Characterization of nucleosome-depleted regions of transcriptionally active chromatin in chicken and human genomes
Bibliographic record
Abstract
The mammalian genome is organized into spatial domains at multiple scales such as compartments, topologically associating domains and chromatin loops. Such folding of the genome is essential to modulate gene expression at the structural and functional level. Histone post-translational modifications (acetylated histones, H3K4me3 and H3K27ac) associated with transcriptionally active chromatin regions are referred to as active histone marks and are often associated with the active compartment (compartment A). Current evidence suggests that protein arginine-N-methyl transferases and their catalyzed histone post-translational modifications, H3R2me2s and H4R3me2a, are also associated with compartment A and are involved in establishing and maintaining the transcriptionally active chromatin state in vertebrate genomes. DNase I sensitivity and dynamic histone acetylation are features of transcribed chromatin. Within the DNase I sensitive region are DNase I hypersensitive sites which are devoid of nucleosomes and mark the presence of regulatory elements (e.g. promoters and enhancers) in the genome. Nucleosomes in the regulatory regions are destabilized by histone post-translational modifications and chromatin remodelling enzymes. Therefore, to understand the organization of transcriptionally active chromatin architecture, it is crucial to characterize the nucleosome-depleted regions of the genome in relation to nucleosome dynamics. For my project, I am investigating the features of nucleosome depleted regions in the chicken and human genomes. I have applied the technique of formaldehyde-assisted isolation of regulatory elements (FAIRE) coupled with next-generation sequencing to map out the position of the regulatory regions in relation to the active marks. FAIRE-sequencing was compared to chromatin immunoprecipitation-sequencing of H3K4me3, H3K27ac, H3R2me2s and H4R3me2a. Based on the sequenced data, FAIRE-sequencing readily identified all of the promoter regions in chicken polychromatic erythrocytes. Further I identified regions that had an atypical chromatin structure in avian and human cells, and in these regions were genes involved in cell identity. Chromatin signatures characterized in active genes, which were involved in different biological processes, were comparable to the chromatin features observed in human genome.
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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 | 0.000 |
| 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) | 0.001 | 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".