Kinetics of chromatin activation and active DNA demethylation in vertebrate cells: Histone acetylation sets the stage for demethylase interactions with DNA resulting in demethylation
Bibliographic record
Abstract
4168 Department of Pharmacology and Therapeutics, McGill University, Montreal Canada. The epigenome programs gene expression profiles of vertebrate cells. Disruption of epigenomic programming is widespread in cancer. The epigenome consists of the chromatin and its modifications such as histone acetylation and histone methylation and a pattern of DNA methylation at the CpG dinucleotide sequence. It was shown that methylated DNA directs the formation of inactive chromatin by recruiting methylated DNA binding proteins, which in turn target histone deacetylase and histone methyltransferase containing complexes to the methylated gene. An alternative hypothesis is that the DNA methylation pattern is a dynamic equilibrium of methylation and demethylation reactions and that the direction of the reaction is determined by chromatin structure. We have previously developed a transient transfection replication-independent active demethylation assay in living HEK 293 cells and showed that either pharmacological induction of histone acetylation by the HDAC inhibitor trichostatin A or a strong promoter triggers active demethylation of the in vitro methylated reporter GFP gene. To test the hypothesis that histone acetylation sets the stage for demethylation by gating the accessibility to demethylase we delineated the time course of epigenomic events leading to active demethylation of DNA and transcription of GFP following TSA treatment using ChIP assays with the pertinent epigenomic status antibodies. We show that histone acetylation occurs rapidly and precedes DNA demethylation. The interaction of pol II with the promoter occurs concomitantly with DNA demethylation and is followed by transcription. Our hypothesis is that demethylation is required for pol II interaction with the promoter. Bisulfite mapping of the state of methylation of CMV promoter bound to pol II is underway to test this hypothesis. Interaction of MBD2/demethylase with the CMV promoter occurs after histone acetylation peaks, which is consistent with the hypothesis that histone acetylation state gates the access of MBD2/demethylase with the CMV promoter. Using antisense and siRNA knock-down of MBD2 we show that MBD2/demethylase interaction with the CMV promoter is responsible for GFP demethylation. To determine whether the same mechanism is responsible for active demethylation of endogenous genes we performed an expression micro-array analysis on TSA treated HEK 293 cells to identify endogenous genes that are demethylated by induction of histone acetylation. This study was supported by the National Cancer Institute of Canada.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".