Analyzing the Contributions of Chromatin Structure in Nuclear Hormone Receptor Activated Transcription In Vivo
Bibliographic record
Abstract
The mouse mammary tumor virus (MMTV) promoter has been used extensively as a model system to examine the role of chromatin structure on transcriptional regulation from a steroid responsive gene ( Fig. 1 ). Early studies demonstrated that the chromatin structure of the MMTV promoter was altered upon glucocorticoid treatment, such that a discrete region became hypersensitive to DNaseI ( 1 ). This hypersensitive region corresponded to the portion of the MMTV promoter that was shown to function as a hormonal enhancer in vivo ( 1 ). Examination of the MMTV promoter stably maintained in mouse mammary cell lines revealed that the MMTV long terminal repeat (LTR) organized into a phased array of six precisely positioned nucleosomes ( A-F ) ( 2 - 4 ). The proximal promoter, containing the hormone response elements (HREs), and binding sites for nuclear factor 1 (NF1), TATA binding protein (TBP), and octamer transcription factors (OTFs) is encompassed by nucleosomes A and B ( 2 , 5 ). Analysis of glucocorticoid activation of the MMTV promoter demonstrated that the glucocorticoid receptor (GR) initiated a cascade of events that led to chromatin disruption upon GR binding to the HREs. Prior to hormonal stimulation the MMTV promoter chromatin structure excluded NF1, TBP, and OTFs from their binding sites ( 6 - 8 ). Treatment with glucocorticoids resulted in activation of the GR, recruitment of coactivators (CoAs) and chromatin remodeling complexes (CRCs), as well as disruption of nucleosome B, subsequent binding of NF1 and OTF, and assembly of a preinitiation complex ( 9 , 10 ). ( A ) Nucleosomal organization of the m M TV promoter. When the m M TV promoter is stably introduced into cells, it is organized into a phased array of nucleosomes ( A-F ). The hormone inducible hypersensitive region (HSR) is positioned over nucleosome B. An expansion of the region encompassed by nucleosomes A and B indicates the binding sites for important transcription factors as well as their approximate distance from the transcription start site (+1). The binding sites for the steroid receptors, hormone response elements (HREs), nuclear factor 1 (NF1), the octamer transcription factors (OTFs) and the TATA-binding protein (TBP) are illustrated. ( B ) Steroid hormones alter m M TV chromatin structure and transcription factor access. In the absence of hormone, nucleosome B is in a repressed conformation, histone H1 is phosphorylated, and transcription factors are excluded from their binding sites. Hormone treatment activates the steroid receptor, which recruits chromatin remodeling complexes (CRCs), and coactivators (CoAs), and ultimately results in a remodeling of nucleosome B to an active chromatin architecture that permits transcription factor binding and transcriptional activation. These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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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 | 0.001 | 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 | 0.001 |
| 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".