Atlas of Genetics and Cytogenetics in Oncology and Haematology

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

RSF1 (remodeling and spacing factor 1)

Written2008-07Tian-Li Wang, Joon T Park
Departments of Gynecology/Obstetrics, Oncology Johns Hopkins Medical Institutions CRBII, Rm: 306 1550 Orleans Street Baltimore, MD 21231, USA

(Note : for Links provided by Atlas : click)


Other namesHBXAP
HGNC (Hugo) RSF1
LocusID (NCBI) 51773
Atlas_Id 44107
Location 11q14.1
Location_base_pair Starts at 77377274 and ends at 77531880 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order gene orientation: centromere -3' RSF1 5'- telomere.
Fusion genes
(updated 2015)
ASPH (8q12.3) / RSF1 (11q14.1)EXT1 (8q24.11) / RSF1 (11q14.1)RSF1 (11q14.1) / HSPA13 (21q11.2)
RSF1 (11q14.1) / INTS4 (11q14.1)RSF1 (11q14.1) / KCTD21 (11q14.1)RSF1 (11q14.1) / KLC2 (11q13.2)
RSF1 (11q14.1) / ODZ4 ()RSF1 (11q14.1) / PHF12 (17q11.2)RSF1 (11q14.1) / TENM4 (11q14.1)
SOCS7 (17q12) / RSF1 (11q14.1)


  Genomic organization of human RSF1.
Description Rsf1 gene is encoded by 16 exons spanning 154.607 Mb that are located on chromosome 11p14.1.
Transcription 5.131 Kb mRNA, the coding sequence is from 121 bp-4446 bp.


Note 1441 amino acids, highly acidic protein (pI 4.94), with calculated molecular mass of 164 kD. SDS-PAGE detected native RSF1 at molecular mass of 200 to 300 kD
Contain a DDT domain, Zinc finger PHD-type domain which was found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation.
RSF1 also contains 3 nuclear localization signal near C-terminus.
  Diagram of the RSF1 protein.
Description Using a variation of the yeast 2-hybrid screen aiming to identify proteins interacting with hepatitis B virus X protein (HBX), Shamay et al (2002a) cloned RSF1 from a spleen cDNA library. Therefore, the initial name of RSF1 was called Hepatitis B virus X-Associated Protein (HBXAP). Using 5'RACE, 3 splice variants were cloned and named HBXAP-alpha, -beta, -gamma, which contains 1431, 1400, and 1189 amino acids, respectively. By characterizing a protein remodeling complex RSF, Loyola A et al has identified two interacting subunits: RSF1 and SNF2H. They used peptide sequence information of RSF1 to clone the full-length cDNA. The deduced sequence contains 1441 amino acids which includes 252 additional amino acids at N-terminus as compared to HBXAP-gamma. Reconstitute experiment by isolating protein complex from coinfection of viruses caring each subunit can recapitulate the chromatin assembly ability and ATPase activity of native complex. They also showed that SNF2H binds to DNA independently of histones. However, RSF1 couldn't bind to DNA unless histones are present.
Expression Highly expressed in heart, skeletal muscle, kidney, and placenta, and expressed weakly in brain and colon.
Localisation Mainly located at cell nucleus. During mitosis, the expression in the nucleus is decreased.
Function RSF1 functions as transcription coactivator when associated with hepatitis B virus X protein (HBX). Shamay et al (2002b) observed the direct interaction between the RSF1 variant, HBXAP-gamma, and HBX. HBXAP-gamma increased hepatitis B viral transcription in an HBX-dependent manner. Furthermore, in the presence of both HBX and HBXAP, the transcription of a nuclear factor kappa-B ( NFKB ) was significantly increased. However, in the presence of HBXAP alone, the transcription of a NFKB was decreased in a dose-dependent manner. Examination of HBXAP-gamma deletion mutants showed that the interaction between HBX and HBXAP-gamma was mediated by the PHD domain in HBXAP-gamma.
RSF1 functions as chromatin remodeling and spacing when associated with SNF2H. Loyola et al reconstituted the RSF complex by overexpressing two subunits, RSF1 and SNF2H. RSF1 assembled nucleosome randomly as a histone chaperone in the nuclei. The resulting nucleosomes were then redistributed into a regularly spaced nucleosome array by the ATP-utilizing nucleosome mobilization factor SNF2H. At the cellular level, Rsf1/SNF2H complex participated in chromatin remodeling by mobilizing nucleosomes in response to a variety of growth modifying signals and environmental cues. Sheu JJ et al found that the induction of RSF1 expression affected the molecular partnership of SNF2H and translocated SNF2H into nuclei where it colocalized with RSF1. To determine which domain in the RSF1 is involved in the binding to SNF2H, a series of RSF1-deletion mutants were generated. Only the fragment that contains DDT, Glu-rich, and PHD motifs could be immunoprecipitated with SNF2H. Ectopic expression of this RSF1 fragment disrupted RSF1/SNF2H complex and resulted in remarkable growth inhibition in ovarian cancer cells with RSF1 gene amplification and overexpression, but not in the cells without detectable RSF1 expression. This finding suggests that interaction between RSF1 and SNF2H may define a survival signal in the tumors overexpressing RSF1.


