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SATB1 (SATB homeobox 1)

Written2009-06Hunter Richards, Terumi Kohwi-Shigematsu
Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Bldg 84-155, University of California, Berkeley, 94720, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namesspecial AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)
Other alias
HGNC (Hugo) SATB1
LocusID (NCBI) 6304
Atlas_Id 44225
Location 3p24.3  [Link to chromosome band 3p24]
Location_base_pair Starts at 18345388 and ends at 18438773 bp from pter ( according to hg19-Feb_2009)  [Mapping SATB1.png]
 
Fusion genes
(updated 2016)
SATB1 (3p24.3) / SATB1 (3p24.3)SSR3 (3q25.31) / SATB1 (3p24.3)

DNA/RNA

Description The gene encompasses 93 kb of genomic DNA in mouse and 91 kb in humans both of which comprise 11 exons, 10 of which are coding.
Transcription GenBank references two mRNA transcript variants in humans: #1 is 5423 bp in length and #2 is 3908 bp. They have identical 3' UTRs whereas variant #1 has a longer 5' UTR. GenBank references one mRNA transcript in mouse: 2922 bp in length.

Protein

 
Description SATB1 is a 763 amino acid protein (~86 kDa molecular weight, migrates as 103kDa on SDS gels) containing six described domains: nuclear localization signal (NLS), PDZ, BUR-binding domain, two Cut repeats (CUT1 and CUT2), and homeodomain (HD). The PDZ domain is a protein-protein interaction module found mostly in signaling proteins. The BUR (Base Unpairing Region) domain is the module responsible for specific recognition of the BURs as opposed to any AT-rich sequence motif. The CUT domain is a DNA-binding motif. The BUR-binding domain includes CUT1 and part of the CUT2 domain. Homeodomains are DNA-binding motifs typically found in transcription factors. Together with the BUR domain and the HD domain, SATB1 confers specific binding with high affinity to the core unwinding elements of BURs. SATB1 is highly conserved between vertebrates.
Expression SATB1 mRNA is expressed abundantly in thymocytes. It is also detected in multiple other progenitor cells and brain neurons.
Localisation Nuclear.
Function SATB1 was identified by virtue of its high affinity and specificity to a DNA probe containing a nucleation site for base-unpairing, a phenomena whereby these sites become continuously unpaired under negative helical strain. Evidence suggests these base unpairing regions (BURs) mark the genome as essential components of chromosomes for tissue-specific gene expression and chromatin accessibility. SATB1 localization is nuclear exhibiting a cage- or honeycomb-like network distribution in thymocytes that is partially resistant to high-salt extraction and is excluded from the heterochromatin compartment. SATB1 tethers its target genes onto the SATB1 network via BURs which reside within the gene loci, and assembles them with chromatin remodeling and histone modification enzymes which SATB1 recruits. In this manner, SATB1 establishes a region-specific epigenetic status and proper nucleosomal positioning at the SATB1 target gene loci. SATB1 is essential for T-cell activation by controlling chromatin looping events, thus bringing remote cytokine genes together for simultaneous induction of these genes. SATB1 has been reported to interact with: CtBP1, SUMO-1, PIAS, Ubc9, PML, HDAC1, p300, RPB11, SNF2H (ISWI), Mi-2, MTA-2, and ACF1.
Homology SATB1 has 59.5% identity to SATB2 (mouse protein sequence; 46.6% for the human protein sequence).

Mutations

Note None identified.

Implicated in

Note
  
Entity Breast cancer
Prognosis In breast cancer SATB1 protein expression levels have high prognostic significance independent of lymph node status.
Oncogenesis In aggressive human breast cancer cell lines and in tissue samples from patients with aggressive breast tumors SATB1 protein is highly expressed. Ectopic expression of SATB1 in non-aggressive breast cancer cells induces metastasis, whereas depletion of SATB1 in highly-aggressive breast cancer cells reverses their metastatic capabilities and other tumorigenic characteristics.
  
