Human Gene SUV39H1 (uc004dkn.3) Description and Page Index
  Description: Homo sapiens suppressor of variegation 3-9 homolog 1 (Drosophila) (SUV39H1), mRNA.
RefSeq Summary (NM_003173): This gene encodes an evolutionarily-conserved protein containing an N-terminal chromodomain and a C-terminal SET domain. The encoded protein is a histone methyltransferase that trimethylates lysine 9 of histone H3, which results in transcriptional gene silencing. Loss of function of this gene disrupts heterochromatin formation and may cause chromosome instability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013].
Transcript (Including UTRs)
   Position: hg19 chrX:48,555,131-48,567,406 Size: 12,276 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chrX:48,555,176-48,565,961 Size: 10,786 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chrX:48,555,131-48,567,406)mRNA (may differ from genome)Protein (412 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Histone-lysine N-methyltransferase SUV39H1; EC=; AltName: Full=Histone H3-K9 methyltransferase 1; Short=H3-K9-HMTase 1; AltName: Full=Lysine N-methyltransferase 1A; AltName: Full=Position-effect variegation 3-9 homolog; AltName: Full=Suppressor of variegation 3-9 homolog 1; Short=Su(var)3-9 homolog 1;
FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3 using monomethylated H3 'Lys- 9' as substrate. Also weakly methylates histone H1 (in vitro). H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. H3 'Lys-9' trimethylation is also required to direct DNA methylation at pericentric repeats. SUV39H1 is targeted to histone H3 via its interaction with RB1 and is involved in many processes, such as repression of MYOD1-stimulated differentiation, regulation of the control switch for exiting the cell cycle and entering differentiation, repression by the PML-RARA fusion protein, BMP-induced repression, repression of switch recombination to IgA and regulation of telomere length. Component of the eNoSC (energy-dependent nucleolar silencing) complex, a complex that mediates silencing of rDNA in response to intracellular energy status and acts by recruiting histone- modifying enzymes. The eNoSC complex is able to sense the energy status of cell: upon glucose starvation, elevation of NAD(+)/NADP(+) ratio activates SIRT1, leading to histone H3 deacetylation followed by dimethylation of H3 at 'Lys-9' (H3K9me2) by SUV39H1 and the formation of silent chromatin in the rDNA locus.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
ENZYME REGULATION: Inhibited by S-adenosyl-L-homocysteine. Negatively regulated by KIAA1967/DBC1.
SUBUNIT: Interacts with H3 and H4 histones. Interacts with GFI1B, DNMT3B, CBX1, CBX4, KIAA1967/DBC1, MBD1, RUNX1, RUNX3, MYOD1, SMAD5 and RB1. Interacts with SBF1 through the SET domain. Interacts with HDAC1 and HDAC2 through the N-terminus and associates with the core histone deacetylase complex composed of HDAC1, HDAC2, RBBP4 and RBBP7. Component of the eNoSC complex, composed of SIRT1, SUV39H1 and RRP8. In case of infection, interacts with HTLV-1 Tax protein, leading to abrogate Tax transactivation of HTLV-1 LTR. Interacts (via SET domain) with MECOM; enhances MECOM transcriptional repression activity (By similarity).
INTERACTION: P68432:- (xeno); NbExp=2; IntAct=EBI-349968, EBI-79764; P45973:CBX5; NbExp=3; IntAct=EBI-349968, EBI-78219; Q13547:HDAC1; NbExp=3; IntAct=EBI-349968, EBI-301834; Q92769:HDAC2; NbExp=3; IntAct=EBI-349968, EBI-301821; Q9UIS9:MBD1; NbExp=5; IntAct=EBI-349968, EBI-867196; O43159:RRP8; NbExp=3; IntAct=EBI-349968, EBI-2008793;
SUBCELLULAR LOCATION: Nucleus. Chromosome, centromere. Note=Associates with centromeric constitutive heterochromatin.
DEVELOPMENTAL STAGE: Accumulates during mitosis at centromeres during prometaphase, but dissociates from the centromere at the meta- to anaphase transition.
DOMAIN: Although the SET domain contains the active site of enzymatic activity, both pre-SET and post-SET domains are required for methyltransferase activity. The SET domain also participates to stable binding to heterochromatin.
PTM: Phosphorylated on serine residues, and to a lesser degree, on threonine residues. The phosphorylated form is stabilized by SBF1 and is less active in its transcriptional repressor function.
PTM: Acetylated at Lys-266, leading to inhibition of enzyme activity. SIRT1-mediated deacetylation relieves this inhibition.
SIMILARITY: Belongs to the histone-lysine methyltransferase family. Suvar3-9 subfamily.
SIMILARITY: Contains 1 chromo domain.
SIMILARITY: Contains 1 post-SET domain.
SIMILARITY: Contains 1 pre-SET domain.
SIMILARITY: Contains 1 SET domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.63 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 130.95 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -14.1045-0.313 Picture PostScript Text
3' UTR -589.521445-0.408 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR023779 - Chromodomain_CS
IPR011381 - Histone_H3-K9_MeTrfase
IPR003616 - Post-SET_dom
IPR007728 - Pre-SET_dom
IPR003606 - Pre-SET_Zn-bd_sub
IPR001214 - SET_dom

