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LDB1 (LIM domain binding 1)

Written2006-11Takeshi Setogawa, Testu Akiyama
Laboratory of Molecular and Genetic Information, Institute for Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)NLI
CLIM2
Other alias
HGNC (Hugo) LDB1
LocusID (NCBI) 8861
Atlas_Id 41135
Location 10q24.32  [Link to chromosome band 10q24]
Location_base_pair Starts at 102106492 and ends at 102120473 bp from pter ( according to hg19-Feb_2009)  [Mapping LDB1.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
LDB1 (10q24.32) / LDB1 (10q24.32)PRICKLE4 (6p21.1) / LDB1 (10q24.32)

DNA/RNA

Description 7kb; 11exons
Transcription 2292 nucleotides mRNA

Protein

Description 375 amino acids; 42.8 kDa protein
Expression Widely expressed
Localisation Nuclear
Function LDB1 is a nuclear protein that contains an N-terminal dimerization domain and a C-terminal LIM interaction domain (LID). LDB1 binds to LIM-homeodomain (LIM-HD) and LIM-only (LMO) proteins. It acts as an adaptor protein that mediates interactions between different classes of transcription factors and their cofactors. LDB1 forms a complex with LKB1, LMO4, and GATA-6. The tumor suppressor LKB1is mutated in Peutz Jeghers syndrome and various sporadic cancers. A complex containing LDB1, LKB1, LMO4, and GATA-6 induces cyclin-dependent kinase inhibitor p21 expression. Targeted deletion of the Ldb1 gene in mice displays multiple developmental defects that reveal a requirement of Ldb1 gene during normal development.

Implicated in

Note
  
Entity Oral squamous cell carcinoma
Oncogenesis LDB1 and LMO4 are frequently detected in less-differentiated and metastasized squamous carcinoma, and overexpressed at the carcinoma invasive front.
  

Bibliography

Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins.
Agulnick AD, Taira M, Breen JJ, Tanaka T, Dawid IB, Westphal H
Nature. 1996 ; 384 (6606) : 270-272.
PMID 8918878
 
A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins.
Bach I, Carrière C, Ostendorff HP, Andersen B, Rosenfeld MG
Genes & development. 1997 ; 11 (11) : 1370-1380.
PMID 9192866
 
Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development.
Chen L, Segal D, Hukriede NA, Podtelejnikov AV, Bayarsaihan D, Kennison JA, Ogryzko VV, Dawid IB, Westphal H
Proceedings of the National Academy of Sciences of the United States of America. 2002 ; 99 (22) : 14320-14325.
PMID 12381786
 
Functional analysis of the nuclear LIM domain interactor NLI.
Jurata LW, Gill GN
Molecular and cellular biology. 1997 ; 17 (10) : 5688-5698.
PMID 9315627
 
LIM-domain-binding protein 1: a multifunctional cofactor that interacts with diverse proteins.
Matthews JM, Visvader JE
EMBO reports. 2003 ; 4 (12) : 1132-1137.
PMID 14647207
 
The LIM-only protein, LMO4, and the LIM domain-binding protein, LDB1, expression in squamous cell carcinomas of the oral cavity.
Mizunuma H, Miyazawa J, Sanada K, Imai K
British journal of cancer. 2003 ; 88 (10) : 1543-1548.
PMID 12771919
 
Functional ablation of the mouse Ldb1 gene results in severe patterning defects during gastrulation.
Mukhopadhyay M, Teufel A, Yamashita T, Agulnick AD, Chen L, Downs KM, Schindler A, Grinberg A, Huang SP, Dorward D, Westphal H
Development (Cambridge, England). 2003 ; 130 (3) : 495-505.
PMID 12490556
 
The tumor suppressor LKB1 induces p21 expression in collaboration with LMO4, GATA-6, and Ldb1.
Setogawa T, Shinozaki-Yabana S, Masuda T, Matsuura K, Akiyama T
Biochemical and biophysical research communications. 2006 ; 343 (4) : 1186-1190.
PMID 16580634
 
