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SMYD2 (SET and MYND domain containing 2)

Written2011-05Hitoshi Tsuda, Shuhei Komatsu
Department of Pathology, Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan (HT); Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan (SK)

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)HSKM-B
ZMYND14
KMT3C
Other aliasMGC119305
HGNC (Hugo) SMYD2
LocusID (NCBI) 56950
Atlas_Id 47098
Location 1q32.3  [Link to chromosome band 1q32]
Location_base_pair Starts at 214454565 and ends at 214510477 bp from pter ( according to hg19-Feb_2009)  [Mapping SMYD2.png]
Fusion genes
(updated 2016)
SMYD2 (1q32.3) / ASNA1 (19p13.2)SMYD2 (1q32.3) / MAGI1 (3p14.1)SMYD2 (1q32.3) / SMYD2 (1q32.3)

DNA/RNA

 
Description 55913 bp, 12 exons.
Transcription 1689 bp mRNA.

Protein

 
Description 433 amino acids. The protein contains SET domain, MYND domain/zinc-finger motif, and cysteine-rich post-SET domain. The SET domain is split into two segments by a MYND domain.
Expression Wide, highly expressed in heart, brain, liver, kidney, thymus, ovary, embryonic tissues (heart, hypothalamus) (Brown et al., 2006).
Localisation Cytoplasmic and nucleus (Brown et al., 2006).
Function Regulation of transcription as a lysine methyltransferase for histone 3, lysine 36 (H3K36) and inhibition of p53's transactivation activity as a lysine methyltransferase for lysine 370 (K370) of p53 through the SET domain (Brown et al., 2006; Huang et al., 2006). Possibly promotion of cell proliferation and/or differentiation through its overexpression/activation-induced inhibition of p53's transactivation activity. Methylation of retinoblastoma (RB) tumor suppressor at lysine 860, that is regulated during cell cycle progression, cellular differentiation ,and in response to DNA damage (Saddic et al., 2010). RB monomethylation at lysine 860 provides a direct binding site for the transcription repressor L3MBTL1. Through interaction with HSP90alpha, SMYD2 histone methyltransferase activity and specificity for histone H3 at lysine 4 (H3K4) are enhanced in vitro (Abu-Farha et al., 2008). SMYD2 gain of function is correlated with the upregulation of 37 and down regulation of 4 genes, the majority of which are involved in the cell cycle, chromatin remodelling, and transcriptional regulation (Abu-Farha et al., 2008).
Homology Xenopus laevis, Zebrafish, Chicken, Gray short-tailed opossum, Mouse, Rat, Rabbit, Pig, Horse, Cattle, Dog, White-tufted-ear marmoset, Rhesus monkey, Sumatran orangutan, Chimpanzee.

Mutations

Note Not found.

Implicated in

Note
  
Entity Esophageal squamous cell carcinoma (ESCC)
Note Frequent overexpression of SMYD2 mRNA and protein was observed in KYSE150 cells with remarkable amplification at 1q32-q41.1 and other ESCC cell lines (11/43 lines, 25.6%). Overexpression of SMYD2 protein was frequently detected in primary tumor samples of ESCC (117/153 cases, 76.5%) as well and significantly correlated with gender, venous invasion, the pT category in the tumor-lymph node-metastasis classification and status of recurrence. Patients with SMYD2-overexpressing tumors had a worse overall rate of survival than those with non-expressing tumors. Knockdown of SMYD2 expression inhibited and ectopic overexpression of SMYD2 promoted the proliferation of ESCC cells in a TP53 mutation-independent but SMYD2 expression dependent manner (Komatsu et al., 2009).
  
  
Entity Thyroid carcinoma and benign thyroid nodule
Note Using differential display-polymerase chain reaction method, the gene expression differences between benign thyroid nodules (BTNs) and follicular and classic variants of papillary thyroid carcinoma (PTC) were evaluated in a group of 42 patients (15 BTNs, 14 follicular variant of PTC and 13 classic variant of PTC). SMYD2 had lower expression in both carcinoma groups than in BTNs (Igci et al., 2011).
  
  
Entity Breast cancer
Note Expression of a group of three genes (MTSS1, RPL37, and SMYD2) evaluated by real-time PCR was shown to be a potential candidate to predict response to neoadjuvant chemotherapy (4 cycles of doxorubicin and cyclophosphamide) in breast cancer patients (Barros Filho et al., 2010).
  

