RBBP4 RB binding protein 4, chromatin remodeling factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: RBBP4provided by HGNC
Official Full Name: RB binding protein 4, chromatin remodeling factorprovided by HGNC
Primary source: HGNC:HGNC:9887
See related: Ensembl:ENSG00000162521 MIM:602923; AllianceGenome:HGNC:9887
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NURF55; RBAP48; lin-53
Summary: This gene encodes a ubiquitously expressed nuclear protein which belongs to a highly conserved subfamily of WD-repeat proteins. It is present in protein complexes involved in histone acetylation and chromatin assembly. It is part of the Mi-2 complex which has been implicated in chromatin remodeling and transcriptional repression associated with histone deacetylation. This encoded protein is also part of co-repressor complexes, which is an integral component of transcriptional silencing. It is found among several cellular proteins that bind directly to retinoblastoma protein to regulate cell proliferation. This protein also seems to be involved in transcriptional repression of E2F-responsive genes. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
Expression: Ubiquitous expression in testis (RPKM 27.2), lymph node (RPKM 20.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p35.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (32651208..32686211)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (32510988..32546003)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (33116809..33151812)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Circ_0110498 facilitates the cisplatin resistance of non-small cell lung cancer by mediating the miR-1287-5p/RBBP4 axis.
Title: Circ_0110498 facilitates the cisplatin resistance of non-small cell lung cancer by mediating the miR-1287-5p/RBBP4 axis.
CircAGO2 promotes colorectal cancer progression by inhibiting heat shock protein family B (small) member 8 via miR-1-3p/retinoblastoma binding protein 4 axis.
Title: CircAGO2 promotes colorectal cancer progression by inhibiting heat shock protein family B (small) member 8 via miR-1-3p/retinoblastoma binding protein 4 axis.
RBBP4 regulates the expression of the Mre11-Rad50-NBS1 (MRN) complex and promotes DNA double-strand break repair to mediate glioblastoma chemoradiotherapy resistance.
Title: RBBP4 regulates the expression of the Mre11-Rad50-NBS1 (MRN) complex and promotes DNA double-strand break repair to mediate glioblastoma chemoradiotherapy resistance.
Overlapping functions of RBBP4 and RBBP7 in regulating cell proliferation and histone H3.3 deposition during mouse preimplantation development.
Title: Overlapping functions of RBBP4 and RBBP7 in regulating cell proliferation and histone H3.3 deposition during mouse preimplantation development.
RBBP4 plays a vital role in the malignant progression of triple-negative breast cancer by regulating epithelial-mesenchymal transition.
Title: RBBP4 plays a vital role in the malignant progression of triple-negative breast cancer by regulating epithelial-mesenchymal transition.
RBBP4-p300 axis modulates expression of genes essential for cell survival and is a potential target for therapy in glioblastoma.
Title: RBBP4-p300 axis modulates expression of genes essential for cell survival and is a potential target for therapy in glioblastoma.
RBBP4 promotes colon cancer malignant progression via regulating Wnt/beta-catenin pathway.
Title: RBBP4 promotes colon cancer malignant progression via regulating Wnt/β-catenin pathway.
The topology of chromatin-binding domains in the NuRD deacetylase complex.
Title: The topology of chromatin-binding domains in the NuRD deacetylase complex.
In summary, this is the first study showing the expression of RBBP4 in colon cancer and revealing that RBBP4 up-regulation is significantly associated with poor prognosis in colon cancer pa- tients.
Title: Retinoblastoma binding protein 4 up-regulation is correlated with hepatic metastasis and poor prognosis in colon cancer patients.
The authors suggest that RBBP4 is linked to HIV-1 transcriptional silencing and that it may be a new type of viral transcription inhibitor.
Title: Retinoblastoma binding protein 4 represses HIV-1 long terminal repeat-mediated transcription by recruiting NR2F1 and histone deacetylase.

