The Silencing Face of DNA Replication: Gene Repression Mediated by DNA Replication Factors
Bibliographic record
Abstract
DNA replication in eukaryotes initiates at multiple origins. The activation of these origins is a critically important event in the life of each cell and is tightly regulated by numerous highly conserved trans-factors. Saccharomyces cerevisiae origins (called Autonomously Replicating Sequences, ARSs) contain a core A element called ACS (ARS Consensus Sequence), plus an array of auxiliary B elements. Most ARSs fire at their chromosomal positions, but there are numerous dormant ARSs as well. Instead of being origins, these dormant ARSs serve as silencer elements, which function in the epigenetic repression of nearby genes. Even more, many DNA replication trans-factors have also been reported to affect gene silencing. This puzzling functional duality of ARS and DNA replication factors has attracted significant interest. Evidence from other species has suggested that the overlap between gene silencing and DNA replication operates in other eukaryotes. In this chapter we will review in detail the activity of ARSs as origins of replication and as silencers. We will focus on sequence dissimilarities between silencer and origin ARSs and will propose a model for the functional duality of DNA replication factors.
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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 | 0.000 | 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 | 0.001 | 0.000 |
| Research integrity | 0.001 | 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 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".