Genome replication perturbs the DNA regulatory environment by displacing DNA-bound proteins, replacing nucleosomes, and introducing dosage imbalance between regions replicating at different S-phase stages. Recently, we showed that these effects are integrated to maintain transcription homeostasis: replicated genes increase in dosage, but their expression remains stable due to replication-dependent epigenetic changes that suppress transcription. Here, we examine whether reduced transcription from replicated DNA results from limited accessibility to regulatory factors by measuring the time-resolved binding of RNA polymerase II (Pol II) and specific transcription factors (TFs) to DNA during S phase in budding yeast. We show that the Pol II binding pattern is largely insensitive to DNA dosage, indicating limited binding to replicated DNA. In contrast, binding of three TFs (Reb1, Abf1, and Rap1) to DNA increases with the increasing DNA dosage. We conclude that the replication-specific chromatin environment remains accessible to regulatory factors but suppresses RNA polymerase recruitment.

基因组复制通过置换与DNA结合的蛋白质，替代核小体并在不同S期阶段复制的区域之间引入剂量失衡，从而扰乱了DNA调控环境。最近，我们证明了这些作用被整合以维持转录稳态：复制的基因剂量增加，但是由于抑制转录的复制依赖性表观遗传变化，它们的表达保持稳定。在这里，我们通过测量出芽酵母中S期的RNA聚合酶II（Pol II）和特定转录因子（TFs）与DNA的时间分辨结合，来检查复制的DNA的转录减少是否是由于对调控因子的有限可达性所致。我们显示，Pol II结合模式对DNA剂量不敏感，表明对复制DNA的结合有限。相反，随着DNA剂量的增加，三个TF（Reb1，Abf1和Rap1）与DNA的结合也会增加。我们得出结论，复制特异性染色质环境仍然可访问调节因素，但抑制RNA聚合酶募集。