  
Entity Acute myeloid leukemia (AML), and lymphoma
Oncogenesis SATB1 positively regulates the PU.1 gene by binding to its distal enhancer. PU.1 is a transcription factor important for B-cell and myeloid development. A single mutation in the distal enhancer dramatically reduces binding by SATB1. SATB1 was found to be an important factor of Xist (X-inactivation specific transcript) silencing in thymic lymphoma cells, potentially by stabilizing Xist transcripts.
  

Breakpoints

Note None known.

Bibliography

SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells.
Agrelo R, Souabni A, Novatchkova M, Haslinger C, Leeb M, Komnenovic V, Kishimoto H, Gresh L, Kohwi-Shigematsu T, Kenner L, Wutz A.
Dev Cell. 2009 Apr;16(4):507-16.
PMID 19386260
 
The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development.
Alvarez JD, Yasui DH, Niida H, Joh T, Loh DY, Kohwi-Shigematsu T.
Genes Dev. 2000 Mar 1;14(5):521-35.
PMID 10716941
 
Tissue-specific nuclear architecture and gene expression regulated by SATB1.
Cai S, Han HJ, Kohwi-Shigematsu T.
Nat Genet. 2003 May;34(1):42-51.
PMID 12692553
 
SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes.
Cai S, Lee CC, Kohwi-Shigematsu T.
Nat Genet. 2006 Nov;38(11):1278-88. Epub 2006 Oct 22.
PMID 17057718
 
An atypical homeodomain in SATB1 promotes specific recognition of the key structural element in a matrix attachment region.
Dickinson LA, Dickinson CD, Kohwi-Shigematsu T.
J Biol Chem. 1997 Apr 25;272(17):11463-70.
PMID 9111059
 
SATB1 cleavage by caspase 6 disrupts PDZ domain-mediated dimerization, causing detachment from chromatin early in T-cell apoptosis.
Galande S, Dickinson LA, Mian IS, Sikorska M, Kohwi-Shigematsu T.
Mol Cell Biol. 2001 Aug;21(16):5591-604.
PMID 11463840
 
SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis.
Han HJ, Russo J, Kohwi Y, Kohwi-Shigematsu T.
Nature. 2008 Mar 13;452(7184):187-93.
PMID 18337816
 
Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus.
Kumar PP, Bischof O, Purbey PK, Notani D, Urlaub H, Dejean A, Galande S.
Nat Cell Biol. 2007 Jan;9(1):45-56. Epub 2006 Dec 17.
PMID 17173041
 
A novel DNA-binding motif in the nuclear matrix attachment DNA-binding protein SATB1.
Nakagomi K, Kohwi Y, Dickinson LA, Kohwi-Shigematsu T.
Mol Cell Biol. 1994 Mar;14(3):1852-60.
PMID 8114718
 
A nuclear targeting determinant for SATB1, a genome organizer in the T cell lineage.
Nakayama Y, Mian IS, Kohwi-Shigematsu T, Ogawa T.
Cell Cycle. 2005 Aug;4(8):1099-106. Epub 2005 Aug 20.
PMID 15970696
 
Phosphorylation of SATB1, a global gene regulator, acts as a molecular switch regulating its transcriptional activity in vivo.
Pavan Kumar P, Purbey PK, Sinha CK, Notani D, Limaye A, Jayani RS, Galande S.
Mol Cell. 2006 Apr 21;22(2):231-43.
PMID 16630892
 
A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia.
Steidl U, Steidl C, Ebralidze A, Chapuy B, Han HJ, Will B, Rosenbauer F, Becker A, Wagner K, Koschmieder S, Kobayashi S, Costa DB, Schulz T, O'Brien KB, Verhaak RG, Delwel R, Haase D, Trumper L, Krauter J, Kohwi-Shigematsu T, Griesinger F, Tenen DG.
J Clin Invest. 2007 Sep;117(9):2611-20.
PMID 17694175
 