Pfam Domains:
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF00856 - SET domain
PF05033 - Pre-SET motif

SCOP Domains:
54160 - Chromo domain-like
82199 - SET domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on O43463
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Protein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0042054 histone methyltransferase activity
GO:0046872 metal ion binding
GO:0046974 histone methyltransferase activity (H3-K9 specific)
GO:0047485 protein N-terminus binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000183 chromatin silencing at rDNA
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006364 rRNA processing
GO:0006974 cellular response to DNA damage stimulus
GO:0007049 cell cycle
GO:0016032 viral process
GO:0030154 cell differentiation
GO:0032259 methylation
GO:0034968 histone lysine methylation
GO:0036123 histone H3-K9 dimethylation
GO:0036124 histone H3-K9 trimethylation
GO:0042754 negative regulation of circadian rhythm
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048511 rhythmic process
GO:0071456 cellular response to hypoxia

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000792 heterochromatin
GO:0000794 condensed nuclear chromosome
GO:0005634 nucleus
GO:0005652 nuclear lamina
GO:0005654 nucleoplasm
GO:0005677 chromatin silencing complex
GO:0005694 chromosome
GO:0033553 rDNA heterochromatin

-  Descriptions from all associated GenBank mRNAs
  AK299900 - Homo sapiens cDNA FLJ57812 complete cds, highly similar to Histone-lysine N-methyltransferase, H3 lysine-9 specific 1 (EC
AF019968 - Homo sapiens Su(var)3-9 homolog (SUV39H) mRNA, complete cds.
BC006238 - Homo sapiens suppressor of variegation 3-9 homolog 1 (Drosophila), mRNA (cDNA clone MGC:10376 IMAGE:3945632), complete cds.
AK298233 - Homo sapiens cDNA FLJ51508 complete cds.
AK312547 - Homo sapiens cDNA, FLJ92918, Homo sapiens suppressor of variegation 3-9 homolog 1 (Drosophila)(SUV39H1), mRNA.
AK223071 - Homo sapiens mRNA for suppressor of variegation 3-9 homolog 1 variant, clone: KAT02327.
JD409693 - Sequence 390717 from Patent EP1572962.
JD499283 - Sequence 480307 from Patent EP1572962.
KJ892234 - Synthetic construct Homo sapiens clone ccsbBroadEn_01628 SUV39H1 gene, encodes complete protein.
CU675305 - Synthetic construct Homo sapiens gateway clone IMAGE:100019282 5' read SUV39H1 mRNA.
AB528514 - Synthetic construct DNA, clone: pF1KB6611, Homo sapiens SUV39H1 gene for suppressor of variegation 3-9 homolog 1, without stop codon, in Flexi system.
DQ895848 - Synthetic construct Homo sapiens clone IMAGE:100010308; FLH188279.01L; RZPDo839A0963D suppressor of variegation 3-9 homolog 1 (Drosophila) (SUV39H1) gene, encodes complete protein.
CR541746 - Homo sapiens full open reading frame cDNA clone RZPDo834E0729D for gene SUV39H1, suppressor of variegation 3-9 homolog 1 (Drosophila); complete cds, incl. stopcodon.
DQ892608 - Synthetic construct clone IMAGE:100005238; FLH188283.01X; RZPDo839A0973D suppressor of variegation 3-9 homolog 1 (Drosophila) (SUV39H1) gene, encodes complete protein.
AK297566 - Homo sapiens cDNA FLJ51507 complete cds, highly similar to Histone-lysine N-methyltransferase, H3lysine-9 specific 1 (EC
