Ribosome footprinting reveals potential roles for spliced leader sequences in translation initiation
Bibliographic record
Abstract
Trans-splicing of a spliced leader (SL) to the 5' ends of mRNAs is used to produce mature mRNAs in several phyla of great importance to human health and marine ecosystems. In some organisms, the SL plays a role in translation, but in other organisms, particularly dinoflagellates, the SL function is poorly understood. We hypothesized dinoflagellate SL can potentially serve to provide a good Kozak consensus to a translation initiation site. Here, we have examined ribosome-protected RNA fragments (RPF) that contain a spliced leader in Dinophyceae, Nematoda, and Euglenozoa. We find that SL's with A/G-rich 3' ends (Dinophyceae and Nematoda) can provide Kozak consensus while those with A/G-poor 3' ends (Euglenozoa) are not involved in translation initiation. The SL-containing RPFs also reveal the use of alternative start codons in both dinoflagellates and nematodes. Overall, our results suggest one possible role of SL's, depending on their sequence, is to increase the efficiency of an initiation site.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".