AUG codons, occasionally near-cognate codons | Footprint-covered regions often start precisely at AUG and near-cognate codons |
| Association between footprint arrangement and putative stop7,* codons | No general association | Footprint-covered regions stop precisely at canonical stop codons | Footprint-covered regions stop precisely at canonical stop codons | Footprint-covered regions stop precisely at canonical stop codons |
| Footprint abundance relative to mRNA abundance7,10,38, | Very low (especially properly-sized footprints) | Low to High, depending on translation efficiency | Low to High, depending on translation efficiency | Low to High, depending on translation efficiency |
| Codon periodicity of footprints7,13,41,90,* | No | Yes | Yes | Often unclear due to generally short length |
| Coding conservation signatures13,38,77,80,98 | No | Often | Sometimes, difficult to assess for very short regions | Unclear, primarily due to short length |
| Identification of protein product by mass spectrometry11,92–97 | No | Often | Sometimes (dependent on length, peptide properties) | Sometimes (dependent on length, peptide properties) |
| Stable physical association of transcript with ribosomes17,39 | Not generally, though may occur in specific cases (eg. tRNAs) | Yes | Yes | Yes |
| Sensitivity of footprints to translation inhibitors39 | No | Yes | Yes | Yes |
| FLOSS (Fragment Length Organization Similarity Score)39,* | High | Low | Low | Low |
| % putative ORF covered by footprints38,* | Low | High | High | Difficult to assess due to frequent uORF overlap |
| Inside/out ratio (local enrichment of footprints within putative ORF)38,* | Low | High | High, Difficult to assess when translated sORFs overlap | Difficult to assess due to frequent uORF overlap |
| Ratio of footprints at putative start codons to footprints at immediately prior codons12,* | Low | High | High | HIgh |
| RRS (Ribosome Release Score)87 | Poor | Good | Sometimes high, but particularly poor in cases of translated sORF overlap | Frequent overlap in uORF translation leads to poor scores, difficult to assess |
| Cellular function determined by genetic or molecular analyses14,82–84 | Sometimes | Sometimes | Rarely, thus far, but important examples exist | Not assayed in many cases, but a subset are regulatory for translation of other ORFs |
| Likelihood based on the above metrics that regions encode functional proteins/peptides | Low | High | High for some, but not for all. Likely to be a heterogenous population with diverse cellular roles. | Unclear. uORF regions predicted to be translated by ribosome profiling likely represent true translation, but resultant peptides may not be stable. |
*
See Glossary, Figure 1c, Figure 2, and Supplementary Figure for class definitions and examples.