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RBBP7 (retinoblastoma binding protein 7)

Written2009-07Neehar Sinha, Ranjan Tamuli
Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati-781 039, Assam, India

(Note : for Links provided by Atlas : click)

Identity

Alias_namesretinoblastoma-binding protein 7
retinoblastoma binding protein 7
RB binding protein 7
Alias_symbol (synonym)RbAp46
Other aliasRBAP46
RBBP-7
MGC138867
MGC138868
HGNC (Hugo) RBBP7
LocusID (NCBI) 5931
Atlas_Id 42065
Location Xp22.2  [Link to chromosome band Xp22]
Location_base_pair Starts at 16844652 and ends at 16869855 bp from pter ( according to hg19-Feb_2009)  [Mapping RBBP7.png]
Fusion genes
(updated 2016)
CTPS2 (Xp22.2) / RBBP7 (Xp22.2)FERMT1 (20p12.3) / RBBP7 (Xp22.2)PSMA7 (20q13.33) / RBBP7 (Xp22.2)
Note RBBP7 is located at contig NP_002884.1 of GenBank. The retinoblastoma binding protein 7 gene symbol for human is RBBP7 whereas the symbol for the same gene for rat and mice is Rbbp7. RBBP7 was one of the two most abundant proteins from HeLa cell lysates that were specifically retained by an RB1 affinity column (Qian et al., 1993). Qian and Lee (1995) isolated cDNAs encoding RBBP7 by screening a HeLa cell cDNA expression library with monoclonal antibodies against RBBP7, which they called as RbAp46. Southern blot analysis indicated that the human genome contains a single copy of the RBBP7 gene.

DNA/RNA

 
Description DNA size 27.75 kb; mRNA size 2021 bp; 12 exons.

Protein

 
Description 425 amino acids; 47.82 kDa protein.

Post translational modifications: Phosphorylation enhances DNA binding. Phosphorylation occurs at position 95, 99, 354, 413 (Serine) and 416 (Threonine). Acetylation brings in a negative charge, acting to neutralise the positive charge on the histones and decreases the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure which is associated with greater levels of gene transcription.
The acetylation sites are: at 2 (Alanine), and 119 (Lysine).

Isoform: The following isoforms have been identified:
- RBBP7.iApr07
- hPA25320.1 (469 aa)
- hPA25320.2 (425 aa)
- hPA25320.3 (410 aa)
- hPA25320.7 (420 aa)

Expression It is widely expressed.
Localisation Nucleus.
Function This protein is an ubiquitously expressed nuclear protein and it belongs to a highly conserved subfamily of WD-repeat proteins. It is found among several proteins that bind directly to retinoblastoma protein, which regulates cell proliferation. The encoded protein is found in many histone deacetylase complexes, including mSin3 co-repressor complex. It is also present in protein complexes involved in chromatin assembly, which include the type B histone acetyltransferase (HAT) complex, which is required for chromatin assembly following DNA replication; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodelling. This protein can interact with BRCA1 tumor-suppressor gene and may have a role in the regulation of cell proliferation and differentiation.
Homology The percent identity below represents identity of RBBP7 over an aligned region in UniGene.
- M. musculus : 100 (percentage identity)
- C. lupus familiaris : 100
- B. taurus : 100
- R. norvegicus : 100
- G.gallus : 96.2
- D. rerio : 94.4

Mutations

Note Two types of mutation have been detected in the RBBP7 gene. A827G is a silent mutation and the other one is a missense type of mutation that changes N276S.

Implicated in

Note
  
Entity Breast cancer
Note RBBP7 (also known as RbAp46) overexpression has shown to inhibit the tumorigenicity of neoplastigenic breast epithelial cells (Li et al., 2003). RBBP7 activates stress-induced apoptosis, the JNK-dependent apoptotic cell death, possibly through upregulation of GADD45 (Growth arrest- and DNA damage-inducible 45). GADD45 binds and activates MAPKKK MTK1/MEK4, the upstream regulator of JNK, triggering JNK-dependent apoptosis. Thus, overexpression of RBBP7 facilitates stress-induced apoptosis and suppresses tumorigenicity of neoplastigenic breast epithelial cells.
  
  
Entity Leukemia
Note Expression level of RBBP7 in initial acute leukemia has been found to be significantly higher than in chronic myelogenous leukemia. The Wilms tumor suppressor gene (WT1) expression level was also correlated with RBBP7 expression. WT1 encodes a zinc finger transcription factor that regulates transcription of its downstream gene. RBBP7 is a downstream effector of WT1 gene, and acts in a similar manner as WT1 does. It has been seen that high expression of RBBP7 suppresses the tumorigenicity of neoplastic breast epithelial cells but its overexpression possibly may induce leukemia. This phenomenon suggests that the regulatory pathway for RbAp46 gene expression in acute leukemia may be different from that in solid tumor.
  
  
Entity Human embryonic kidney (HEK) 293 cell tumorigenesis
Note High levels of RbAp46 suppress the tumorigenicity of adenovirus-transformed human embryonic kidney 293 cells. High level of RbAp46 resulted in G2/M cell population and augmented apoptosis in serum starved cells. It is possible that overexpression of RbAp46 may interfere with normal cell cycle and/or enhance apoptotic cell death which inhibits the transformation of tumor cells.
  

