RNA-seq in CRAMP1 and SUZ12 knockout KBM-7 cells
The essential role of the core histones (H2A, H2B, H3 and H4) in DNA packaging has been well understood for decades, but the function of the linker histone (H1) remains enigmatic. H1 compacts nucleosome arrays in vitro, but the multiple H1 subtypes and variants encoded in mammalian genomes (11 in both mice and humans) hamper genetic studies to determine H1 function in vivo. Challenging the prevailing view that linker histones are a general feature of heterochromatin, here we show a critical requirement for linker histones in the function of Polycomb Repressive complex 2 (PRC2). Through a CRISPR/Cas9 genetic screen in a fluorescent reporter cell line responsive to PRC2 perturbation, we identified an essential requirement for the poorly characterised gene CRAMP1 in PRC2-mediated repression. CRAMP1 localises to the promoters of all expressed H1 genes where it acts as a positive transcriptional regulator. Ablation of CRAMP1 provides a unique tool to simultaneously deplete all linker histones, which results in selective decompaction of H3K27me3-marked loci and derepression of PRC2 target genes without concomitant loss of PRC2 occupancy or enzymatic activity. Strikingly, in contrast to the broad genomic distribution previously ascribed to H1, we find that linker histones selectively localise to genomic loci marked by H3K27me3 across diverse cell types and organisms. Altogether, our data demonstrate a prominent role for linker histones in epigenetic repression by PRC2. Overall design: Total RNA was extracted from wild-type, CRAMP1 knockout or SUZ12 knockout KBM-7 cells. Three independent CRAMP1 knockout clones and two independent SUZ12 knockout clones were used as biological replicates.