Investigating the interplay between the Tup1-Cyc8 and Swi-Snf chromatin remodelling complexes in Saccharomyces cerevisiae
Bibliographic record
Abstract
Swi-Snf is an ATP dependent chromatin remodelling complex which acts as a coactivator of gene transcription by its ability to open up densely packed chromatin by removal of nucleosomes.Conversely, Tup1-Cyc8 is a co-repressor complex that has the ability to position nucleosomes at the promotors of genes, forming a more closed chromatin state which is repressive towards transcription.The antagonistic activity of these two complexes has recently been shown to regulate 102 genes by RNA-Seq analysis.In this study I have validated the subset of genes suggested to be under the coregulation of Swi-Snf and Tup1-Cyc8 using gene-specific RT-qPCR and ChIP analysis.Using ChIP analysis of Snf2 and Tup1 proteins at gene promotors, examples of some of the co-regulated genes were shown to be under the direct control of Swi-Snf and Tup1-Cyc8.The data also revealed that at these co-regulated genes Tup1 occupancy was dependent on Snf2.Furthermore, Tup1 can persist at co-regulated genes in the absence of Cyc8 and that this retention of Tup1 is Snf2 dependent.Finally, the data revealed that there may be two models of co-regulation.In model one, Tup-Cyc8 occupies the promotor of target genes to bring about repression.In the absence of Tup1-Cyc8, Swi-Snf is recruited resulting in gene activation.In model two, Swi-Snf and Tup1-Cyc8 both occupy the promotors of target genes with Swi-Snf becoming further enriched upon target gene activation in the absence of Tup1-Cyc8.Moreover, preliminary data might suggest that the two complexes interact with one another via the Swi3 and Cyc8 proteins.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.005 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.000 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".