Publications

• SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells.

  Hamamoto R., Furukawa Y., Morita M., Iimura Y., Silva F.P., Li M., Yagyu R., Nakamura Y.

  Colorectal and hepatocellular carcinomas are some of the leading causes of cancer deaths worldwide, but the mechanisms that underly these malignancies are not fully understood. Here we report the identification of SMYD3, a gene that is over-expressed in the majority of colorectal carcinomas and he ... >> More

  Colorectal and hepatocellular carcinomas are some of the leading causes of cancer deaths worldwide, but the mechanisms that underly these malignancies are not fully understood. Here we report the identification of SMYD3, a gene that is over-expressed in the majority of colorectal carcinomas and hepatocellular carcinomas. Introduction of SMYD3 into NIH3T3 cells enhanced cell growth, whereas genetic knockdown with small-interfering RNAs (siRNAs) in cancer cells resulted in significant growth suppression. SMYD3 formed a complex with RNA polymerase II through an interaction with the RNA helicase HELZ and transactivated a set of genes that included oncogenes, homeobox genes and genes associated with cell-cycle regulation. SMYD3 bound to a motif, 5'-CCCTCC-3', present in the promoter region of downstream genes such as Nkx2.8. The SET domain of SMYD3 showed histone H3-lysine 4 (H3-K4)-specific methyltransferase activity, which was enhanced in the presence of the heat-shock protein HSP90A. Our findings suggest that SMYD3 has histone methyltransferase activity and plays an important role in transcriptional regulation as a member of an RNA polymerase complex. Furthermore, activation of SMYD3 may be a key factor in human carcinogenesis. << Less

  Nat. Cell Biol. 6:731-740(2004) [PubMed] [EuropePMC]

  This publication is cited by 3 other entries.

• ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation.

  Nakamura T., Mori T., Tada S., Krajewski W., Rozovskaia T., Wassell R., Dubois G., Mazo A., Croce C.M., Canaani E.

  ALL-1 is a member of the human trithorax/Polycomb gene family and is also involved in acute leukemia. ALL-1 is present within a stable, very large multiprotein supercomplex composed of > or =29 proteins. The majority of the latter are components of the human transcription complexes TFIID (includin ... >> More

  ALL-1 is a member of the human trithorax/Polycomb gene family and is also involved in acute leukemia. ALL-1 is present within a stable, very large multiprotein supercomplex composed of > or =29 proteins. The majority of the latter are components of the human transcription complexes TFIID (including TBP), SWI/SNF, NuRD, hSNF2H, and Sin3A. Other components are involved in RNA processing or in histone methylation. The complex remodels, acetylates, deacetylates, and methylates nucleosomes and/or free histones. The complex's H3-K4 methylation activity is conferred by the ALL-1 SET domain. Chromatin immunoprecipitations show that ALL-1 and other complex components examined are bound at the promoter of an active ALL-1-dependent Hox a9 gene. In parallel, H3-K4 is methylated, and histones H3 and H4 are acetylated at this promoter. << Less

  Mol. Cell 10:1119-1128(2002) [PubMed] [EuropePMC]

  This publication is cited by 4 other entries.

• Characterization of a novel WHSC1-associated SET domain protein with H3K4 and H3K27 methyltransferase activity.

  Kim S.M., Kee H.J., Eom G.H., Choe N.W., Kim J.Y., Kim Y.S., Kim S.K., Kook H., Kook H., Seo S.B.

  Evolutionary conserved SET domains were originally identified in three Drosophila proteins: suppressor of variegation (Su (var) 3-9), enhancer of zeste (E(z)), and the trithorax. Some of the SET-domain containing proteins have been known to elicit methylation of histone lysine residues. Based on a ... >> More

  Evolutionary conserved SET domains were originally identified in three Drosophila proteins: suppressor of variegation (Su (var) 3-9), enhancer of zeste (E(z)), and the trithorax. Some of the SET-domain containing proteins have been known to elicit methylation of histone lysine residues. Based on a search for SET-domain containing proteins using bioinformatic tools, we identified and subsequently named a novel SET domain as WHISTLE, that has histone methyltransferase (HMTase) activity. To characterize WHISTLE, we performed an HMTase assay, mass spectrometric analysis, lysine specificity, and transfection assays. Mass spectrometric and immunoblot analysis revealed that WHISTLE di-methylates H3K4 and di-, and tri-methylates H3K27 of histones. Overexpression of WHISTLE repressed transcription of the SV40 promoter. Our results suggest that WHISTLE is a novel SET domain containing a protein with specific H3K4 and H3K27 HMTase activity. << Less

  Biochem. Biophys. Res. Commun. 345:318-323(2006) [PubMed] [EuropePMC]

  This publication is cited by 5 other entries.

• Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation.

  Nishioka K., Chuikov S., Sarma K., Erdjument-Bromage H., Allis C.D., Tempst P., Reinberg D.

  A novel histone methyltransferase, termed Set9, was isolated from human cells. Set9 contains a SET domain, but lacks the pre- and post-SET domains. Set9 methylates specifically lysine 4 (K4) of histone H3 (H3-K4) and potentiates transcription activation. The histone H3 tail interacts specifically ... >> More

  A novel histone methyltransferase, termed Set9, was isolated from human cells. Set9 contains a SET domain, but lacks the pre- and post-SET domains. Set9 methylates specifically lysine 4 (K4) of histone H3 (H3-K4) and potentiates transcription activation. The histone H3 tail interacts specifically with the histone deacetylase NuRD complex. Methylation of histone H3-K4 by Set9 precludes the association of NuRD with the H3 tail. Moreover, methylation of H3-K4 impairs Suv39h1-mediated methylation at K9 of H3 (H3-K9). The interplay between the Set9 and Suv39h1 histone methyltransferases is specific, as the methylation of H3-K9 by the histone methyltransferase G9a was not affected by Set9 methylation of H3-K4. Our studies suggest that Set9-mediated methylation of H3-K4 functions in transcription activation by competing with histone deacetylases and by precluding H3-K9 methylation by Suv39h1. Our results suggest that the methylation of histone tails can have distinct effects on transcription, depending on its chromosomal location, the combination of posttranslational modifications, and the enzyme (or protein complex) involved in the particular modification. << Less

  Genes Dev. 16:479-489(2002) [PubMed] [EuropePMC]

• Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures.

  Hu P., Zhang Y.

  Histone lysine methylation is emerging as an important mechanism to regulate chromatin structure and gene activity. To provide theoretical understanding of its reaction mechanism and product specificity, ab initio quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations and mole ... >> More

  Histone lysine methylation is emerging as an important mechanism to regulate chromatin structure and gene activity. To provide theoretical understanding of its reaction mechanism and product specificity, ab initio quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations and molecular dynamics simulations have been carried out to investigate the histone lysine methyltransferase SET7/9. It is found that the methyl-transfer reaction catalyzed by SET7/9 is a typical in-line S(N)2 nucleophilic substitution reaction with a transition state of 70% dissociative character. The calculated average free energy barrier at the MP2(6-31+G) QM/MM level is 20.4 +/-1.1 kcal/mol, consistent with the activation barrier of 20.9 kcal/mol estimated from the experimental reaction rate. The barrier fluctuation has a strong correlation with the nucleophilic attack distance and angle in the reactant complex. The calculation results show that the product specificity of SET7/9 as a monomethyltransferase is achieved by disrupting the formation of near-attack conformations for the dimethylation reaction. << Less

  J. Am. Chem. Soc. 128:1272-1278(2006) [PubMed] [EuropePMC]

• PR Domain-containing Protein 7 (PRDM7) Is a Histone 3 Lysine 4 Trimethyltransferase.

  Blazer L.L., Lima-Fernandes E., Gibson E., Eram M.S., Loppnau P., Arrowsmith C.H., Schapira M., Vedadi M.

  PR domain-containing protein 7 (PRDM7) is a primate-specific histone methyltransferase that is the result of a recent gene duplication of PRDM9. The two proteins are highly homologous, especially in the catalytic PR/SET domain, where they differ by only three amino acid residues. Here we report th ... >> More

  PR domain-containing protein 7 (PRDM7) is a primate-specific histone methyltransferase that is the result of a recent gene duplication of PRDM9. The two proteins are highly homologous, especially in the catalytic PR/SET domain, where they differ by only three amino acid residues. Here we report that PRDM7 is an efficient methyltransferase that selectively catalyzes the trimethylation of H3 lysine 4 (H3K4) both in vitro and in cells. Through selective mutagenesis we have dissected the functional roles of each of the three divergent residues between the PR domains of PRDM7 and PRDM9. These studies indicate that after a single serine to tyrosine mutation at residue 357 (S357Y), PRDM7 regains the substrate specificities and catalytic activities similar to its evolutionary predecessor, including the ability to efficiently methylate H3K36. << Less

  J. Biol. Chem. 291:13509-13519(2016) [PubMed] [EuropePMC]

  This publication is cited by 3 other entries.

