Inseparable RNA binding and chromatin modification activities of a nucleosome-interacting surface in EZH2 [ChIP-seq]

Polycomb repressive complex 2 (PRC2) interacts with RNAs in cells, but there is no consensus on how RNA regulates its canonical functions, including chromatin modification and the maintenance of transcription programs in lineage-committed cells. We assayed two separation-of-function mutants of the catalytic subunit EZH2, defective in RNA binding but active in methyltransferase. We find that part of the RNA-binding surface of EZH2 is required for chromatin modification, yet this activity is independent of RNA. Mechanistically, the RNA-binding surface within EZH2 is required for chromatin modification in vitro and in cells, through interactions with nucleosomal DNA. Contrarily, an RNA-binding defective mutant exhibited normal chromatin modification activity in vitro and in lineage-committed cells, accompanied by normal gene repression activity. Collectively, we show that part of the RNA-binding surface of PRC2, rather than the RNA-binding activity per se, is required for the histone methylation of chromatin in vitro and in cells. Overall design: Quantitative ChIP sequencing with exogenous mouse reference genome spike in (ChIP-Rx) in human K562 cells for PRC2 components, EZH2 & SUZ12, as well as histone modification H3K27me3. Cas9 expressing K562 cells were transduced with lentiviruses containing gRNAs targeting EZH2 as well as rescue constructs to express EZH2-WT, -mt1, -mt2 and -dEZH2.