Transcription Factor Binding to Replicated DNA

Abstract

Summary: 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. : During genome replication, mRNA synthesis from replicated genes is inhibited. Bar-Ziv et al. find that transcription factors (TFs) are recruited to replicated promoters but RNA polymerase II (Pol II) binding is buffered. Their work suggests that the unique chromatin environment during DNA replication limits the ability of TFs to recruit Pol II. Keywords: transcription, replication, chromatin, DNA, transcription factor, RNA polymerase