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ARID5B (AT rich interactive domain 5B (MRF1-like))

Written2013-08Heng Xu, Jun J Yang
Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 DannyThomas Place, MS 313, Memphis, TN 38105-2794, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namesAT rich interactive domain 5B (MRF1-like)
Alias_symbol (synonym)FLJ21150
MRF2
Other aliasDESRT
MRF-2
HGNC (Hugo) ARID5B
LocusID (NCBI) 84159
Atlas_Id 51529
Location 10q21.2  [Link to chromosome band 10q21]
Location_base_pair Starts at 62049211 and ends at 62096948 bp from pter ( according to hg19-Feb_2009)  [Mapping ARID5B.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)
ARID5B (10q21.2) / ABLIM1 (10q25.3)ARID5B (10q21.2) / ARID5B (10q21.2)ARID5B (10q21.2) / CDAN1 (15q15.2)
ARID5B (10q21.2) / CREB5 (7p15.1)ARID5B (10q21.2) / DIS3L2 (2q37.1)ARID5B (10q21.2) / NOTCH2 (1p12)
ARID5B (10q21.2) / RPL13 (16q24.3)C20orf27 (20p13) / ARID5B (10q21.2)FLNA (Xq28) / ARID5B (10q21.2)
HDLBP (2q37.3) / ARID5B (10q21.2)
Note ARID5B (AT rich interactive domain 5B (MRF1-like)) encodes a possible transcription factor with chromatin remodeling activities. It may be involved in hematopoietic cell development and differentiation (Novershtern et al., 2011). Single nucleotide polymorphisms (SNPs) within this gene are associated with susceptibility to childhood acute lymphoblastic leukemia (Papaemmanuil et al., 2009; Treviño et al., 2009), rheumatoid arthritis (Okada et al., 2012), and systemic lupus erythematosus (Yang et al., 2013).

DNA/RNA

 
  Illustration of transcriptions of human ARID5B gene.
Description The ARID5B gene is composed of 10 exons spanning ~200 kb on chr 10q21.2. Two alternative splicing variants have been identified. Both transcripts share exons 5 to 10 but the short isoform (7032 bp) lacks a portion of the 5' coding region of the long transcript (7948 bp).

Protein

Description ARID5B belongs to a family of DNA binding proteins characterized by a conserved AT-rich interaction domain (ARID). The ARID domain, a helix-turn-helix motif, recognizes a core sequence AAT(C/T). Alternatively-spliced transcription variants encoding two isoforms have been identified, and the short isoform has a truncated N-terminal compared to the long isoform.
Expression ARID5B is expressed is in a variety of tissues and cell types, particularly in uterus, smooth muscle, placenta, and CD19+ B cells.
Localisation ARID5B contains nuclei location signal (NLS) and may primarily function as a transcription regulator within the nucleus.
Function ARID5B was identified as one of the intermediate early effector genes of the platelet-derived growth factor (PDGF). It forms a histone H3K9Me2 demethylase complex with PHD finger protein 2 and regulates the transcription of target genes involved in adipogenesis and liver development. ARID5B also plays a role in hematopoietic cell development and differentiation, plausibly as a transcription factor.

Implicated in

Note
  
Entity Acute lymphoblastic leukemia (ALL)
Note Single nucleotide polymorphisms (SNPs) in this gene (e.g., rs10821936) are strongly associated with susceptibility to childhood ALL, particularly hyperdiploid B-lineage ALL. Also, ARID5B SNPs were also related to ALL relapse, with the disease susceptibility alleles always linked to poorer treatment outcome. However, the molecular mechanisms of how ARID5B contributes to leukemogenesis and relapse remain unclear.
  
  
Entity Endometrial carcinoma
Note Recurrent somatic mutations in ARID5B have also been described in endometrial carcinoma and is particularly enriched in the MSI subtype (23,1%).
  
  
Entity Rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE)
Note SNPs in this gene (e.g., rs10821944 in RA and rs4948496 in SLE) are associated with RA and SLE, both of which are autoimmune diseases but with distinct clinical characteristics.
  

