Asymmetric partition of parental histone (H3-H4)2 tetramers onto replicating DNA strands

In eukaryotic cells, inheritable changes in gene expression in response to environmental and developmental stimuli is associated with changes in histone modifications and relies on the passage of these changes into daughter cells during cell division, a process that remains elusive. Here, we show that parental histone (H3-H4)2 tetramers, the primary carrier of epigenetic modifications, are assembled into nucleosomes onto both replicating leading and lagging strands, with a preference for lagging strands of DNA replication forks. This asymmetric distribution of parental (H3-H4)2 is exacerbated in cells lacking Dpb3 and Dpb4, two subunits of DNA polymerase Pol ε. Dpb3-Dpb4 binds (H3-H4)2 and participates in the transfer of parental (H3-H4)2 tetramers onto leading strands of DNA replication forks. Cells lacking Dpb3 and Dpb4 exhibits defects in epigenetic inheritance. These results reveal a previously undocumented mechanism of histone segregation and a direct role for Pol ε in this poorly understood process. We synchronized yeast cells (Wile type and other mutant cells) at G1 and released into early S phase in the presence of BrdU, and hydroxyurea (HU). We then performed BrdU immunoprecipitation using anti-BrdU antibodies following single-strand DNA library preparation and sequencing (ssSeq). we also performed protein ChIP followed by single-strand DNA sequencing (ChIP-ssSeq) for Dpb3, Dpb4, H3K56ac, H3K4me3, T7-tag, and HA-tag. The sequencing tag was mapped to both Watson (red) and Crick (blue) strands of the reference genome.