Chromatin binding of CFP1 mutants in C127 mouse cell lines. [C127_ChIPseq]

Chromatin modifications and the promoter associated epigenome are thought to be important for the regulation of gene expression. However, the mechanisms by which chromatin modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed target gene promoters through CFP1 which engages in a unique form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). CFP1 defines SET1 complex occupancy on chromatin and its multivalent interactions are required for the SET1 complex to place H3K4me3. In the absence of CFP1, gene expression is perturbed suggesting that the normal targeting and function of SET1 complex is central to creating an appropriately functioning vertebrate promoter associated epigenome. Overall design: C127 mouse cell line was used to investigate the occupancy of variuos chromatin binding proteins, including CFP1, KDM2B and RNA PolII, as well as the genome-wide distribution of H3K4me3. In addition, novel C127 cell lines were generated that expressed different forms of a GFP-tagged CFP1 protein to compare the binding properties of wild-type CFP1 with single point mutants within its binding domains. The cell lines generated include GFP-CFP1 wild-type , GFP-CFP1 CXXC mutant, GFP-CFP1 PHD mutant, a double GFP-CFP1 PHD and CXXC mutant, GFP-CPF1 SID mutant, along with a GFP control.