The LIM-domain binding protein Ldb1 and its partner LMO2 act as negative regulators of erythroid differentiation.
Visvader JE, Mao X, Fujiwara Y, Hahm K, Orkin SH
Proceedings of the National Academy of Sciences of the United States of America. 1997 ; 94 (25) : 13707-13712.
PMID 9391090
 

Citation

This paper should be referenced as such :
Akiyama, T ; Setogawa, T
LDB1 (LIM domain binding 1)
Atlas Genet Cytogenet Oncol Haematol. 2007;11(3):167-168.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/LDB1ID41135ch10q24.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  del(11)(p12p13) LMO2


External links

Nomenclature
HGNC (Hugo)LDB1   6532
Cards
AtlasLDB1ID41135ch10q24
Entrez_Gene (NCBI)LDB1  8861  LIM domain binding 1
AliasesCLIM-2; CLIM2; LDB-1; NLI
GeneCards (Weizmann)LDB1
Ensembl hg19 (Hinxton)ENSG00000198728 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000198728 [Gene_View]  chr10:102106492-102120473 [Contig_View]  LDB1 [Vega]
ICGC DataPortalENSG00000198728
TCGA cBioPortalLDB1
AceView (NCBI)LDB1
Genatlas (Paris)LDB1
WikiGenes8861
SOURCE (Princeton)LDB1
Genetics Home Reference (NIH)LDB1
Genomic and cartography
GoldenPath hg38 (UCSC)LDB1  -     chr10:102106492-102120473 -  10q24.32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LDB1  -     10q24.32   [Description]    (hg19-Feb_2009)
EnsemblLDB1 - 10q24.32 [CytoView hg19]  LDB1 - 10q24.32 [CytoView hg38]
Mapping of homologs : NCBILDB1 [Mapview hg19]  LDB1 [Mapview hg38]
OMIM603451   
Gene and transcription
Genbank (Entrez)AB016485 AB250384 AF064491 AF068652 AK300588
RefSeq transcript (Entrez)NM_001113407 NM_001321612 NM_003893
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LDB1
Cluster EST : UnigeneHs.672935 [ NCBI ]
CGAP (NCI)Hs.672935
Alternative Splicing GalleryENSG00000198728
Gene ExpressionLDB1 [ NCBI-GEO ]   LDB1 [ EBI - ARRAY_EXPRESS ]   LDB1 [ SEEK ]   LDB1 [ MEM ]
Gene Expression Viewer (FireBrowse)LDB1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8861
GTEX Portal (Tissue expression)LDB1
Human Protein AtlasENSG00000198728-LDB1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ86U70   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ86U70  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ86U70
Splice isoforms : SwissVarQ86U70
PhosPhoSitePlusQ86U70
Domains : Interpro (EBI)LDB1    LIM-bd/SEUSS   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)LDB1
DMDM Disease mutations8861
Blocks (Seattle)LDB1
PDB (SRS)2XJY    2XJZ    2YPA   
PDB (PDBSum)2XJY    2XJZ    2YPA   
PDB (IMB)2XJY    2XJZ    2YPA   
PDB (RSDB)2XJY    2XJZ    2YPA   
Structural Biology KnowledgeBase2XJY    2XJZ    2YPA   
SCOP (Structural Classification of Proteins)2XJY    2XJZ    2YPA   
CATH (Classification of proteins structures)2XJY    2XJZ    2YPA   
SuperfamilyQ86U70
Human Protein Atlas [tissue]ENSG00000198728-LDB1 [tissue]
Peptide AtlasQ86U70
HPRD09144
IPIIPI00856078   IPI00428954   IPI00760574   
Protein Interaction databases
DIP (DOE-UCLA)Q86U70
IntAct (EBI)Q86U70
FunCoupENSG00000198728
BioGRIDLDB1
STRING (EMBL)LDB1
ZODIACLDB1
Ontologies - Pathways
QuickGOQ86U70
Ontology : AmiGOnuclear chromatin  transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery  RNA polymerase II activating transcription factor binding  enhancer sequence-specific DNA binding  gastrulation with mouth forming second  hair follicle development  chromatin binding  transcription corepressor activity  protein binding  nucleus  transcription factor complex  transcription, DNA-templated  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  multicellular organism development  anterior/posterior axis specification  epithelial structure maintenance  Wnt signaling pathway  enzyme binding  cerebellar Purkinje cell differentiation  cellular component assembly  neuron differentiation  LIM domain binding  LIM domain binding  regulation of cell migration  cell leading edge  regulation of DNA-templated transcription, elongation  somatic stem cell population maintenance  protein homodimerization activity  protein complex  regulation of kinase activity  protein self-association  histone H3-K4 acetylation  negative regulation of erythrocyte differentiation  positive regulation of cell adhesion  negative regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  positive regulation of hemoglobin biosynthetic process  regulation of focal adhesion assembly  