Submit: New GeneRIF Correction See all GeneRIFs (38)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	The SIN3/HDAC complex, composed of SIN3A, SAP30, SAP18, HDAC-1 AND -2 and RbAp46/48 ,except SAP30, interacts with HIV-1 Tat in Jurkat cell	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

SHGC-30801 (e-PCR)
- UniSTS:53772

D1S1793E (e-PCR)
- UniSTS:57108

D8S2279 (e-PCR)
- UniSTS:473907

sY3084 (e-PCR)
- UniSTS:515126

SHGC-74547 (e-PCR)
- UniSTS:62015

ha1305 (e-PCR)
- UniSTS:515424

D10S16 (e-PCR)
- UniSTS:155756

RH70422 (e-PCR)
- UniSTS:44677

SHGC-57292 (e-PCR)
- UniSTS:70538

SYNCOILIN__5360 (e-PCR)
- UniSTS:464581

GDB:631802 (e-PCR)
- UniSTS:158429

RH102670 (e-PCR)
- UniSTS:97004

RH16653 (e-PCR)
- UniSTS:9976

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
contributes_to ATP-dependent activity, acting on DNA	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	NAS Non-traceable Author Statement more info	PubMed
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to nucleosomal DNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in DNA replication-dependent chromatin assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in brain development	NAS Non-traceable Author Statement more info	PubMed
involved_in chromatin remodeling	HDA more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of cell migration	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of cell population proliferation	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in nucleosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cell fate specification	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of stem cell differentiation	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of ATPase complex	IDA Inferred from Direct Assay more info	PubMed
part_of CAF-1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of CAF-1 complex	IPI Inferred from Physical Interaction more info	PubMed
part_of ESC/E(Z) complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ESC/E(Z) complex	IDA Inferred from Direct Assay more info	PubMed
part_of NURF complex	IDA Inferred from Direct Assay more info	PubMed
part_of NURF complex	IPI Inferred from Physical Interaction more info	PubMed
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NuRD complex	IDA Inferred from Direct Assay more info	PubMed
part_of NuRD complex	NAS Non-traceable Author Statement more info	PubMed
part_of Sin3-type complex	NAS Non-traceable Author Statement more info	PubMed
part_of chromatin	HDA more info	PubMed
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
part_of histone deacetylase complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
part_of protein-containing complex	HDA more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-binding protein RBBP4

Names: CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; MSI1 protein homolog; RBBP-4; chromatin assembly factor 1 subunit C; chromatin assembly factor I p48 subunit; chromatin assembly factor/CAF-1 p48 subunit; nucleosome-remodeling factor subunit RBAP48; retinoblastoma-binding protein 4; retinoblastoma-binding protein p48

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001135255.2 → NP_001128727.1 histone-binding protein RBBP4 isoform b

See identical proteins and their annotated locations for NP_001128727.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is one aa shorter compared to isoform a.

Source sequence(s)

AC114489, AK222779, DC315298

Consensus CDS

CCDS44105.1

UniProtKB/Swiss-Prot

Q09028

Related

ENSP00000398242.3, ENST00000414241.7

Conserved Domains (3) summary

sd00039
Location:127 → 174

7WD40; WD40 repeat [structural motif]

pfam12265
Location:18 → 87

CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex

cl29593
Location:121 → 402

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001135256.2 → NP_001128728.1 histone-binding protein RBBP4 isoform c

See identical proteins and their annotated locations for NP_001128728.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.

Source sequence(s)

AC114489, AK222779, AK299251

Consensus CDS

CCDS44106.1

UniProtKB/Swiss-Prot

Q09028

Related

ENSP00000396057.2, ENST00000458695.6

Conserved Domains (3) summary

sd00039
Location:93 → 140

7WD40; WD40 repeat [structural motif]

pfam12265
Location:1 → 53

CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex

cl29593
Location:87 → 368

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_005610.3 → NP_005601.1 histone-binding protein RBBP4 isoform a

See identical proteins and their annotated locations for NP_005601.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC114489, AK312571, DC315298

Consensus CDS

CCDS366.1

UniProtKB/Swiss-Prot

B2R6G9, B4DRH0, D3DPQ3, P31149, Q09028, Q53H02, Q96BV9

Related

ENSP00000362592.4, ENST00000373493.10

Conserved Domains (3) summary

sd00039
Location:128 → 175

7WD40; WD40 repeat [structural motif]

pfam12265
Location:19 → 88

CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex

cl29593
Location:122 → 403

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...