SATB1 targets chromatin remodelling to regulate genes over long distances.
Yasui D, Miyano M, Cai S, Varga-Weisz P, Kohwi-Shigematsu T.
Nature. 2002 Oct 10;419(6907):641-5.
PMID 12374985
 
The genomic sequences bound to special AT-rich sequence-binding protein 1 (SATB1) in vivo in Jurkat T cells are tightly associated with the nuclear matrix at the bases of the chromatin loops.
de Belle I, Cai S, Kohwi-Shigematsu T.
J Cell Biol. 1998 Apr 20;141(2):335-48.
PMID 9548713
 

Citation

This paper should be referenced as such :
Richards, H ; Kohwi-Shigematsu, T
SATB1 (SATB homeobox 1)
Atlas Genet Cytogenet Oncol Haematol. 2010;14(5):479-481.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SATB1ID44225ch3p24.html


External links

Nomenclature
HGNC (Hugo)SATB1   10541
Cards
AtlasSATB1ID44225ch3p24
Entrez_Gene (NCBI)SATB1  6304  SATB homeobox 1
Aliases
GeneCards (Weizmann)SATB1
Ensembl hg19 (Hinxton)ENSG00000182568 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000182568 [Gene_View]  chr3:18345388-18438773 [Contig_View]  SATB1 [Vega]
ICGC DataPortalENSG00000182568
TCGA cBioPortalSATB1
AceView (NCBI)SATB1
Genatlas (Paris)SATB1
WikiGenes6304
SOURCE (Princeton)SATB1
Genetics Home Reference (NIH)SATB1
Genomic and cartography
GoldenPath hg38 (UCSC)SATB1  -     chr3:18345388-18438773 -  3p24.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SATB1  -     3p24.3   [Description]    (hg19-Feb_2009)
EnsemblSATB1 - 3p24.3 [CytoView hg19]  SATB1 - 3p24.3 [CytoView hg38]
Mapping of homologs : NCBISATB1 [Mapview hg19]  SATB1 [Mapview hg38]
OMIM602075   
Gene and transcription
Genbank (Entrez)AA001621 AB209761 AK124253 AK127242 AU127749
RefSeq transcript (Entrez)NM_001131010 NM_001195470 NM_001322871 NM_001322872 NM_001322873 NM_001322874 NM_001322875 NM_001322876 NM_002971
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SATB1
Cluster EST : UnigeneHs.593276 [ NCBI ]
CGAP (NCI)Hs.593276
Alternative Splicing GalleryENSG00000182568
Gene ExpressionSATB1 [ NCBI-GEO ]   SATB1 [ EBI - ARRAY_EXPRESS ]   SATB1 [ SEEK ]   SATB1 [ MEM ]
Gene Expression Viewer (FireBrowse)SATB1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6304
GTEX Portal (Tissue expression)SATB1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ01826   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ01826  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ01826
Splice isoforms : SwissVarQ01826
PhosPhoSitePlusQ01826
Domaine pattern : Prosite (Expaxy)CUT (PS51042)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)CUT_dom    CUTL    Homeobox-like    Homeobox_dom    Lambda_DNA-bd_dom    ULD   
Domain families : Pfam (Sanger)CUT (PF02376)    CUTL (PF16557)    Homeobox (PF00046)    ULD (PF16534)   
Domain families : Pfam (NCBI)pfam02376    pfam16557    pfam00046    pfam16534   
Domain families : Smart (EMBL)CUT (SM01109)  HOX (SM00389)  
Conserved Domain (NCBI)SATB1
DMDM Disease mutations6304
Blocks (Seattle)SATB1
PDB (SRS)1YSE    2L1P    2MW8    2O49    2O4A    3NZL    3TUO   
PDB (PDBSum)1YSE    2L1P    2MW8    2O49    2O4A    3NZL    3TUO   
PDB (IMB)1YSE    2L1P    2MW8    2O49    2O4A    3NZL    3TUO   
PDB (RSDB)1YSE    2L1P    2MW8    2O49    2O4A    3NZL    3TUO   
Structural Biology KnowledgeBase1YSE    2L1P    2MW8    2O49    2O4A    3NZL    3TUO   
SCOP (Structural Classification of Proteins)1YSE    2L1P    2MW8    2O49    2O4A    3NZL    3TUO   
CATH (Classification of proteins structures)1YSE    2L1P    2MW8    2O49    2O4A    3NZL    3TUO   