Ontology : EGO-EBInuclear chromatin  transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery  RNA polymerase II activating transcription factor binding  enhancer sequence-specific DNA binding  gastrulation with mouth forming second  hair follicle development  chromatin binding  transcription corepressor activity  protein binding  nucleus  transcription factor complex  transcription, DNA-templated  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  multicellular organism development  anterior/posterior axis specification  epithelial structure maintenance  Wnt signaling pathway  enzyme binding  cerebellar Purkinje cell differentiation  cellular component assembly  neuron differentiation  LIM domain binding  LIM domain binding  regulation of cell migration  cell leading edge  regulation of DNA-templated transcription, elongation  somatic stem cell population maintenance  protein homodimerization activity  protein complex  regulation of kinase activity  protein self-association  histone H3-K4 acetylation  negative regulation of erythrocyte differentiation  positive regulation of cell adhesion  negative regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  positive regulation of hemoglobin biosynthetic process  regulation of focal adhesion assembly  
Pathways : BIOCARTAMulti-step Regulation of Transcription by Pitx2 [Genes]   
Pathways : KEGGTranscriptional misregulation in cancer   
NDEx NetworkLDB1
Atlas of Cancer Signalling NetworkLDB1
Wikipedia pathwaysLDB1
Orthology - Evolution
OrthoDB8861
GeneTree (enSembl)ENSG00000198728
Phylogenetic Trees/Animal Genes : TreeFamLDB1
HOVERGENQ86U70
HOGENOMQ86U70
Homologs : HomoloGeneLDB1
Homology/Alignments : Family Browser (UCSC)LDB1
Gene fusions - Rearrangements
Tumor Fusion PortalLDB1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLDB1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LDB1
dbVarLDB1
ClinVarLDB1
1000_GenomesLDB1 
Exome Variant ServerLDB1
ExAC (Exome Aggregation Consortium)ENSG00000198728
GNOMAD BrowserENSG00000198728
Genetic variants : HAPMAP8861
Genomic Variants (DGV)LDB1 [DGVbeta]
DECIPHERLDB1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLDB1 
Mutations
ICGC Data PortalLDB1 
TCGA Data PortalLDB1 
Broad Tumor PortalLDB1
OASIS PortalLDB1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLDB1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLDB1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LDB1
DgiDB (Drug Gene Interaction Database)LDB1
DoCM (Curated mutations)LDB1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LDB1 (select a term)
intoGenLDB1
NCG5 (London)LDB1
Cancer3DLDB1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603451   
Orphanet
DisGeNETLDB1
MedgenLDB1
Genetic Testing Registry LDB1
NextProtQ86U70 [Medical]
TSGene8861
GENETestsLDB1
Target ValidationLDB1
Huge Navigator LDB1 [HugePedia]
snp3D : Map Gene to Disease8861
BioCentury BCIQLDB1
ClinGenLDB1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8861
Chemical/Pharm GKB GenePA30316
Clinical trialLDB1
Miscellaneous
canSAR (ICR)LDB1 (select the gene name)
Probes
Litterature
PubMed55 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLDB1
EVEXLDB1
GoPubMedLDB1
iHOPLDB1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:54:26 CET 2017

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