• Crystal structure and functional analysis of the histone methyltransferase SET7/9.

  Wilson J., Jing C., Walker P., Martin S., Howell S., Blackburn G., Gamblin S., Xiao B.

  Methylation of lysine residues in the N-terminal tails of histones is thought to represent an important component of the mechanism that regulates chromatin structure. The evolutionarily conserved SET domain occurs in most proteins known to possess histone lysine methyltransferase activity. We pres ... >> More

  Methylation of lysine residues in the N-terminal tails of histones is thought to represent an important component of the mechanism that regulates chromatin structure. The evolutionarily conserved SET domain occurs in most proteins known to possess histone lysine methyltransferase activity. We present here the crystal structure of a large fragment of human SET7/9 that contains a N-terminal beta-sheet domain as well as the conserved SET domain. Mutagenesis identifies two residues in the C terminus of the protein that appear essential for catalytic activity toward lysine-4 of histone H3. Furthermore, we show how the cofactor AdoMet binds to this domain and present biochemical data supporting the role of invariant residues in catalysis, binding of AdoMet, and interactions with the peptide substrate. << Less

  Cell 111:105-115(2002) [PubMed] [EuropePMC]

• Structure and catalytic mechanism of the human histone methyltransferase SET7/9.

  Xiao B., Jing C., Wilson J.R., Walker P.A., Vasisht N., Kelly G., Howell S., Taylor I.A., Blackburn G.M., Gamblin S.J.

  Acetylation, phosphorylation and methylation of the amino-terminal tails of histones are thought to be involved in the regulation of chromatin structure and function. With just one exception, the enzymes identified in the methylation of specific lysine residues on histones (histone methyltransfera ... >> More

  Acetylation, phosphorylation and methylation of the amino-terminal tails of histones are thought to be involved in the regulation of chromatin structure and function. With just one exception, the enzymes identified in the methylation of specific lysine residues on histones (histone methyltransferases) belong to the SET family. The high-resolution crystal structure of a ternary complex of human SET7/9 with a histone peptide and cofactor reveals that the peptide substrate and cofactor bind on opposite surfaces of the enzyme. The target lysine accesses the active site of the enzyme and the S-adenosyl-l-methionine (AdoMet) cofactor by inserting its side chain into a narrow channel that runs through the enzyme, connecting the two surfaces. Here we show from the structure and from solution studies that SET7/9, unlike most other SET proteins, is exclusively a mono-methylase. The structure indicates the molecular basis of the specificity of the enzyme for the histone target, and allows us to propose a model for the methylation reaction that accounts for the role of many of the residues that are invariant across the SET family. << Less

  Nature 421:652-656(2003) [PubMed] [EuropePMC]

  This publication is cited by 3 other entries.

• Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase.

  Wang H., Cao R., Xia L., Erdjument-Bromage H., Borchers C., Tempst P., Zhang Y.

  Methylation of histone H3 at lysine 9 by SUV39H1 and subsequent recruitment of the heterochromatin protein HP1 has recently been linked to gene silencing. In addition to lysine 9, histone H3 methylation also occurs at lysines 4, 27, and 36. Here, we report the purification, molecular identificatio ... >> More

  Methylation of histone H3 at lysine 9 by SUV39H1 and subsequent recruitment of the heterochromatin protein HP1 has recently been linked to gene silencing. In addition to lysine 9, histone H3 methylation also occurs at lysines 4, 27, and 36. Here, we report the purification, molecular identification, and functional characterization of an H3-lysine 4-specific methyltransferase (H3-K4-HMTase), SET7. We demonstrate that SET7 methylates H3-K4 in vitro and in vivo. In addition, we found that methylation of H3-K4 and H3-K9 inhibit each other. Furthermore, H3-K4 and H3-K9 methylation by SET7 and SUV39H1, respectively, have differential effects on subsequent histone acetylation by p300. Thus, our study provides a molecular explanation to the differential effects of H3-K4 and H3-K9 methylation on transcription. << Less

  Mol. Cell 8:1207-1217(2001) [PubMed] [EuropePMC]