Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 109; no. 32; pp. 12950 - 12955
• Main Authors: Arita, Kyohei, Isogai, Shin, Oda, Takashi, Unoki, Motoko, Sugita, Kazuya, Sekiyama, Naotaka, Kuwata, Keiko, Hamamoto, Ryuji, Tochio, Hidehito, Sato, Mamoru, Ariyoshi, Mariko, Shirakawa, Masahiro
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 07.08.2012; National Acad Sciences
• Subjects: Binding sites; Biological Sciences; CCAAT-Enhancer-Binding Proteins - genetics; CCAAT-Enhancer-Binding Proteins - metabolism; Cells; Chemical equilibrium; Chromatography, Affinity; Chromatography, Gel; Chromatography, Ion Exchange; Chromatography, Liquid; Cloning, Molecular; Crystal structure; Crystallography, X-Ray; DNA; DNA methylation; Electrophoretic Mobility Shift Assay; Epigenetics; Escherichia coli; genes; Histones; Histones - metabolism; Humans; Hydrogen bonds; Magnetic Resonance Spectroscopy; Methylation; Models, Molecular; Multiprotein Complexes - chemistry; Phosphorylation; Polymerase Chain Reaction; Protein Binding; Protein Subunits - metabolism; Proteins; Research universities; Tandem Mass Spectrometry; transcription (genetics); Ubiquitin-Protein Ligases
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1203701109

Multiple covalent modifications on a histone tail are often recognized by linked histone reader modules. UHRF1 [ubiquitin-like, containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1], an essential factor for maintenance of DNA methylation, contains linked two-histone reader modules, a tandem Tudor domain and a PHD finger, tethered by a 17-aa linker, and has been implicated to link histone modifications and DNA methylation. Here, we present the crystal structure of the linked histone reader modules of UHRF1 in complex with the amino-terminal tail of histone H3. Our structural and biochemical data provide the basis for combinatorial readout of unmodified Arg-2 (H3-R2) and methylated Lys-9 (H3-K9) by the tandem tudor domain and the PHD finger. The structure reveals that the intermodule linker plays an essential role in the formation of a histone H3–binding hole between the reader modules by making extended contacts with the tandem tudor domain. The histone H3 tail fits into the hole by adopting a compact fold harboring a central helix, which allows both of the reader modules to simultaneously recognize the modification states at H3-R2 and H3-K9. Our data also suggest that phosphorylation of a linker residue can modulate the relative position of the reader modules, thereby altering the histone H3–binding mode. This finding implies that the linker region plays a role as a functional switch of UHRF1 involved in multiple regulatory pathways such as maintenance of DNA methylation and transcriptional repression.