Bibliography

PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B.
Baba A, Ohtake F, Okuno Y, Yokota K, Okada M, Imai Y, Ni M, Meyer CA, Igarashi K, Kanno J, Brown M, Kato S.
Nat Cell Biol. 2011 Jun;13(6):668-75. doi: 10.1038/ncb2228. Epub 2011 May 1.
PMID 21532585
 
Integrated genomic characterization of endometrial carcinoma.
Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA.
Nature. 2013 May 2;497(7447):67-73. doi: 10.1038/nature12113.
PMID 23636398
 
Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs.
Lahoud MH, Ristevski S, Venter DJ, Jermiin LS, Bertoncello I, Zavarsek S, Hasthorpe S, Drago J, de Kretser D, Hertzog PJ, Kola I.
Genome Res. 2001 Aug;11(8):1327-34.
PMID 11483573
 
Densely interconnected transcriptional circuits control cell states in human hematopoiesis.
Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, McConkey ME, Habib N, Yosef N, Chang CY, Shay T, Frampton GM, Drake AC, Leskov I, Nilsson B, Preffer F, Dombkowski D, Evans JW, Liefeld T, Smutko JS, Chen J, Friedman N, Young RA, Golub TR, Regev A, Ebert BL.
Cell. 2011 Jan 21;144(2):296-309. doi: 10.1016/j.cell.2011.01.004.
PMID 21241896
 
Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population.
Okada Y, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Kawaguchi T, Stahl EA, Kurreeman FA, Nishida N, Ohmiya H, Myouzen K, Takahashi M, Sawada T, Nishioka Y, Yukioka M, Matsubara T, Wakitani S, Teshima R, Tohma S, Takasugi K, Shimada K, Murasawa A, Honjo S, Matsuo K, Tanaka H, Tajima K, Suzuki T, Iwamoto T, Kawamura Y, Tanii H, Okazaki Y, Sasaki T, Gregersen PK, Padyukov L, Worthington J, Siminovitch KA, Lathrop M, Taniguchi A, Takahashi A, Tokunaga K, Kubo M, Nakamura Y, Kamatani N, Mimori T, Plenge RM, Yamanaka H, Momohara S, Yamada R, Matsuda F, Yamamoto K.
Nat Genet. 2012 Mar 25;44(5):511-6. doi: 10.1038/ng.2231.
PMID 22446963
 
Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia.
Papaemmanuil E, Hosking FJ, Vijayakrishnan J, Price A, Olver B, Sheridan E, Kinsey SE, Lightfoot T, Roman E, Irving JA, Allan JM, Tomlinson IP, Taylor M, Greaves M, Houlston RS.
Nat Genet. 2009 Sep;41(9):1006-10. doi: 10.1038/ng.430. Epub 2009 Aug 16.
PMID 19684604
 
DNA-binding properties of ARID family proteins.
Patsialou A, Wilsker D, Moran E.
Nucleic Acids Res. 2005 Jan 7;33(1):66-80. Print 2005.
PMID 15640446
 
PDGF signaling specificity is mediated through multiple immediate early genes.
Schmahl J, Raymond CS, Soriano P.
Nat Genet. 2007 Jan;39(1):52-60. Epub 2006 Dec 3.
PMID 17143286
 
Germline genomic variants associated with childhood acute lymphoblastic leukemia.
Trevino LR, Yang W, French D, Hunger SP, Carroll WL, Devidas M, Willman C, Neale G, Downing J, Raimondi SC, Pui CH, Evans WE, Relling MV.
Nat Genet. 2009 Sep;41(9):1001-5. doi: 10.1038/ng.432. Epub 2009 Aug 16.
PMID 19684603
 
Associations of variations in the MRF2/ARID5B gene with susceptibility to type 2 diabetes in the Japanese population.
Wang G, Watanabe M, Imai Y, Hara K, Manabe I, Maemura K, Horikoshi M, Ozeki A, Itoh C, Sugiyama T, Kadowaki T, Yamazaki T, Nagai R.
J Hum Genet. 2012 Nov 26;57(11):727-33. doi: 10.1038/jhg.2012.101. Epub 2012 Sep 13.
PMID 22971728
 
ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia.
Xu H, Cheng C, Devidas M, Pei D, Fan Y, Yang W, Neale G, Scheet P, Burchard EG, Torgerson DG, Eng C, Dean M, Antillon F, Winick NJ, Martin PL, Willman CL, Camitta BM, Reaman GH, Carroll WL, Loh M, Evans WE, Pui CH, Hunger SP, Relling MV, Yang JJ.
J Clin Oncol. 2012 Mar 1;30(7):751-7. doi: 10.1200/JCO.2011.38.0345. Epub 2012 Jan 30.
PMID 22291082
 
Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations.
Xu H, Yang W, Perez-Andreu V, Devidas M, Fan Y, Cheng C, Pei D, Scheet P, Burchard EG, Eng C, Huntsman S, Torgerson DG, Dean M, Winick NJ, Martin PL, Camitta BM, Bowman WP, Willman CL, Carroll WL, Mullighan CG, Bhojwani D, Hunger SP, Pui CH, Evans WE, Relling MV, Loh ML, Yang JJ.
J Natl Cancer Inst. 2013 May 15;105(10):733-42. doi: 10.1093/jnci/djt042. Epub 2013 Mar 19.
PMID 23512250
 
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
Yang W, Tang H, Zhang Y, Tang X, Zhang J, Sun L, Yang J, Cui Y, Zhang L, Hirankarn N, Cheng H, Pan HF, Gao J, Lee TL, Sheng Y, Lau CS, Li Y, Chan TM, Yin X, Ying D, Lu Q, Leung AM, Zuo X, Chen X, Tong KL, Zhou F, Diao Q, Tse NK, Xie H, Mok CC, Hao F, Wong SN, Shi B, Lee KW, Hui Y, Ho MH, Liang B, Lee PP, Cui H, Guo Q, Chung BH, Pu X, Liu Q, Zhang X, Zhang C, Chong CY, Fang H, Wong RW, Sun Y, Mok MY, Li XP, Avihingsanon Y, Zhai Z, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Gao F, Shotelersuk V, Kang X, Ying SK, Zhang L, Wong WH, Zhu D, Fung SK, Zeng F, Lai WM, Wong CM, Ng IO, Garcia-Barcelo MM, Cherny SS, Shen N, Tam PK, Sham PC, Ye DQ, Yang S, Zhang X, Lau YL.
Am J Hum Genet. 2013 Jan 10;92(1):41-51. doi: 10.1016/j.ajhg.2012.11.018. Epub 2012 Dec 27.
PMID 23273568
 
A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
Yuan YC, Whitson RH, Liu Q, Itakura K, Chen Y.
Nat Struct Biol. 1998 Nov;5(11):959-64.
PMID 9808040
 

Citation

This paper should be referenced as such :
Xu, H ; Yang, JJ
ARID5B (AT rich interactive domain 5B (MRF1-like))
Atlas Genet Cytogenet Oncol Haematol. 2014;18(3):150-151.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/ARID5BID51529ch10q21.html


