Genome binding/occupancy profiling by high throughput sequencing
Summary
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.
Overall design
ChIP-Seq and ChOR-seq measuring chromatin occupancy for H3K27me3, H2AK119ub, H2A.Z, H2BK120ub, pan-H2A, pan-H3 in wildtype (WT) or Ring1B-mAID BAP1dTAG Ring1AKO mouse embryonic stem cells with corresponding clickedInputs controls in two biological replicates. CHOR-seq involves a 10min EdU labelling step, followed by a chase in medium without EdU (T15-T720; in min) or immediate harvesting (T0). Optional treatments are indicated. ClickedInputs are the corresponding inputs from the ChOR-seq time course where the EdU-labelled fraction has been clicked to Biotin, Streptavidin-purified and libraries generated.
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