H3K4me3 recognition by the COMPASS complex guides de novo histone methylation to restore the symmetric distribution of H3K4me3 following DNA replication

During DNA replication, histones in nucleosomes ahead of DNA replication forks are evicted and then distributed equally onto leading and lagging strands. Mcm2, a subunit of the replicative MCM helicase, participates in the transfer of parental H3-H4 marked by H3K4me3 to lagging strands. Mutations in Mcm2 (Mcm2-3A) result in enrichment of H3K4me3 at leading strands following DNA replication. Here, we show that mcm2-3A mutant cells partially recover the H3K4me3 lost at lagging strands, with a faster recovery at highly transcribed genes than lowly ones, before mitosis. Furthermore, the H3K4 methyltransferase complex COMPASS is essential in the recovery of H3K4me3, irrespective of transcription status. Finally, H3K4me3 recognition (read) by COMPASS is also important for the restoration (write) of this mark. We suggest that both gene transcription and the “read and write” mechanism contribute to the restoration of H3K4me3, with the later mechanism more important for lowly transcribed chromatin. Overall design: We synchronized yeast cells (Wild type, mcm2-3A mutant and Swd1 KO and Spp1 KO using the conditional degradation system) at G1 and released into early S phase in the presence of BrdU. 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 RNA Pol II (RNA Pol II CTD Ser5p), H3K4me3, H3K56ac. And eSPAN for H3K4me3, H3K56ac. The sequencing tag was mapped to both Watson (red) and Crick (blue) strands of the reference genome.