L08238 - Human MG44 mRNA, 5' end.
JD153987 - Sequence 135011 from Patent EP1572962.
JD059414 - Sequence 40438 from Patent EP1572962.
JD446003 - Sequence 427027 from Patent EP1572962.
JD099518 - Sequence 80542 from Patent EP1572962.
JD423981 - Sequence 405005 from Patent EP1572962.
JD151843 - Sequence 132867 from Patent EP1572962.
JD340530 - Sequence 321554 from Patent EP1572962.
JD403773 - Sequence 384797 from Patent EP1572962.
JD166868 - Sequence 147892 from Patent EP1572962.
JD459709 - Sequence 440733 from Patent EP1572962.
JD245363 - Sequence 226387 from Patent EP1572962.
JD493982 - Sequence 475006 from Patent EP1572962.
JD356076 - Sequence 337100 from Patent EP1572962.
JD452904 - Sequence 433928 from Patent EP1572962.
JD074654 - Sequence 55678 from Patent EP1572962.
JD160154 - Sequence 141178 from Patent EP1572962.
JD062882 - Sequence 43906 from Patent EP1572962.
JD270307 - Sequence 251331 from Patent EP1572962.
JD115271 - Sequence 96295 from Patent EP1572962.
JD115272 - Sequence 96296 from Patent EP1572962.
JD052680 - Sequence 33704 from Patent EP1572962.
JD378032 - Sequence 359056 from Patent EP1572962.
JD469355 - Sequence 450379 from Patent EP1572962.
JD209397 - Sequence 190421 from Patent EP1572962.
JD342022 - Sequence 323046 from Patent EP1572962.
JD375551 - Sequence 356575 from Patent EP1572962.
JD242164 - Sequence 223188 from Patent EP1572962.
JD559148 - Sequence 540172 from Patent EP1572962.
JD205301 - Sequence 186325 from Patent EP1572962.
JD066015 - Sequence 47039 from Patent EP1572962.
JD193842 - Sequence 174866 from Patent EP1572962.
JD357925 - Sequence 338949 from Patent EP1572962.
JD500131 - Sequence 481155 from Patent EP1572962.
JD516665 - Sequence 497689 from Patent EP1572962.
JD302463 - Sequence 283487 from Patent EP1572962.
JD178006 - Sequence 159030 from Patent EP1572962.
AF075109 - Homo sapiens full length insert cDNA YU40D04.
JD174404 - Sequence 155428 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00310 - Lysine degradation

Reactome (by CSHL, EBI, and GO)

Protein O43463 (Reactome details) participates in the following event(s):

R-HSA-427528 Formation of energy-dependent Nucleolar Silencing Complex (eNoSC)
R-HSA-427514 eNoSC deacetylates histone H3
R-HSA-427527 eNoSC dimethylates histone H3 at lysine-9
R-HSA-4827382 SUV39H1 (KMT1A), SUV39H2 (KTM1B), SETDB1 (KMT1E), SETDB2 (KMT1F) methylate dimethyl-lysine-10 of histone H3 (H3K9)
R-HSA-427359 SIRT1 negatively regulates rRNA expression
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-3214841 PKMTs methylate histone lysines
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-74160 Gene expression (Transcription)
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6E8, KMT1A, NM_003173, NP_003164, O43463, Q53G60, Q6FHK6, SUV39H, SUV91_HUMAN
UCSC ID: uc004dkn.3
RefSeq Accession: NM_003173
Protein: O43463 (aka SUV91_HUMAN or SU91_HUMAN)
CCDS: CCDS14304.1, CCDS65252.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_003173.2
exon count: 6CDS single in 3' UTR: no RNA size: 2745
ORF size: 1239CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2667.00frame shift in genome: no % Coverage: 99.42
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.