Bibliography

WT1-mediated pathway of transcriptional regulation and leukemia.
Duan WM, Chen ZX.
Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2002 Aug;10(4):366-70. (REVIEW)
PMID 12513776
 
Rb-associated protein 46 (RbAp46) suppresses the tumorigenicity of adenovirus-transformed human embryonic kidney 293 cells.
Guan LS, Li GC, Chen CC, Liu LQ, Wang ZY.
Int J Cancer. 2001 Aug 1;93(3):333-8.
PMID 11433396
 
High expression of RbAp46 gene in patients with acute leukemia or chronic myelogenous leukemia in blast crisis.
Hu SY, Chen ZX, Gu WY, Cen JN, Zhao Y.
Chin Med J (Engl). 2005 Aug 5;118(15):1295-8.
PMID 16117885
 
Overexpression of RbAp46 facilitates stress-induced apoptosis and suppresses tumorigenicity of neoplastigenic breast epithelial cells.
Li GC, Guan LS, Wang ZY.
Int J Cancer. 2003 Jul 20;105(6):762-8.
PMID 12767060
 
Retinoblastoma suppressor associated protein 46 (RbAp46) attenuates the beta-catenin/TCF signaling through up-regulation of GSK-3beta expression.
Li GC, Wang ZY.
Anticancer Res. 2006 Nov-Dec;26(6B):4511-8.
PMID 17201172
 
Immunohistochemical analysis of possible chemoresistance markers identified by micro-arrays on serous ovarian carcinomas.
Tetu B, Popa I, Bairati I, L'Esperance S, Bachvarova M, Plante M, Harel F, Bachvarov D.
Mod Pathol. 2008 Aug;21(8):1002-10. Epub 2008 May 23.
PMID 18500265
 
Aberrant expression of X-linked genes RbAp46, Rsk4, and Cldn2 in breast cancer.
Thakur A, Rahman KW, Wu J, Bollig A, Biliran H, Lin X, Nassar H, Grignon DJ, Sarkar FH, Liao JD.
Mol Cancer Res. 2007 Feb;5(2):171-81.
PMID 17314274
 
RbAp46 inhibits estrogen-stimulated progression of neoplastigenic breast epithelial cells.
Zhang TF, Yu SQ, Wang ZY.
Anticancer Res. 2007 Sep-Oct;27(5A):3205-9.
PMID 17970062
 
Expressive profile of retinoblastoma-associated protein 46 and its clinical significance in acute leukemias.
Zhou JC, Zhang GS.
Zhonghua Xue Ye Xue Za Zhi. 2005 Feb;26(2):86-9.
PMID 15921624
 

Citation

This paper should be referenced as such :
Sinha, N ; Tamuli, R
RBBP7 (retinoblastoma binding protein 7)
Atlas Genet Cytogenet Oncol Haematol. 2010;14(6):578-580.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/RBBP7ID42065chXp22.html


