The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B

KDM5B is a histone H3K4me2/3 demethylase. The PHD1 domain of KDM5B is critical for demethylation, but the mechanism underlying the action of this domain is unclear. In this paper, we observed that PHDIKDMSB interacts with unmethylated H3K4me0. Our NMR structure of PHDIKDMSB in complex with H3K4me0 revealed that the binding mode is slightly different from that of other reported PHD fingers. The disruption of this interaction by double mutations on the residues in the interface （L325A/D328A） decreases the H3K4me2/3 demethylation activity of KDM5B in cells by approximately 50% and increases the transcriptional repression of tumor suppressor genes by approximately twofold. These findings imply that PHDIKDMSB may help maintain KDM5B at target genes to mediate the demethylation activities of KDM5B.

NMR Studies on the Interaction between Oncogene RET G-Quadruplex and Berberine

of main observation and conclusion RET G-quadruplex DNA(G4-DNA)is formed in the promoter region of RET protein,which is involved in the initiation and progression of human cancers.Berberine inhibits cancer cell growth through interactions with RET G4-DNA,but how it binds to RET G4-DNA remains unknown.Previously,we reported that colchicine selectively bound to RET G4-DNA,but the structural basis of its binding selectivity is still unclear.Here,mainly by NMR,we demonstrated how berberine bound to RET G4-DNA in a means different from colchicine,and implied several key determinants for small molecules specifically binding to one G4-DNA.

Dimeric G-quadruplex DNA Structure in the Proximal Promoter of VEGFR-2 Reveals a New Drug Target to Inhibit Tumor Angiogenesis

Vascular endothelial growth factor(VEGF)regulates tumor angiogenesis,which is active on the endothelium via VEGF receptor 2(VEGFR-2).The proximal promoter region of VEGFR-2(termed as VEGFR-2 DNA)is guanine-rich,forming G-quadruplex(G4)structures.Here,we demonstrate that VEGFR-2 DNA consists of one symmetrically dimeric 14-mer G4-DNA and one 12-mer sequence-palindromic dsDNA.This G4-DNA adopts an unprecedented folding with five stacked tetrads linked by four broken strands.Its 5’-end part contains an A-tetrad A^(1)•A^(4)•A^(1’)•A^(4’)and one G-tetrad G^(3)•G^(5)•G^(3’)•G^(5’)with two V-shaped loops and two one-nt edge-type loops.Its 3’-end part includes three G-tetrads G^(10)•G^(6)•G^(10’)•G^(6’),G^(11)•G^(7)•G^(11’)•G^(7’)(central)and G^(12)•G^(8)•G^(12’)•G^(8’)spanned by two double-chain-reversal one-nt(C^(9)or C^(9’))loops.Bases G^(13)and G^(13’)stack with G-tetrad G^(12)•G^(8)•G^(12’)•G^(8’).These characteristics make this G4-DNA more stable than reported VEGFR-17T G4 structure.The dsDNA connects with G4-DNA without any interactions,generating a linear assembly with G4-DNA structural bulges.These studies uncover new structural features of VEGFR-2 DNA as a potential drug target by inhibiting VEGFR-2 expression,thereby tumor angiogenesis.

Structural Basis of RACK7 PHD Domain to Read a Pediatric Glioblastoma-Associated Histone Mutation H3.3G34R

Histone point mutations,including missense mutations on histone H3 at positions 27(K27M),34(G34R/V,G34W,G34L)and 36(K36M),were identified as potential cancer driver mutations.H3.3G34R/V mutations account for pediatric glioblastomas(GBM).RACK7(also known as ZMYND8,PRKCBP1)was recently reported to specifically bind H3.3G34R through its PHD(plant homedomain)domain(PHDRACK7)in vitro and in H3.3G34R pediatric glioblastoma cells,playing key roles in H3.3G34R-mediated gene transcription.Herein,we provided both biochemical and NMR structural evidences that PHDRACK7 recognized histone H3.3G34R mutant via a mechanism distinet from all other reported PHD domains.Except the reported residue D104,two new sites D108 and L121 of PHD^(RACK7) were found necessary for the interactions between PHD^(RACK7) and histone H3.3G34R peptide.Our results provided a potential molecular basis for pediatric GBM driven by the H3.3G34R mutation.