Bibliography

The tale of two domains: proteomics and genomics analysis of SMYD2, a new histone methyltransferase.
Abu-Farha M, Lambert JP, Al-Madhoun AS, Elisma F, Skerjanc IS, Figeys D.
Mol Cell Proteomics. 2008 Mar;7(3):560-72. Epub 2007 Dec 7.
PMID 18065756
 
Gene trio signatures as molecular markers to predict response to doxorubicin cyclophosphamide neoadjuvant chemotherapy in breast cancer patients.
Barros Filho MC, Katayama ML, Brentani H, Abreu AP, Barbosa EM, Oliveira CT, Goes JC, Brentani MM, Folgueira MA.
Braz J Med Biol Res. 2010 Dec;43(12):1225-31. Epub 2010 Nov 26.
PMID 21103787
 
Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex.
Brown MA, Sims RJ 3rd, Gottlieb PD, Tucker PW.
Mol Cancer. 2006 Jun 28;5:26.
PMID 16805913
 
Repression of p53 activity by Smyd2-mediated methylation.
Huang J, Perez-Burgos L, Placek BJ, Sengupta R, Richter M, Dorsey JA, Kubicek S, Opravil S, Jenuwein T, Berger SL.
Nature. 2006 Nov 30;444(7119):629-32. Epub 2006 Nov 15.
PMID 17108971
 
Differential expression of a set of genes in follicular and classic variants of papillary thyroid carcinoma.
Igci YZ, Arslan A, Akarsu E, Erkilic S, Igci M, Oztuzcu S, Cengiz B, Gogebakan B, Cakmak EA, Demiryurek AT.
Endocr Pathol. 2011 Jun;22(2):86-96.
PMID 21509594
 
Overexpression of SMYD2 relates to tumor cell proliferation and malignant outcome of esophageal squamous cell carcinoma.
Komatsu S, Imoto I, Tsuda H, Kozaki KI, Muramatsu T, Shimada Y, Aiko S, Yoshizumi Y, Ichikawa D, Otsuji E, Inazawa J.
Carcinogenesis. 2009 Jul;30(7):1139-46. Epub 2009 May 7.
PMID 19423649
 
Methylation of the retinoblastoma tumor suppressor by SMYD2.
Saddic LA, West LE, Aslanian A, Yates JR 3rd, Rubin SM, Gozani O, Sage J.
J Biol Chem. 2010 Nov 26;285(48):37733-40. Epub 2010 Sep 24.
PMID 20870719
 

Citation

This paper should be referenced as such :
Tsuda, H ; Komatsu, S
SMYD2 (SET, MYND domain containing 2)
Atlas Genet Cytogenet Oncol Haematol. 2011;15(11):972-973.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SMYD2ID47098ch1q32.html