SuperfamilyQ01826
Human Protein AtlasENSG00000182568
Peptide AtlasQ01826
HPRD03647
IPIIPI00009804   IPI00555719   IPI00925809   IPI00926916   IPI00926252   IPI00925653   IPI00924983   IPI00926120   IPI00925426   
Protein Interaction databases
DIP (DOE-UCLA)Q01826
IntAct (EBI)Q01826
FunCoupENSG00000182568
BioGRIDSATB1
STRING (EMBL)SATB1
ZODIACSATB1
Ontologies - Pathways
QuickGOQ01826
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II regulatory region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  chromatin binding  double-stranded DNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  nuclear heterochromatin  chromatin organization  chromatin remodeling  transcription, DNA-templated  epidermis development  viral process  nuclear matrix  histone methylation  nuclear body  PML body  CD4-positive, alpha-beta T cell differentiation  CD8-positive, alpha-beta T cell differentiation  activated T cell proliferation  reflex  execution phase of apoptosis  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II regulatory region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  chromatin binding  double-stranded DNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  nuclear heterochromatin  chromatin organization  chromatin remodeling  transcription, DNA-templated  epidermis development  viral process  nuclear matrix  histone methylation  nuclear body  PML body  CD4-positive, alpha-beta T cell differentiation  CD8-positive, alpha-beta T cell differentiation  activated T cell proliferation  reflex  execution phase of apoptosis  
REACTOMEQ01826 [protein]
REACTOME PathwaysR-HSA-111465 [pathway]   
NDEx NetworkSATB1
Atlas of Cancer Signalling NetworkSATB1
Wikipedia pathwaysSATB1
Orthology - Evolution
OrthoDB6304
GeneTree (enSembl)ENSG00000182568
Phylogenetic Trees/Animal Genes : TreeFamSATB1
HOVERGENQ01826
HOGENOMQ01826
Homologs : HomoloGeneSATB1
Homology/Alignments : Family Browser (UCSC)SATB1
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSATB1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SATB1
dbVarSATB1
ClinVarSATB1
1000_GenomesSATB1 
Exome Variant ServerSATB1
ExAC (Exome Aggregation Consortium)SATB1 (select the gene name)
Genetic variants : HAPMAP6304
Genomic Variants (DGV)SATB1 [DGVbeta]
DECIPHERSATB1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSATB1 
Mutations
ICGC Data PortalSATB1 
TCGA Data PortalSATB1 
Broad Tumor PortalSATB1
OASIS PortalSATB1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSATB1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSATB1
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 SATB1
DgiDB (Drug Gene Interaction Database)SATB1
DoCM (Curated mutations)SATB1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SATB1 (select a term)
intoGenSATB1
NCG5 (London)SATB1
Cancer3DSATB1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602075   
Orphanet
MedgenSATB1
Genetic Testing Registry SATB1
NextProtQ01826 [Medical]
TSGene6304
GENETestsSATB1
Target ValidationSATB1
Huge Navigator SATB1 [HugePedia]
snp3D : Map Gene to Disease6304
BioCentury BCIQSATB1
ClinGenSATB1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6304
Chemical/Pharm GKB GenePA34951
Clinical trialSATB1
Miscellaneous
canSAR (ICR)SATB1 (select the gene name)
Probes
Litterature
PubMed138 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSATB1
EVEXSATB1
GoPubMedSATB1
iHOPSATB1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 18 17:14:03 CEST 2017

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