Eviction of repressor PRC1 via RNA-binding of PHC1 promotes stress-induced transcription

Proteins of the Polycomb group (PcG) maintain cellular states through epigenetic control of gene expression. It is still heavily debated how RNAs modulate the function of these chromatin factors. To identify PcG RNA-binding proteins, we screened a library of HEK293T expressing PcG proteins for their binding potential using CLIP and PARCLIP. We find that RNA-binding is not as pervasive as suggested, but rather focused on few mostly core PcG proteins. Since the relationship between core-PRC1 and RNA has not been previously studied, we sequenced RNAs bound to PHC1, showing a 5’ enrichment at transcripts with lower expression. Drosophila mutants and overexpression of RNA-binding deficient PHC1, show binding to be essential to fast induction of response genes upon heat-shock and LPS/TNF treatment. ChIP at sequential time points reveals a lack of Polymerase S2 phosphorylation. Altogether, the RNA-PHC1-PRC1 axis aids rapid induction of immediate-early genes. We performed two replicates of PARCLIP on PRC1 member PHC1. From this we determined binding sites and strength in relation to two replicates of total nuclear RNA-Seq. As control, 2 replicates of RNAPII PARCLIP were used. To determine the functional mechanism of binding, we generated two replicates each of ChIP-Seq data of mutant and wt PHC1 as well as one replicate each of H3K27me3, H3K4me3, RNA Polymerase II and EZH2. All sequencing experiments were performed in HEK293T T-Rex cells.