Selected-GenAtlas references SOURCE GeneCards NCBI Gene Swiss-Prot Ensembl
HGNC UniGene Nucleotide OMIM UCSC
Home Page
Symbol SETDB1 contributors: mct/pgu - updated : 17-01-2014
HGNC name SET domain, bifurcated 1
HGNC id 10761
Location 1q21.3      Physical location : 150.898.814 - 150.937.220
Synonym name
  • ERG-associated protein with SET domain
  • histone-lysine N-methyltransferase, H3lysine-9 specific 4
  • histone-lysine N-methyltransferase SETDB1
  • H3-K9-HMTase 4
  • lysine N-methyltransferase 1E
  • histone H3-K9 methyltransferase 4
  • Synonym symbol(s) KIAA0067, ESET, KG1T, KMT1E
    TYPE functioning gene
    STRUCTURE 38.57 kb     22 Exon(s)
    Genomic sequence alignment details
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked N status confirmed
    Map cen - D1S514 - D1S2347 - SETDB1 - D1S2858 - D1S305 - D1S2635 - qter
    Authors GeneMap (98)
    Physical map
    FLJ12528 1q21.3 threonyl-tRNA synthetase ECM1 1q21.1-q21.2 extracellular matrix protein 1 TSRC1 1q21.3 thrombospondin repeat containing 1 FLJ13544 1q21.3 hypothetical protein FLJ13544 MCL1 1q21 myeloid cell leukemia sequence 1 (BCL2-related) ENSA 1q21.2 endosulfine alpha GPP34R 1q21.3 GPP34-related protein DKFZP434A1315 1q21.3 hypothetical protein DKFZp434A1315 CTSS 1q21 cathepsin S CTSK 1q21 cathepsin K (pycnodysostosis) ARNT 1q21 aryl hydrocarbon receptor nuclear translocator HCP1 1q21.3 cytochrome c, somatic pseudogene SETDB1 1q21 SET domain, bifurcated 1 LASS2 1q11 LAG1 longevity assurance homolog 2 (S. cerevisiae) ANXA9 1q21 annexin A9 FLJ11280 1q21.3 hypothetical protein FLJ11280 BNIPL 1q21.2 BCL2/adenovirus E1B 19kD interacting protein like HTCD37 1q21 TcD37 homolog FLJ20519 1q21.3 hypothetical protein FLJ20519 SPEC1 1q21.2 hypothetical protein FLJ20519 AF1Q 1q21 hypothetical protein FLJ20519 MGC29891 1q21.3 hypothetical protein MGC29891 SEMA6C 1q21.2 sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C FLJ23467 1q21.3 hypothetical protein FLJ23467 LOC388695 1 similar to hypothetical protein SB145 SCNM1 1q21.3 sodium channel modifier 1 TMOD4 1q12 tropomodulin 4 (muscle) TCFL1 1q21 transcription factor-like 1 PIP5K1A 1q22-q24 phosphatidylinositol-4-phosphate 5-kinase, type I, alpha PSMD4 1q21.3 proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 KIAA1441 1q21.3 KIAA1441 protein PIK4CB 1q21 phosphatidylinositol 4-kinase, catalytic, beta polypeptide RFX5 1q21 regulatory factor X, 5 (influences HLA class II expression) SELENBP1 1q21-q22 selenium binding protein 1 PSMB4 1q21 proteasome (prosome, macropain) subunit, beta type, 4 POGZ 1q21.1 pogo transposable element with ZNF domain
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    22 - 4449 - 1291 - 1994 7584044
    22 - 4446 - 1290 - -
    9 - 1507 - 397 - -
    Type widely
       expressed in (based on citations)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestivemouth   highly
     thymus   highly
     tonsils   highly
    Nervousbrain   highly Mus musculusFetal
    Reproductivefemale systembreastmammary gland  
     male systemtestis  highly
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Blood / Hematopoieticbone marrow   
    cell lineage
    cell lines
    at STAGE
  • N-terminal tudor domain, mediating protein-protein interactions region and a SUMO interaction motif (SIM) whose mutation greatly reduced the ability of SETDB1 to associate with promyelocytic leukemia nuclear body (PML-NB) , related to the nuclear export of SETDB1, and having two nuclear export signal motifs
  • a pre-set and post-set domains are all required for methyltransferase activity
  • one methyl-binding (MBD) domain
  • C-terminal SET domain that catalyzes methylation of histone H3 at lysine 9, an unusual bifurcated SET domain, multifunctional chromatin regulator (130AA)
  • conjugated PhosphoP
    mono polymer complex