Somatic Chromosome 11q is one of the most common targets for allelic imbalance alteration in human cancers. Several candidate tumor-promoting genes were postulated previously. In ovarian carcinoma, Shih et al, has pinpointed a minimal amplicon spanning from 76.6 to 78.4 Mb on the chromosome 11q, which harbor 13 genes. Rsf1 was identified as the gene with most consistent correlation between gene amplification and transcription up-regulation.

Implicated in

Entity Ovarian cancer
Prognosis Shih et al found that amplification of Rsf1 locus was correlated with shorter overall survival of ovarian cancer patients.
Cytogenetics Amplification of 11q13 detected an ovarian cancer cell line, OVCAR3.
Oncogenesis Shih et al found that the amplification of chr11q13 is associated with RSF1 protein over-expression. siRNA knockdown experiment in OVCAR3 cell, which harbor Rsf-1 amplification, demonstrated it is essential for tumor cell survival.
Mao TL et al found that RSF1 overexpression was observed in 25% of high-grade ovarian serous carcinomas and in less than 7% of low-grade ovarian serous carcinoma and ovarian endometrioid. RSF1 does not express in any of the ovarian serous borderline tumors, ovarian clear cell carcinomas, ovarian mucinous carcinomas, and normal ovaries. Overexpression of RSF1 was significantly associated with high-grade ovarian serous carcinoma (P < 0.05) as compared with other types of ovarian tumors, demonstrating that RSF1 expression is primarily confined to high-grade serous carcinoma, the most aggressive ovarian cancer.


Hepatitis B virus pX interacts with HBXAP, a PHD finger protein to coactivate transcription.
Shamay M, Barak O, Doitsh G, Ben-Dor I, Shaul Y.
J Biol Chem. 2002b Mar 22;277(12):9982-8. Epub 2002 Jan 11.
PMID 11788598
HBXAP, a novel PHD-finger protein, possesses transcription repression activity.
Shamay M, Barak O, Shaul Y.
Genomics. 2002a Apr;79(4):523-9.
PMID 11944984
Functional analysis of the subunits of the chromatin assembly factor RSF.
Loyola A, Huang JY, LeRoy G, Hu S, Wang YH, Donnelly RJ, Lane WS, Lee SC, Reinberg D.
Mol Cell Biol. 2003 Oct;23(19):6759-68.
PMID 12972596
Amplification of a chromatin remodeling gene, Rsf-1/HBXAP, in ovarian carcinoma.
Shih IeM, Sheu JJ, Santillan A, Nakayama K, Yen MJ, Bristow RE, Vang R, Parmigiani G, Kurman RJ, Trope CG, Davidson B, Wang TL.
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):14004-9. Epub 2005 Sep 19.
PMID 16172393
Expression of Rsf-1, a chromatin-remodeling gene, in ovarian and breast carcinoma.
Mao TL, Hsu CY, Yen MJ, Gilks B, Sheu JJ, Gabrielson E, Vang R, Cope L, Kurman RJ, Wang TL, Shih IeM.
Hum Pathol. 2006 Sep;37(9):1169-75. Epub 2006 Jul 7.
PMID 16938522
The roles of human sucrose nonfermenting protein 2 homologue in the tumor-promoting functions of Rsf-1.
Sheu JJ, Choi JH, Yildiz I, Tsai FJ, Shaul Y, Wang TL, Shih IeM.
Cancer Res. 2008 Jun 1;68(11):4050-7.
PMID 18519663


