Replication‐dependent repression of SV40 early transcription occurs by placement of a nucleosome over early regulatory elements

Abstract

We have previously shown that during the Simian Virus 40 (SV40) life‐cycle, DNA replication serves as an epigenetic switch by introducing H3K9me1 into newly replicated SV40 minichromosomes in order to repress early transcription in these newly‐replicated minichromosomes. While these studies demonstrated that epigenetics played a critical role in regulation of SV40 transcription, they did not directly address the exact mechanism of how the introduction of H3K9me1 repressed early transcription. We have now analyzed the location of nucleosomes in SV40 wild‐type 776 and the repression‐defective mutant cs1085 using a ChIP‐Seq like approach and confirmed that there is a significant increase in minichromosomes lacking a nucleosome over the early regulatory region in the cs1085 repression‐defective mutant minchromosomes compared to the wild‐type minichromosomes. In addition, we have shown that nucleosomes containing H3K9me1 are preferentially found within the early regulatory region in the wild‐type minichromosomes. These results suggest replication‐dependent repression of early transcription occurs by a mechanism in which nucleosomes specifically containing H3K9me1 are targeted to locations within the early regulatory region including the binding site of TBP and RNA Polymerase II. These specifically located nucleosomes would serve as a physical barrier to prevent the binding of the factors necessary for initiation of early transcription.