External links

Nomenclature
HGNC (Hugo)ARID5B   17362
Cards
AtlasARID5BID51529ch10q21
Entrez_Gene (NCBI)ARID5B  84159  AT-rich interaction domain 5B
AliasesDESRT; MRF-2; MRF2
GeneCards (Weizmann)ARID5B
Ensembl hg19 (Hinxton)ENSG00000150347 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000150347 [Gene_View]  chr10:62049211-62096948 [Contig_View]  ARID5B [Vega]
ICGC DataPortalENSG00000150347
TCGA cBioPortalARID5B
AceView (NCBI)ARID5B
Genatlas (Paris)ARID5B
WikiGenes84159
SOURCE (Princeton)ARID5B
Genetics Home Reference (NIH)ARID5B
Genomic and cartography
GoldenPath hg38 (UCSC)ARID5B  -     chr10:62049211-62096948 +  10q21.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)ARID5B  -     10q21.2   [Description]    (hg19-Feb_2009)
EnsemblARID5B - 10q21.2 [CytoView hg19]  ARID5B - 10q21.2 [CytoView hg38]
Mapping of homologs : NCBIARID5B [Mapview hg19]  ARID5B [Mapview hg38]
OMIM608538   
Gene and transcription
Genbank (Entrez)AI149153 AK024803 AK123882 AK296921 AL049471
RefSeq transcript (Entrez)NM_001244638 NM_032199
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)ARID5B
Cluster EST : UnigeneHs.535297 [ NCBI ]
CGAP (NCI)Hs.535297
Alternative Splicing GalleryENSG00000150347
Gene ExpressionARID5B [ NCBI-GEO ]   ARID5B [ EBI - ARRAY_EXPRESS ]   ARID5B [ SEEK ]   ARID5B [ MEM ]
Gene Expression Viewer (FireBrowse)ARID5B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)84159
GTEX Portal (Tissue expression)ARID5B
Human Protein AtlasENSG00000150347-ARID5B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14865   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ14865  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14865
Splice isoforms : SwissVarQ14865
PhosPhoSitePlusQ14865
Domaine pattern : Prosite (Expaxy)ARID (PS51011)   
Domains : Interpro (EBI)ARID5B    ARID_dom   
Domain families : Pfam (Sanger)ARID (PF01388)   
Domain families : Pfam (NCBI)pfam01388   
Domain families : Smart (EMBL)BRIGHT (SM00501)  
Conserved Domain (NCBI)ARID5B
DMDM Disease mutations84159
Blocks (Seattle)ARID5B
PDB (SRS)1IG6    2OEH   
PDB (PDBSum)1IG6    2OEH   
PDB (IMB)1IG6    2OEH   
PDB (RSDB)1IG6    2OEH   
Structural Biology KnowledgeBase1IG6    2OEH   
SCOP (Structural Classification of Proteins)1IG6    2OEH   
CATH (Classification of proteins structures)1IG6    2OEH   
SuperfamilyQ14865
Human Protein Atlas [tissue]ENSG00000150347-ARID5B [tissue]
Peptide AtlasQ14865
IPIIPI00399164   IPI00455219   IPI00908840   
Protein Interaction databases
DIP (DOE-UCLA)Q14865
IntAct (EBI)Q14865
FunCoupENSG00000150347
BioGRIDARID5B
STRING (EMBL)ARID5B
ZODIACARID5B
Ontologies - Pathways
QuickGOQ14865
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II regulatory region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  liver development  DNA binding  transcription coactivator activity  protein binding  nucleus  nucleoplasm  transcription, DNA-templated  histone demethylation  histone demethylase activity  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of sequence-specific DNA binding transcription factor activity  adipose tissue development  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II regulatory region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  liver development  DNA binding  transcription coactivator activity  protein binding  nucleus  nucleoplasm  transcription, DNA-templated  histone demethylation  histone demethylase activity  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of sequence-specific DNA binding transcription factor activity  adipose tissue development  
REACTOMEQ14865 [protein]
REACTOME PathwaysR-HSA-3214842 [pathway]   
NDEx NetworkARID5B
Atlas of Cancer Signalling NetworkARID5B
Wikipedia pathwaysARID5B
Orthology - Evolution
OrthoDB84159
GeneTree (enSembl)ENSG00000150347
Phylogenetic Trees/Animal Genes : TreeFamARID5B
HOVERGENQ14865
HOGENOMQ14865
Homologs : HomoloGeneARID5B
Homology/Alignments : Family Browser (UCSC)ARID5B
Gene fusions - Rearrangements
Fusion : MitelmanARID5B/ABLIM1 [10q21.2/10q25.3]  
Fusion: TCGA_MDACCARID5B 10q21.2 ABLIM1 10q25.3 BRCA
Tumor Fusion PortalARID5B
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerARID5B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ARID5B
dbVarARID5B
ClinVarARID5B
1000_GenomesARID5B 
Exome Variant ServerARID5B
ExAC (Exome Aggregation Consortium)ENSG00000150347
GNOMAD BrowserENSG00000150347
Genetic variants : HAPMAP84159
Genomic Variants (DGV)ARID5B [DGVbeta]
DECIPHERARID5B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisARID5B 
Mutations
ICGC Data PortalARID5B 
TCGA Data PortalARID5B 
Broad Tumor PortalARID5B
OASIS PortalARID5B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICARID5B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDARID5B
intOGen PortalARID5B
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch ARID5B
DgiDB (Drug Gene Interaction Database)ARID5B
DoCM (Curated mutations)ARID5B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ARID5B (select a term)
intoGenARID5B
NCG5 (London)ARID5B
Cancer3DARID5B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM608538   
Orphanet
DisGeNETARID5B
MedgenARID5B
Genetic Testing Registry ARID5B
NextProtQ14865 [Medical]
TSGene84159
GENETestsARID5B
Target ValidationARID5B
Huge Navigator ARID5B [HugePedia]
snp3D : Map Gene to Disease84159
BioCentury BCIQARID5B
ClinGenARID5B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD84159
Chemical/Pharm GKB GenePA134943193
Clinical trialARID5B
Miscellaneous
canSAR (ICR)ARID5B (select the gene name)
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=ARID5B
Probes
Litterature
PubMed67 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineARID5B
EVEXARID5B
GoPubMedARID5B
iHOPARID5B
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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