Dynamic regulation of histone H3K9 is linked to the switch between replication and transcription at the Dbf4 origin-promoter locus

Abstract

The co-regulation of DNA replication and gene transcription is still poorly understood. To gain a better understanding of this important control mechanism, we examined the DNA replication and transcription using the Dbf4 origin-promoter and Dbf4 pseudogene models. We found that origin firing and Dbf4 transcription activity were inversely regulated in a cell cycle-dependent manner. We also found that proteins critical for the regulation of replication (ORC, MCM), transcription (SP1, TFIIB), and cohesin (Smc1, Smc3) and Mediator functions (Med1, Med12) interact with specific sites within and the surrounding regions of the Dbf4 locus in a cell cycle-dependent manner. As expected, replication initiation occurred within a nucleosome-depleted region, and nucleosomes flanked the 2 replication initiation zones. Further, the histone H3 in this region was distinctly acetylated or trimethylated on lysine 9 in a cell cycledependent fluctuation pattern: H3K9ac was most prevalent when the Dbf4 transcription level was highest whereas the H3K9me3 level was greatest during and just after replication. The KDM4A histone demethylase, which is responsible for the H3K9me3 modification, was enriched at the Dbf4 origin in a manner coinciding with H3K9me3. Finally, HP1g, a protein known to interact with H3K9me3 in the heterochromatin was also found enriched at the origin during DNA replication, indicating that H3K9me3 may be required for the regulation of replication at both heterochromatin and euchromatin regions. Taken together, our data show that mammalian cells employ an extremely sophisticated and multilayered co-regulation mechanism for replication and transcription in a highly coordinated manner.

Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3 and SIRT1

“…If such a mechanism also exists in mammals, an appealing hypothesis is that HDAC3 is responsible for erasing this replication-associated acetylation. Indeed, HDAC3 was shown to be associated with DNA replication in mammalian cells (Kylie, Romero et al, 2016) and HDAC3 null mouse cells show replication defects and DNA damage (Bhaskara, Chyla et al, 2008). Further analysis of HDAC2 and HDAC3 localization during mitosis is needed to support this hypothesis.…”

Accurate Identification of DNA Replication Origin by Fusing Epigenomics and Chromatin Interaction Information

“…To explore the conservative pattern of epigenome preference for DNA replication initiation, the ChIP-seq peaks of histone modification and transcription factors in K562 cell line from the ENCODE database were mapped to corresponding ORI regions. Previous research has shown that H3K9me3 has the highest level during and just after replication in HeLa S3 cells, in which H3K9me3 may be required for the regulation of replication at both heterochromatin and euchromatin regions [ 60 ]. However, we found that H3K9me3 is not significantly distributed in the ORI regions from IGV map ( Figure 2(a) ) and colocalization frequencies ( Figure 2(b) ).…”