This paper should be referenced as such :
Wang, TL ; Park, JT
RSF1 (remodeling, spacing factor 1)
Atlas Genet Cytogenet Oncol Haematol. 2009;13(6):426-428.
Free journal version : [ pdf ]   [ DOI ]
On line version :

External links

HGNC (Hugo)RSF1   18118
Entrez_Gene (NCBI)RSF1  51773  remodeling and spacing factor 1
GeneCards (Weizmann)RSF1
Ensembl hg19 (Hinxton)ENSG00000048649 [Gene_View]  chr11:77377274-77531880 [Contig_View]  RSF1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000048649 [Gene_View]  chr11:77377274-77531880 [Contig_View]  RSF1 [Vega]
ICGC DataPortalENSG00000048649
TCGA cBioPortalRSF1
AceView (NCBI)RSF1
Genatlas (Paris)RSF1
SOURCE (Princeton)RSF1
Genomic and cartography
GoldenPath hg19 (UCSC)RSF1  -     chr11:77377274-77531880 -  11q14.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)RSF1  -     11q14.1   [Description]    (hg38-Dec_2013)
EnsemblRSF1 - 11q14.1 [CytoView hg19]  RSF1 - 11q14.1 [CytoView hg38]
Mapping of homologs : NCBIRSF1 [Mapview hg19]  RSF1 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AF059317 AF227948 AF380176 AK001268 AK096617
RefSeq transcript (Entrez)NM_016578
RefSeq genomic (Entrez)NC_000011 NC_018922 NT_167190 NW_004929380
Consensus coding sequences : CCDS (NCBI)RSF1
Cluster EST : UnigeneHs.593415 [ NCBI ]
CGAP (NCI)Hs.593415
Alternative Splicing : Fast-db (Paris)GSHG0006040
Alternative Splicing GalleryENSG00000048649
Gene ExpressionRSF1 [ NCBI-GEO ]     RSF1 [ SEEK ]   RSF1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96T23 (Uniprot)
NextProtQ96T23  [Medical]  [Publications]
With graphics : InterProQ96T23
Splice isoforms : SwissVarQ96T23 (Swissvar)
Domaine pattern : Prosite (Expaxy)ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)Rsf-1    WHIM1_dom    WHIM2_dom    WHIM3_domain    Zinc_finger_PHD-type_CS    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING/FYVE/PHD   
Related proteins : CluSTrQ96T23
Domain families : Pfam (Sanger)PHD (PF00628)    WHIM1 (PF15612)    WHIM2 (PF15613)    WHIM3 (PF15614)   
Domain families : Pfam (NCBI)pfam00628    pfam15612    pfam15613    pfam15614   
Domain families : Smart (EMBL)PHD (SM00249)  
DMDM Disease mutations51773
Blocks (Seattle)Q96T23
Human Protein AtlasENSG00000048649
Peptide AtlasQ96T23
IPIIPI00290652   IPI00514411   IPI00982445   IPI01010155   IPI00977965   IPI00976511   IPI00981883   
Protein Interaction databases
IntAct (EBI)Q96T23
Ontologies - Pathways
Ontology : AmiGOprotein binding  nucleus  nucleoplasm  nucleoplasm  nucleosome assembly  nucleosome assembly  chromatin remodeling  DNA-templated transcription, initiation  zinc ion binding  nucleosome positioning  ATPase activity  RSF complex  CENP-A containing nucleosome assembly  histone binding  negative regulation of DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of viral transcription  
