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Browse RBBP4

Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Nucleus.
Domain PF12265 Histone-binding protein RBBP4 or subunit C of CAF1 complex
PF00400 WD domain
Function

Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; 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 remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.

> Gene Ontology
 
Biological Process GO:0006260 DNA replication
GO:0006323 DNA packaging
GO:0006333 chromatin assembly or disassembly
GO:0006334 nucleosome assembly
GO:0006335 DNA replication-dependent nucleosome assembly
GO:0006336 DNA replication-independent nucleosome assembly
GO:0006338 chromatin remodeling
GO:0006476 protein deacetylation
GO:0016570 histone modification
GO:0016575 histone deacetylation
GO:0031055 chromatin remodeling at centromere
GO:0031497 chromatin assembly
GO:0034080 CENP-A containing nucleosome assembly
GO:0034508 centromere complex assembly
GO:0034723 DNA replication-dependent nucleosome organization
GO:0034724 DNA replication-independent nucleosome organization
GO:0034728 nucleosome organization
GO:0035601 protein deacylation
GO:0040029 regulation of gene expression, epigenetic
GO:0043044 ATP-dependent chromatin remodeling
GO:0043434 response to peptide hormone
GO:0043486 histone exchange
GO:0045814 negative regulation of gene expression, epigenetic
GO:0060416 response to growth hormone
GO:0061641 CENP-A containing chromatin organization
GO:0065004 protein-DNA complex assembly
GO:0071103 DNA conformation change
GO:0071824 protein-DNA complex subunit organization
GO:0072331 signal transduction by p53 class mediator
GO:0098732 macromolecule deacylation
GO:1901652 response to peptide
GO:1901796 regulation of signal transduction by p53 class mediator
Molecular Function GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0000987 core promoter proximal region sequence-specific DNA binding
GO:0001158 enhancer sequence-specific DNA binding
GO:0001159 core promoter proximal region DNA binding
GO:0003682 chromatin binding
GO:0004407 histone deacetylase activity
GO:0008094 DNA-dependent ATPase activity
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0016887 ATPase activity
GO:0019213 deacetylase activity
GO:0031490 chromatin DNA binding
GO:0031491 nucleosome binding
GO:0031492 nucleosomal DNA binding
GO:0033558 protein deacetylase activity
GO:0035326 enhancer binding
GO:0042393 histone binding
GO:0042623 ATPase activity, coupled
GO:0042826 histone deacetylase binding
GO:0043566 structure-specific DNA binding
Cellular Component GO:0000118 histone deacetylase complex
GO:0000785 chromatin
GO:0000790 nuclear chromatin
GO:0016580 Sin3 complex
GO:0016581 NuRD complex
GO:0016589 NURF complex
GO:0017053 transcriptional repressor complex
GO:0031010 ISWI-type complex
GO:0031519 PcG protein complex
GO:0033186 CAF-1 complex
GO:0034708 methyltransferase complex
GO:0035097 histone methyltransferase complex
GO:0035098 ESC/E(Z) complex
GO:0044454 nuclear chromosome part
GO:0070603 SWI/SNF superfamily-type complex
GO:0070822 Sin3-type complex
GO:0090545 CHD-type complex
GO:0090568 nuclear transcriptional repressor complex
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-5619507: Activation of HOX genes during differentiation
R-HSA-5617472: Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-1640170: Cell Cycle
R-HSA-69278: Cell Cycle, Mitotic
R-HSA-2559583: Cellular Senescence
R-HSA-2262752: Cellular responses to stress
R-HSA-3247509: Chromatin modifying enzymes
R-HSA-4839726: Chromatin organization
R-HSA-73886: Chromosome Maintenance
R-HSA-606279: Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-1266738: Developmental Biology
R-HSA-427389: ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-212165: Epigenetic regulation of gene expression
R-HSA-1538133: G0 and Early G1
R-HSA-69275: G2/M Transition
R-HSA-74160: Gene Expression
R-HSA-212436: Generic Transcription Pathway
R-HSA-3214815: HDACs deacetylate histones
R-HSA-453279: Mitotic G1-G1/S phases
R-HSA-453274: Mitotic G2-G2/M phases
R-HSA-774815: Nucleosome assembly
R-HSA-2559580: Oxidative Stress Induced Senescence
R-HSA-3214841: PKMTs methylate histone lysines
R-HSA-212300: PRC2 methylates histones and DNA
R-HSA-156711: Polo-like kinase mediated events
R-HSA-5250913: Positive epigenetic regulation of rRNA expression
R-HSA-73854: RNA Polymerase I Promoter Clearance
R-HSA-73864: RNA Polymerase I Transcription
R-HSA-73762: RNA Polymerase I Transcription Initiation
R-HSA-504046: RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription
R-HSA-5633007: Regulation of TP53 Activity
R-HSA-6804758: Regulation of TP53 Activity through Acetylation
R-HSA-3700989: Transcriptional Regulation by TP53
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between RBBP4 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of RBBP4 in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NS NA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell logFC: -1.92; FDR: 0.04110 Resistant to T cell-mediated killing
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NS NA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NS NA/NS
24476824shRNAmelanomaB16Primary screen NA/NS NA/NS
24476824shRNAmelanomaB16Secondary screen NA/NS NA/NS
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of RBBP4 in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.160.406
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.0320.987
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.30.827
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.2420.504
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590.1980.932
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.2980.92
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.0050.989
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.0660.973
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.0840.968
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 48-0.0930.957
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.6210.811
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.1910.00342
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of RBBP4 in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27733.72.711
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 01407.1-7.11
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27593.71.720.532
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21170001
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38272.602.61
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22134.504.51
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11139.109.10.458
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 6116.7016.71
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of RBBP4. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of RBBP4. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by RBBP4.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of RBBP4. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of RBBP4 expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between RBBP4 and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolRBBP4
Nameretinoblastoma binding protein 4
Aliases RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location1p35.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting RBBP4 collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.