DNA polymerase α interacts with H3-H4 and facilitates the transfer to parental histones to lagging strand

How parental histones, the carriers of epigenetic modifications, are deposited onto replicating DNA remains poorly understood. Here, we develop the eSPAN method (enrichment and sequencing of protein associated nascent DNA) in mouse embryonic stem (ES) cells, which detects the distribution of histones with distinct modifications on leading and lagging strands in a relatively small number of cells. We show that DNA polymerase α (Pol α), which synthesizes primers used for synthesis of both leading and lagging strands, binds histone H3-H4 preferentially. The Pol α mutant defective in histone binding in vitro impairs the transfer of parental H3-H4 to lagging strand in both yeast and mouse ES cells. Finally, dysregulation of both coding genes and non-coding endogenous retroviruses (ERVs) is detected in mutant ES cells defective in parental histone transfer. Together, we report an efficient eSPAN method for analysis of DNA replication coupled processes in mouse ES cells and reveal the mechanism of Pol α in parental histone transfer.