Polycomb repressive complexes 1 and 2 independently and dynamically regulate euchromatin during cerebellar neurodevelopment

Polycomb Repressive Complexes (PRCs) are known for chemically modifying histones to compact chromatin structure and repress transcription. Broadly speaking, PRC1 monoubiquitinates histone 2A at lysine 119 (H2AK119ub), and PRC2 methylates histone H3 lysine 27 (H3K27me3, H3K27me2 and H3K27me1), but the scope and functions of these activities are complicated by a multiplicity of factors involving distinct cellular contexts and compositions of both complexes. Because epigenetic dysregulation is associated with neurodevelopmental disorders, but little is known about normal PRC activities in neurons, we used CUT&RUN to map PRC-dependent histone modifications in the mouse cerebellum at two postnatal timepoints (day 12 and 3 months). We find that H2AK119ub appears within both heterochromatin and euchromatin as the cerebellum matures, becoming enriched within active enhancers and promoters while being depleted from heterochromatin. Unexpectedly, the PRC1 product H2AK119ub appeared frequently without the accompaniment of the PRC2 product H3K27me3; leading to a much more dynamic chromatin state than when these two marks colocalized. Deposition of H2AK119ub at loci with the chromatin signature of active cis-regulatory elements tended to also gain the euchromatin-associated modifications H3K4me3 and H3K27ac during neurodevelopment. Importantly, deposition of H2AK119ub within both bivalent and H3K4me3-only promoters reduced transcription of downstream genes. The pattern of H2AK119ub deposition was specific to the cerebellum compared to liver and kidney. We then show that the PRC2 product H3K27me1 formed euchromatic zones that alternated with heterochromatic zones dominated by H3K27me3. Between the early and late timepoints H3K27me1 became enriched within a subset of expressed gene bodies and depleted from most other genes while remaining uncorrelated with the abundance of the corresponding mRNAs. Our data lead us to propose that deposition of H2AK119ub and H3K27me1 during cerebellar development likely fine-tunes the activity of cis-regulatory elements and transcription, respectively, and that PRC1 and PRC2 activities become uncoupled in the mature brain.