Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression
Bibliographic record
Abstract
Abstract What genes and regulatory sequences make humans and apes that share substantial genes but show distinct phenotypes has puzzled researchers for decades. Genomic studies have examined species-specific genes and regulatory sequences (e.g., transcription factor binding sites, TFBS); birth, loss, and changes in these genes and sequences can greatly drive speciation and evolution. However, those involved in epigenetic regulation - species-specific lncRNA genes and regulatory sequences - remain poorly explored. We identified human-specific (HS) lncRNAs from GENCODE-annotated human lncRNAs, predicted their DNA binding domains (DBDs) and binding sites (DBSs) genome-wide, analyzed DBSs in modern humans (CEU, CHB, and YRI), archaic humans (Altai Neanderthals, Denisovans, and Vindija Neanderthals), and their counterparts in chimpanzees, and analyzed how DBSs influence gene expression in modern and archaic humans. Our results suggest that HS lncRNAs and their DBSs have substantially rewired gene expression human-specifically, the rewiring has evolved continuously from archaic to modern humans, and rewired gene expression has promoted brain development, made humans adapt to new environments and lifestyles, and caused differences in modern humans.
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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 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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 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".