Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [RNA-Seq]

Neural progenitor cells exhibit developmental plasticity, as they are able to commit to different developmental trajectories in response to external stimuli. How these decisions are stabilized at the molecular level remains a highly active area of research. One way to stably integrate external stimuli into cell fate decisions is through epigenetic marks. H4K16ac represents a unique epigenetic mark, as it modulates chromatin compaction and is the only known active histone modification that is transmitted intergenerationally. The deposition of H4K16ac is mediated by the evolutionarily conserved MSL acetyltransferase complex (MSLc), via its catalytic subunit MOF, and mutations in its components have been linked to neurodevelopmental disorders. To dissect the role of the MSLc, we employed a multi-pronged strategy combining both chronic and acute depletion models. Deletion of the MSLc structural backbone Msl1 in vivo resulted in embryonic lethality by E10, and single-cell multi-omics analysis revealed a systemic disruption in lineage commitment within the neuroectoderm. To distinguish primary molecular functions from secondary developmental consequences, we complemented this with a rapid degradation system in vitro, coupled to directed differentiation into two distinct neural lineages. We found that the MSLc facilitates accessibility at regulatory elements in the early stages of lineage commitment during neurogenesis. We observe a significant decrease in enhancer-promoter contacts in a specific subset of neurodevelopmental genes. In the absence of MSLc this gene group fails to reach adequate gene expression levels upon differentiation, resulting in abnormal morphology. Intriguingly, MSLc loss later on during differentiation does not phenocopy this. Our work reveals MSLc-mediated gene priming as a crucial mechanism potentiating the transcriptional activation of neurodevelopmental gene programs. Our study describes a new mode of epigenetic regulation which cements initial cell fate decisions and provides molecular insights into MSLc-associated developmental disorders. Overall design: WT vs KO experiments: Global transcriptomic differences in a chronic MSL1 depletion model (MSL1 KO) during Neuronal differentiation. WT vs dN experiments: Global transcriptomic differences in a chronic MSL1 truncation model (dN-MSL1-F) during Neuronal differentiation. MSL1-AID experiments: Global transcriptomic differences in response to MSL1 depletion via the additin of Auxin to the cell culture medium. MSL1 depletion was carried out either in short term, like 24h MSL1 depletion in NPCs, or throughout entire stages of the directed in vitro differentiation (Auxin treatment: Day0-7, Day7-14 or Day0-14 during Neuronal differentiation or Day0-3 during Astrocyte differentiation). At least three replicates were sequenced per condition.