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 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 | 0.000 |
| 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 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".