    interspecies homolog to murine Setdb1 (92.5pc)
    homolog to rattus Setdb1 (94.5pc)
  • histone-lysine methyltransferase family
  • Suvar3-9 subfamily
  • CATEGORY enzyme
    SUBCELLULAR LOCALIZATION     plasma membrane
  • associated with non pericentromeric regions of chromatin
  • excluded from nucleoli and islands of condensed chromatin
  • basic FUNCTION
  • contributing to silencing of euchromatic genes by KRAB zinc-finger proteins
  • histone H3 (K9) methyltransferase, mediating histone methylation
  • functioning in transcription regulation and modification of local chromatin and involved in maintaining hetrochromatin
  • coordinates with AKT1 to silence gene expression
  • chromatin-associated protein, effector of SUMO-dependent changes in chromatin structure and gene expression
  • essential role in the control of developmentally regulated gene expression programs in embryonic stem (ES) cells
  • epigenetic role in the temporal and tissue-specific gene expression that results in proper control of brain development
  • controls hypertrophic differentiation of growth plate chondrocytes and endochondral ossification during embryogenesis and postnatal development
  • its expression plays an essential role in the maintenance of articular cartilage by preventing articular chondrocytes from terminal differentiation and may have implications in joint diseases such as osteoarthritis
  • is a critical regulator of osteoblast differentiation during bone development
  • CELLULAR PROCESS nucleotide, chromatin organization, methylation
    nucleotide, transcription, regulation
    a component
  • complexing with ATF7IP/MDB1 (complex facilitating the formation of heterochromatic domains, and emphasizing the role of MCAF/AM family proteins in epigenetic control)
  • complex at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1
  • associating with CHAF1B-CBX5 chaperone complex and monomethylating K9 on non nucleosomal histone H3, thus providing H3K9me1 for subsequent trimethylation by SUV39H1/H2 in pericentric regions
  • forms a multimeric complex with SUV39H1 and other H3K9 methyltransferases
    small molecule
  • TRIM28, ERG
  • interacting with ESCO2
  • interacting with CBX1, CBX5, DNMT3A, HDAC1, HDAC2
  • interacting with SIN3A, SIN3B, DNMT3B and SUMO2
  • can bind to HIV-1 Tat and methylate it, thus regulating the transcriptional activity of the viral LTR
  • nuclear interacting partner of AKT1
  • ZNF274 binding sites co-localize with SETDB1, TRIM28, and H3K9me3 at the 3prime ends of zinc finger genes
  • JARID2 functions as a transcriptional repressor of target genes, including NOTCH1, through a novel process involving the modification of H3K9 methylation via specific interaction with SETDB1 during heart development
  • MAT2A interacts with histone methyltransferase SETDB1 and inhibits PTGS2 gene expression
  • associates with histone deacetylase 4 to bind and inhibit the activity of RUNX2, a hypertrophy-promoting transcription factor
  • cell & other
    Other targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins
    corresponding disease(s)
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    constitutional     --over  
    markedly increased in Huntington's disease
    tumoral   amplification    
    focally amplified in non-small-cell lung cancer, small-cell lung cancer, ovarian cancer, hepatocellular carcinoma and breast cancer
    tumoral     --over  
    may potentially contribute to melanoma formation by abrogating oncogene-induced senescence
    Variant & Polymorphism
    Candidate gene
    Therapy target
    neurologyneurodegenerativehuntington chorea
    regulation of the gene is important to neuronal survival and, as such, may be a promising treatment in HD patients
  • Eset-deficient mice are thus characterized by defective long bone growth and trabecular bone formation