Recycling of H2A-H2B provides short-term memory of chromatin states [SCAR-Seq]

Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. We show that H2AK119ub, H2BK120ub, and H2A.Z are recycled quantitatively and accurately during DNA replication. H2A-H2B are recycled symmetrically to daughter strands largely independent of known H3-H4 recycling pathways. Post-replication, H2A-H2B modifications are rapidly restored, and the rapid wave of H2AK119ub supports accurate restoration of H3K27me3. This work reveals epigenetic transmission of H2A-H2B modification during DNA replication and identifies H3-H4 and H2A-H2B crosstalk in epigenome propagation. We propose that rapid short-term memory of recycled H2A-H2B modifications facilitates reestablishment of slow, long-term chromatin state memory. SCAR-seq (Sister Chromatids After Replication) time-series measuring histone partition of H3K27me3, H2AK119ub, H2A.Z and H4K20me0 in wildtype (WT), MCM2 histone-binding mutant (MCM2-2A), Pola1 histone-binding mutant (Pola1-3A), or Pole4 KO mouse embryonic stem cells (Parental WT cells, 2 MCM2-2A clones, 2 Pola1-3A clones, 2 Pole4KO clones, >2 replicates per cell line, stranded input controls). SCAR-seq time-series measuring histone partition of H3K27me3 or JARID2 in Ring1B-mAID Ring1AKO MCM2-2A cells by either depleting H2AK119ub by the addition of indole-3-acetic acid (IAA) or corresponding DMSO treatment as a control.