Ontology : EGO-EBIprotein binding  nucleus  nucleoplasm  nucleoplasm  nucleosome assembly  nucleosome assembly  chromatin remodeling  DNA-templated transcription, initiation  zinc ion binding  nucleosome positioning  ATPase activity  RSF complex  CENP-A containing nucleosome assembly  histone binding  negative regulation of DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of viral transcription  
REACTOMEQ96T23 [protein]
REACTOME PathwaysREACT_115566 Cell Cycle [pathway]
Protein Interaction DatabaseRSF1
Atlas of Cancer Signalling NetworkRSF1
Wikipedia pathwaysRSF1
Gene fusions - Rearrangements
Fusion : MitelmanASPH/RSF1 [8q12.3/11q14.1]  [t(8;11)(q12;q14)]  
Fusion : MitelmanEXT1/RSF1 [8q24.11/11q14.1]  [t(8;11)(q24;q14)]  
Fusion : MitelmanRSF1/HSPA13 [11q14.1/21q11.2]  [t(11;21)(q14;q11)]  
Fusion : MitelmanRSF1/INTS4 [11q14.1/11q14.1]  [t(11;11)(q14;q14)]  
Fusion : MitelmanRSF1/KCTD21 [11q14.1/11q14.1]  [t(11;11)(q14;q14)]  
Fusion : MitelmanRSF1/KLC2 [11q14.1/11q13.2]  [t(11;11)(q13;q14)]  
Fusion : MitelmanRSF1/PHF12 [11q14.1/17q11.2]  [t(11;17)(q14;q11)]  
Fusion : MitelmanRSF1/TENM4 [11q14.1/11q14.1]  [t(11;11)(q14;q14)]  
Fusion : MitelmanSOCS7/RSF1 [17q12/11q14.1]  [t(11;17)(q14;q12)]  
Fusion: TCGAASPH 8q12.3 RSF1 11q14.1 BRCA
Fusion: TCGAEXT1 8q24.11 RSF1 11q14.1 BRCA
Fusion: TCGANCOR1 17p12 RSF1 11q14.1 BRCA
Fusion: TCGARSF1 11q14.1 HSPA13 21q11.2 BRCA
Fusion: TCGARSF1 11q14.1 INTS4 11q14.1 LUSC SKCM
Fusion: TCGARSF1 11q14.1 KCTD21 11q14.1 OV
Fusion: TCGARSF1 11q14.1 KLC2 11q13.2 LGG
Fusion: TCGARSF1 11q14.1 ODZ4 BRCA
Fusion: TCGARSF1 11q14.1 PHF12 17q11.2 BRCA
Fusion: TCGASOCS7 17q12 RSF1 11q14.1 LUAD
Polymorphisms : SNP, variants
NCBI Variation ViewerRSF1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RSF1
Exome Variant ServerRSF1
SNP (GeneSNP Utah)RSF1
Genetic variants : HAPMAPRSF1
Genomic Variants (DGV)RSF1 [DGVbeta]
ICGC Data PortalRSF1 
TCGA Data PortalRSF1 
Tumor PortalRSF1
TCGA Copy Number PortalRSF1
Somatic Mutations in Cancer : COSMICRSF1 
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
DoCM (Curated mutations)RSF1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
DECIPHER (Syndromes)11:77377274-77531880
CONAN: Copy Number AnalysisRSF1 
Mutations and Diseases : HGMDRSF1
NextProtQ96T23 [Medical]
Huge Navigator RSF1 [HugePedia]  RSF1 [HugeCancerGEM]
snp3D : Map Gene to Disease51773
DGIdb (Drug Gene Interaction db)RSF1
BioCentury BCIQRSF1
General knowledge
Homologs : HomoloGeneRSF1
Homology/Alignments : Family Browser (UCSC)RSF1
Phylogenetic Trees/Animal Genes : TreeFamRSF1
Chemical/Protein Interactions : CTD51773
Chemical/Pharm GKB GenePA29210
Clinical trialRSF1
Cancer Resource (Charite)ENSG00000048649
Other databases
PubMed57 Pubmed reference(s) in Entrez
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Nov 28 14:32:30 CET 2015

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us