Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing in Neurospora crassa

Here we utilize a forward genetics approach in Neurospora crassa to identify novel effectors of Polycomb repression. We recovered several mutant alleles of a gene (NCU07505),which we deemed effector of Polycomb repression 1 (epr-1), encoding a protein with a bromo-adjacent homology (BAH) domain and plant homeodomain (PHD) finger. Although epr-1mutants display phenotypic and gene expression changes similar to strains lacking PRC2 components, H3K27 methylation is notably unaffected. We demonstrate that EPR-1 forms nuclear foci, reminiscent of Polycomb bodies {Pirrotta:2012br}, and its genomic distribution is limited to and dependent upon H3K27-methylated chromatin, which it recognizes through its BAH domain. Finally, we discover that EPR-1 homologs are widely distributed across eukaryotes, contrary to previous reports {LopezGonzalez:2014id, Li:2018kg}, suggesting an ancient role of EPR-1 homologs in Polycomb repression that was secondarily lost in select lineages. Overall design: ChIP-seq: We perform H3K27me2/3 ChIP-seq in ?epr-1 strains to determine the effests of loss of epr-1 on H3K27me2/3 distribution. We perform GFP ChIP of GFP-tagged EPR-1 (WT, PHD, and BAH) to determine the genomic localization of EPR-1. RNA-seq: We performed polyA-RNAseq on ?epr-1 strains and compared gene expression levels to previously published data sets from wild type and ?set-7 (in Series GSE82222). DamID-seq: We performed DamID-seq on Dam tagged EPR-1 in a wild type and ?eed background and a Dam tagged EPR-1 PHD mutatnt to determine the chromatin targets of EPR-1.