The structural insight into the biological role of PHD fingers
Bibliographic record
Abstract
Covalent modifications of histone tails and protein domains that bind these epigenetic marks are essential components of the chromatin remodeling and gene expression machinery. The PHD (plant homeodomain) finger is found in many transcriptional regulators and chromatin‐associating complexes, however the overall biological role of this module remains unclear. Recently, it was found that a subset of PHD fingers recognizes histone H3 tri‐methylated at lysine 4 (H3K4me3). In this study, we characterize the binding specificity of the PHD finger family using a set of biochemical, crystallographic and spectroscopic approaches. We compare the crystal structures of the H3K4me3‐bound PHD fingers, identify the binding sites for methylated histone H3 tails by resonance perturbation analysis and mutagenesis, and measure the binding affinities by tryptophan fluorescence. Our results provide novel insight into the molecular mechanisms underlying the activity of the histone‐binding PHD fingers, and further our understanding on how the histone code is read.
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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 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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".