Mechanics of DNA Replication and Transcription Guide the Asymmetric Distribution of RNAPol2 and New Nucleosomes on Replicated Daughter Genomes

Replication of the eukaryotic genome occurs in the context of chromatin. Chromatin is commonly thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture occurring during genomic replication. In order to better understand the transmission of gene expression states from one cell generation to the next we have developed a method for following chromatin structure dynamics during replication: ChIP NChAP (Chromatin Immuno-Precipitation and Nascent Chromatin Avidin Pulldown), which we used to monitor RNApol2 and new nucleosome binding to newly-replicated daughter genomes in S. Cerevisiae. The strand specificity of our libraries allowed us to uncover the inherently asymmetric distribution of RNApol2 and H3K56ac-a mark of new histones- on daughter chromatids after replication. Our results show a range of distributions on thousands of genes from symmetric to asymmetric with shifts from one strand to the other throughout S-phase. We propose a two-step model of chromatin assembly on nascent DNA which provides a mechanistic framework for the regulation of asymmetric segregation of maternal histones, and discuss our model for chromatin assembly in the context of a mechanism for gene expression buffering without a direct role for H3K56ac.