Repressor elements provide insights into tissue development and phenotypes in pigs
Bibliographic record
Abstract
Repressor elements play important roles in economic phenotypes of the pig, however, these elements remain poorly characterized. Here, we used H3K27me3, ATAC-seq and RNA-seq data derived from six tissues from three embryonic layers to identify 2 034 super repressor elements (SREs) and 22 223 typical repressor elements (TREs) in the pig genome. Among the identified repressor elements, many are shared by mesodermal and ectodermal tissues. SREs tightly regulate their target genes (within a specific genomic region, SREs act on a small number of target genes with strong effects) while the regulation by TREs is looser (TREs act on a wider range of target genes with weaker effects). Furthermore, in neuronal tissues, repressor element regulated genes start to be repressed during the stage of differentiation of stem cells to progenitor cells. Many regulatory elements were found to cooperate with each other (and have additive effects) to regulate the expression of KLF4. This study provides the first comprehensive pig repressor element map and should be a crucial reference for future studies on REs.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| 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 | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".