Protocol for the purification and crystallization of the Drosophila melanogaster Cfp1PHD domain in complex with an H3K4me3 peptide

The tri-methylation of histone H3 on K4 (H3K4me3) is a key epigenetic modification that is predominantly found at active gene promoters and is deposited by the complex of proteins associated with SET1 (COMPASS). CXXC zinc finger protein 1 (Cfp1) regulates this process by recruiting SET1 to chromatin and recognizing H3K4me3 via its plant homeodomain (Cfp1^PHD). Here, we present a protocol for the purification and crystallization of the Drosophila melanogaster Cfp1^PHD domain in complex with an H3K4me3 peptide (PDB: 9C0O). We describe steps for obtaining highly pure Cfp1^PHD and diffraction-quality crystals. We then detail procedures for rapidly identifying crystals containing the H3K4me3-bound form of the Cfp1^PHD domain. For complete details on the use and execution of this protocol, please refer to Grégoire et al.¹.