External links

Nomenclature
HGNC (Hugo)SMYD2   20982
Cards
AtlasSMYD2ID47098ch1q32
Entrez_Gene (NCBI)SMYD2  56950  SET and MYND domain containing 2
AliasesHSKM-B; KMT3C; ZMYND14
GeneCards (Weizmann)SMYD2
Ensembl hg19 (Hinxton)ENSG00000143499 [Gene_View]  chr1:214454565-214510477 [Contig_View]  SMYD2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000143499 [Gene_View]  chr1:214454565-214510477 [Contig_View]  SMYD2 [Vega]
ICGC DataPortalENSG00000143499
TCGA cBioPortalSMYD2
AceView (NCBI)SMYD2
Genatlas (Paris)SMYD2
WikiGenes56950
SOURCE (Princeton)SMYD2
Genetics Home Reference (NIH)SMYD2
Genomic and cartography
GoldenPath hg19 (UCSC)SMYD2  -     chr1:214454565-214510477 +  1q32.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SMYD2  -     1q32.3   [Description]    (hg38-Dec_2013)
EnsemblSMYD2 - 1q32.3 [CytoView hg19]  SMYD2 - 1q32.3 [CytoView hg38]
Mapping of homologs : NCBISMYD2 [Mapview hg19]  SMYD2 [Mapview hg38]
OMIM610663   
Gene and transcription
Genbank (Entrez)AF070592 AF226053 AK091590 AK098683 AK313868
RefSeq transcript (Entrez)NM_020197
RefSeq genomic (Entrez)NC_000001 NC_018912 NT_004487 NW_004929294
Consensus coding sequences : CCDS (NCBI)SMYD2
Cluster EST : UnigeneHs.66170 [ NCBI ]
CGAP (NCI)Hs.66170
Alternative Splicing GalleryENSG00000143499
Gene ExpressionSMYD2 [ NCBI-GEO ]   SMYD2 [ EBI - ARRAY_EXPRESS ]   SMYD2 [ SEEK ]   SMYD2 [ MEM ]
Gene Expression Viewer (FireBrowse)SMYD2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)56950
GTEX Portal (Tissue expression)SMYD2
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NRG4   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NRG4  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NRG4
Splice isoforms : SwissVarQ9NRG4
Catalytic activity : Enzyme2.1.1.- [ Enzyme-Expasy ]   2.1.1.-2.1.1.- [ IntEnz-EBI ]   2.1.1.- [ BRENDA ]   2.1.1.- [ KEGG ]   
PhosPhoSitePlusQ9NRG4
Domaine pattern : Prosite (Expaxy)SET (PS50280)    ZF_MYND_1 (PS01360)    ZF_MYND_2 (PS50865)   
Domains : Interpro (EBI)SET_dom    TPR-like_helical_dom    Znf_MYND   
Domain families : Pfam (Sanger)SET (PF00856)    zf-MYND (PF01753)   
Domain families : Pfam (NCBI)pfam00856    pfam01753   
Domain families : Smart (EMBL)SET (SM00317)  
Conserved Domain (NCBI)SMYD2
DMDM Disease mutations56950
Blocks (Seattle)SMYD2
PDB (SRS)3RIB    3S7B    3S7D    3S7F    3S7J    3TG4    3TG5    4O6F    4WUY    4YND   
PDB (PDBSum)3RIB    3S7B    3S7D    3S7F    3S7J    3TG4    3TG5    4O6F    4WUY    4YND   
PDB (IMB)3RIB    3S7B    3S7D    3S7F    3S7J    3TG4    3TG5    4O6F    4WUY    4YND   
PDB (RSDB)3RIB    3S7B    3S7D    3S7F    3S7J    3TG4    3TG5    4O6F    4WUY    4YND   
Structural Biology KnowledgeBase3RIB    3S7B    3S7D    3S7F    3S7J    3TG4    3TG5    4O6F    4WUY    4YND   
SCOP (Structural Classification of Proteins)3RIB    3S7B    3S7D    3S7F    3S7J    3TG4    3TG5    4O6F    4WUY    4YND   
CATH (Classification of proteins structures)3RIB    3S7B    3S7D    3S7F    3S7J    3TG4    3TG5    4O6F    4WUY    4YND   
SuperfamilyQ9NRG4
Human Protein AtlasENSG00000143499
Peptide AtlasQ9NRG4
HPRD15406
IPIIPI00024641   IPI01018827   IPI00879642   IPI01015726   
Protein Interaction databases
DIP (DOE-UCLA)Q9NRG4
IntAct (EBI)Q9NRG4
FunCoupENSG00000143499
BioGRIDSMYD2
STRING (EMBL)SMYD2
ZODIACSMYD2
Ontologies - Pathways
QuickGOQ9NRG4
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II core binding  p53 binding  protein binding  nucleus  nucleoplasm  cytoplasm  cytosol  transcription, DNA-templated  heart development  negative regulation of cell proliferation  histone H3-K36 methylation  lysine N-methyltransferase activity  protein-lysine N-methyltransferase activity  histone-lysine N-methyltransferase activity  peptidyl-lysine monomethylation  peptidyl-lysine dimethylation  regulation of DNA damage response, signal transduction by p53 class mediator  metal ion binding  histone methyltransferase activity (H3-K36 specific)  regulation of signal transduction by p53 class mediator  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II core binding  p53 binding  protein binding  nucleus  nucleoplasm  cytoplasm  cytosol  transcription, DNA-templated  heart development  negative regulation of cell proliferation  histone H3-K36 methylation  lysine N-methyltransferase activity  protein-lysine N-methyltransferase activity  histone-lysine N-methyltransferase activity  peptidyl-lysine monomethylation  peptidyl-lysine dimethylation  regulation of DNA damage response, signal transduction by p53 class mediator  metal ion binding  histone methyltransferase activity (H3-K36 specific)  regulation of signal transduction by p53 class mediator  
REACTOMEQ9NRG4 [protein]
REACTOME Pathways3214841 [pathway]   6804760 [pathway]   
NDEx NetworkSMYD2
Atlas of Cancer Signalling NetworkSMYD2
Wikipedia pathwaysSMYD2
Orthology - Evolution
OrthoDB56950
GeneTree (enSembl)ENSG00000143499
Phylogenetic Trees/Animal Genes : TreeFamSMYD2
HOVERGENQ9NRG4
HOGENOMQ9NRG4
Homologs : HomoloGeneSMYD2
Homology/Alignments : Family Browser (UCSC)SMYD2
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMYD2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMYD2
dbVarSMYD2
ClinVarSMYD2
1000_GenomesSMYD2 
Exome Variant ServerSMYD2
ExAC (Exome Aggregation Consortium)SMYD2 (select the gene name)
Genetic variants : HAPMAP56950
Genomic Variants (DGV)SMYD2 [DGVbeta]
DECIPHER (Syndromes)1:214454565-214510477  ENSG00000143499
CONAN: Copy Number AnalysisSMYD2 
Mutations
ICGC Data PortalSMYD2 
TCGA Data PortalSMYD2 
Broad Tumor PortalSMYD2
OASIS PortalSMYD2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMYD2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMYD2
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SMYD2
DgiDB (Drug Gene Interaction Database)SMYD2
DoCM (Curated mutations)SMYD2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMYD2 (select a term)
intoGenSMYD2
NCG5 (London)SMYD2
Cancer3DSMYD2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610663   
Orphanet
MedgenSMYD2
Genetic Testing Registry SMYD2
NextProtQ9NRG4 [Medical]
TSGene56950
GENETestsSMYD2
Huge Navigator SMYD2 [HugePedia]
snp3D : Map Gene to Disease56950
BioCentury BCIQSMYD2
ClinGenSMYD2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD56950
Chemical/Pharm GKB GenePA134930268
Clinical trialSMYD2
Miscellaneous
canSAR (ICR)SMYD2 (select the gene name)
Probes
Litterature
PubMed35 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMYD2
EVEXSMYD2
GoPubMedSMYD2
iHOPSMYD2
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:49:45 CET 2017

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