External links

Nomenclature
HGNC (Hugo)RBBP7   9890
Cards
AtlasRBBP7ID42065chXp22
Entrez_Gene (NCBI)RBBP7  5931  RB binding protein 7, chromatin remodeling factor
AliasesRbAp46
GeneCards (Weizmann)RBBP7
Ensembl hg19 (Hinxton)ENSG00000102054 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000102054 [Gene_View]  chrX:16844652-16869855 [Contig_View]  RBBP7 [Vega]
ICGC DataPortalENSG00000102054
TCGA cBioPortalRBBP7
AceView (NCBI)RBBP7
Genatlas (Paris)RBBP7
WikiGenes5931
SOURCE (Princeton)RBBP7
Genetics Home Reference (NIH)RBBP7
Genomic and cartography
GoldenPath hg38 (UCSC)RBBP7  -     chrX:16844652-16869855 -  Xp22.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RBBP7  -     Xp22.2   [Description]    (hg19-Feb_2009)
EnsemblRBBP7 - Xp22.2 [CytoView hg19]  RBBP7 - Xp22.2 [CytoView hg38]
Mapping of homologs : NCBIRBBP7 [Mapview hg19]  RBBP7 [Mapview hg38]
OMIM300825   
Gene and transcription
Genbank (Entrez)AK091911 AK127332 AK291567 AK310309 BC114500
RefSeq transcript (Entrez)NM_001198719 NM_002893
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)RBBP7
Cluster EST : UnigeneHs.495755 [ NCBI ]
CGAP (NCI)Hs.495755
Alternative Splicing GalleryENSG00000102054
Gene ExpressionRBBP7 [ NCBI-GEO ]   RBBP7 [ EBI - ARRAY_EXPRESS ]   RBBP7 [ SEEK ]   RBBP7 [ MEM ]
Gene Expression Viewer (FireBrowse)RBBP7 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5931
GTEX Portal (Tissue expression)RBBP7
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ16576   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ16576  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ16576
Splice isoforms : SwissVarQ16576
PhosPhoSitePlusQ16576
Domaine pattern : Prosite (Expaxy)WD_REPEATS_1 (PS00678)    WD_REPEATS_2 (PS50082)    WD_REPEATS_REGION (PS50294)   
Domains : Interpro (EBI)G-protein_beta_WD-40_rep    Histone-bd_RBBP4_N    WD40/YVTN_repeat-like_dom    WD40_repeat    WD40_repeat_CS    WD40_repeat_dom   
Domain families : Pfam (Sanger)CAF1C_H4-bd (PF12265)    WD40 (PF00400)   
Domain families : Pfam (NCBI)pfam12265    pfam00400   
Domain families : Smart (EMBL)WD40 (SM00320)  
Conserved Domain (NCBI)RBBP7
DMDM Disease mutations5931
Blocks (Seattle)RBBP7
PDB (SRS)3CFS    3CFV   
PDB (PDBSum)3CFS    3CFV   
PDB (IMB)3CFS    3CFV   
PDB (RSDB)3CFS    3CFV   
Structural Biology KnowledgeBase3CFS    3CFV   
SCOP (Structural Classification of Proteins)3CFS    3CFV   
CATH (Classification of proteins structures)3CFS    3CFV   
SuperfamilyQ16576
Human Protein AtlasENSG00000102054
Peptide AtlasQ16576
HPRD04231
IPIIPI00395865   IPI00552530   IPI00642026   IPI00647914   IPI00646512   IPI00879702   IPI00947052   IPI00947544   IPI00947393   
Protein Interaction databases
DIP (DOE-UCLA)Q16576
IntAct (EBI)Q16576
FunCoupENSG00000102054
BioGRIDRBBP7
STRING (EMBL)RBBP7
ZODIACRBBP7
Ontologies - Pathways
QuickGOQ16576
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  RNA binding  histone deacetylase activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytosol  DNA replication  transcription, DNA-templated  multicellular organism development  cell proliferation  histone deacetylation  NuRD complex  negative regulation of cell growth  CENP-A containing nucleosome assembly  ESC/E(Z) complex  negative regulation of gene expression, epigenetic  response to steroid hormone  cellular heat acclimation  regulation of signal transduction by p53 class mediator  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  RNA binding  histone deacetylase activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytosol  DNA replication  transcription, DNA-templated  multicellular organism development  cell proliferation  histone deacetylation  NuRD complex  negative regulation of cell growth  CENP-A containing nucleosome assembly  ESC/E(Z) complex  negative regulation of gene expression, epigenetic  response to steroid hormone  cellular heat acclimation  regulation of signal transduction by p53 class mediator  
Pathways : BIOCARTAThe PRC2 Complex Sets Long-term Gene Silencing Through Modification of Histone Tails [Genes]   
REACTOMEQ16576 [protein]
REACTOME PathwaysR-HSA-73762 [pathway]   
NDEx NetworkRBBP7
Atlas of Cancer Signalling NetworkRBBP7
Wikipedia pathwaysRBBP7
Orthology - Evolution
OrthoDB5931
GeneTree (enSembl)ENSG00000102054
Phylogenetic Trees/Animal Genes : TreeFamRBBP7
HOVERGENQ16576
HOGENOMQ16576
Homologs : HomoloGeneRBBP7
Homology/Alignments : Family Browser (UCSC)RBBP7
Gene fusions - Rearrangements
Fusion : MitelmanCTPS2/RBBP7 [Xp22.2/Xp22.2]  [t(X;X)(p22;p22)]  
Fusion: TCGACTPS2 Xp22.2 RBBP7 Xp22.2 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRBBP7 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RBBP7
dbVarRBBP7
ClinVarRBBP7
1000_GenomesRBBP7 
Exome Variant ServerRBBP7
ExAC (Exome Aggregation Consortium)RBBP7 (select the gene name)
Genetic variants : HAPMAP5931
Genomic Variants (DGV)RBBP7 [DGVbeta]
DECIPHERRBBP7 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRBBP7 
Mutations
ICGC Data PortalRBBP7 
TCGA Data PortalRBBP7 
Broad Tumor PortalRBBP7
OASIS PortalRBBP7 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRBBP7  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDRBBP7
intOGen PortalRBBP7
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 RBBP7
DgiDB (Drug Gene Interaction Database)RBBP7
DoCM (Curated mutations)RBBP7 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RBBP7 (select a term)
intoGenRBBP7
NCG5 (London)RBBP7
Cancer3DRBBP7(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300825   
Orphanet
MedgenRBBP7
Genetic Testing Registry RBBP7
NextProtQ16576 [Medical]
TSGene5931
GENETestsRBBP7
Target ValidationRBBP7
Huge Navigator RBBP7 [HugePedia]
snp3D : Map Gene to Disease5931
BioCentury BCIQRBBP7
ClinGenRBBP7
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5931
Chemical/Pharm GKB GenePA34254
Clinical trialRBBP7
Miscellaneous
canSAR (ICR)RBBP7 (select the gene name)
Probes
Litterature
PubMed133 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRBBP7
EVEXRBBP7
GoPubMedRBBP7
iHOPRBBP7
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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