Proper parental histone allocation is required for mouse embryonic stem cell differentiation and histone post-transcription modification inheritance

To understand whether parental histone PTM landscape plays roles in cell differentiation, we perturbed parental histone PTM allocation by mutating histone chaperone MCM2 on its histone binding domain (MCM2-2A mutation), disrupted only the histone transferring of MCM2 protein in mouse embryonic stem cells (ESCs). Combining single-cell transcriptomics and epigenomics with lineage barcoding, we found that MCM2-2A mutant ESCs cannot be fully differentiated to neuronal precursor cells (NPCs), causing by the redistribution of H3K27me3, and subsequently NPC related gene expression. Here, we show that the parental histone allocation plays an important role in the establishment of chromatin landscapes, altering ESC differentiational potential, shaping expression programs and cell heterogeneity. We used mouse embryonic stem cell and differentiation neuronal precursor cells (Wild type and MCM2-2A mutant cells). H3K27me3, H3K4me3 and H3K9me3 CUT&Tag, H3.3 CUT&Tag in ESCs, H3K27me3 eSPAN in ESCs, H3.3 espan in ESCs, scRNA-seq of ESCs and D7 NPCs, scCUT&Tag of H3K27me3 in ESCs, MINCE-seq in ESCs, Repli-ATAC-seq in ESCs, ATAC-seq in ESCs and CUT&RUN in ESCs, D3 NPCs and D7 NPCs were implemented. Parts of experiments above were also implemented in POLE3-/-, HIRA-/- and HIRA-/- MCM2-2A ESCs.