Mapping Chromatin Composition of Transcription Factor Binding Sites in HEK293 Cells Using Histone Modifications
Bibliographic record
Abstract
Histone modifications play key roles in regulating gene expression and shaping chromatin structure. The interplay between histone modifications, transcription factor specificity, and DNA sequence remains poorly understood. I examined the distribution and enrichment patterns of several histone marks at promoters, TF binding sites, and transposable elements. Active marks were enriched at promoter regions, while repressive marks were primarily seen in heterochromatin regions. Histone marks analysis over 137 transcription factor binding sites showed two major enrichment patterns for CpG-binding and KRAB-ZNF proteins. TFBS analysis revealed that CpG-binding TFs showed a clear depletion of active histone marks precisely at the TFBSs. Younger KRAB ZNFs were heavily enriched at younger retrotransposons, while older KRABs had low enrichment over older retrotransposons. This project provides a detailed histone modification dataset for the HEK293 cell line, offering novel insights into histone modification dynamics, TF-histone mark relationships, and the evolutionary interplay between histones, TFs and repeat elements.
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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 | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
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".