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

2013-08-01   Heng Xu  , Jun J Yang  

Department of Pharmaceutical Sciences, St. Jude Childrens Research Hospital, 262 DannyThomas Place, MS 313, Memphis, TN 38105-2794, USA

Identity

HGNC
ARID5B
LOCATION
10q21.2
LOCUSID
84159
ALIAS
DESRT,MRF-2,MRF2
FUSION GENES
Show Gene Fusions

DNA/RNA

Atlas Image
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).

Proteins

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

Entity name
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 name
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 name
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.

Article Bibliography

Pubmed IDLast YearTitleAuthors
215325852011PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B.Baba A et al
236363982013Integrated genomic characterization of endometrial carcinoma.Kandoth C et al
114835732001Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs.Lahoud MH et al
212418962011Densely interconnected transcriptional circuits control cell states in human hematopoiesis.Novershtern N et al
224469632012Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population.Okada Y et al
196846042009Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia.Papaemmanuil E et al
156404462005DNA-binding properties of ARID family proteins.Patsialou A et al
171432862007PDGF signaling specificity is mediated through multiple immediate early genes.Schmahl J et al
196846032009Germline genomic variants associated with childhood acute lymphoblastic leukemia.Treviño LR et al
229717282012Associations of variations in the MRF2/ARID5B gene with susceptibility to type 2 diabetes in the Japanese population.Wang G et al
222910822012ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia.Xu H et al
235122502013Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations.Xu H et al
232735682013Meta-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 et al
98080401998A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.Yuan YC et al

Other Information

Locus ID:

NCBI: 84159
MIM: 608538
HGNC: 17362
Ensembl: ENSG00000150347

Variants:

dbSNP: 84159
ClinVar: 84159
TCGA: ENSG00000150347
COSMIC: ARID5B

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000150347ENST00000279873Q14865
ENSG00000150347ENST00000309334Q14865
ENSG00000150347ENST00000644638A0A2R8Y5F2

Expression (GTEx)

0
10
20
30
40
50
60
70
80
Adipose - Subcutaneous
Adipose - Visceral
Adrenal Gland
Artery - Aorta
Artery - Tibial
Bladder
Brain - Amygdala
Brain - Anterior cingulate cortex
Brain - Caudate
Brain - Cerebellar Hemisphere
Brain - Cerebellum
Brain - Cortex
Brain - Frontal Cortex
Brain - Hippocampus
Brain - Hypothalamus
Brain - Nucleus accumbens
Brain - Putamen
Brain - Spinal cord
Brain - Substantia nigra
Breast - Mammary Tissue
Cells - Cultured fibroblasts
Cells - EBV - transformed lymphocytes
Cervix - Ectocervix
Cervix - Endocervix
Colon - Sigmoid
Colon - Transverse
Esophagus - Gastroesophageal Junction
Esophagus - Mucosa
Esophagus - Muscularis
Fallopian Tube
Heart - Atrial Appendage
Heart - Left Ventricle
Kidney - Cortex
Kidney - Medulla
Liver
Lung
Minor Salivary Gland
Muscle - Skeletal
Nerve - Tibial
Ovary
Pancreas
Pituitary
Prostate
Skin - Not Sun Exposed
Skin - Sun Exposed
Small Intestine - Terminal Ileum
Spleen
Stomach
Testis
Thyroid
Uterus
Vagina
Whole Blood

Pathways

PathwaySourceExternal ID
Chromatin organizationREACTOMER-HSA-4839726
Chromatin modifying enzymesREACTOMER-HSA-3247509
HDMs demethylate histonesREACTOMER-HSA-3214842

Protein levels (Protein atlas)

Not detected
Low
Medium
High
cerebral cortex
cerebellum
hippocampus
caudate
thyroid gland
parathyroid gland
adrenal gland
nasopharynx
bronchus
lung
oral mucosa
salivary gland
esophagus
stomach 1
stomach 2
duodenum
small intestine
colon
rectum
liver
gallbladder
pancreas
kidney
urinary bladder
testis
epididymis
seminal vesicle
prostate
vagina
ovary
fallopian tube
endometrium 1
endometrium 2
cervix, uterine
placenta
breast
heart muscle
smooth muscle
skeletal muscle
soft tissue 1
soft tissue 2
adipose tissue
skin 1
skin 2
appendix
spleen
lymph node
tonsil
bone marrow

PharmGKB

Entity IDNameTypeEvidenceAssociationPKPDPMIDs
PA446155Precursor Cell Lymphoblastic Leukemia-LymphomaDiseaseClinicalAnnotationassociatedPK24712521
PA449841haloperidolChemicalMultilinkAnnotationassociated27023437
PA450428methotrexateChemicalClinicalAnnotationassociatedPK24712521

References

Pubmed IDYearTitleCitations
375780682024ARID5B, IKZF1, GATA3, CEBPE, and CDKN2A germline polymorphisms and predisposition to childhood acute lymphoblastic leukemia.0
382241862024ARID5B-mediated LINC01128 epigenetically activated pyroptosis and apoptosis by promoting the formation of the BTF3/STAT3 complex in β2GPI/anti-β2GPI-treated monocytes.0
387389682024Constitutional and acquired genetic variants in ARID5B in pediatric B-cell precursor acute lymphoblastic leukemia.0
375780682024ARID5B, IKZF1, GATA3, CEBPE, and CDKN2A germline polymorphisms and predisposition to childhood acute lymphoblastic leukemia.0
382241862024ARID5B-mediated LINC01128 epigenetically activated pyroptosis and apoptosis by promoting the formation of the BTF3/STAT3 complex in β2GPI/anti-β2GPI-treated monocytes.0
387389682024Constitutional and acquired genetic variants in ARID5B in pediatric B-cell precursor acute lymphoblastic leukemia.0
367085852023Association of two ARID5B gene variant single nucleotide polymorphisms with acute lymphoblastic leukemia in the Egyptian population.0
369524662023Contributions of ARID5B, IKZF1, PIP4K2A, and GATA3 Gene Polymorphisms to Childhood Acute Lymphoblastic Leukemia in a Chinese Population.0
370965022023[Correlation between ARID5B Gene SNP and MTX Resistance in Children with ALL].0
374836042023ARID5B regulates fatty acid metabolism and proliferation at the Pre-B cell stage during B cell development.0
379489992023ARID5B promoted the histone demethylation of SORBS2 and hampered the metastasis of ovarian cancer.1
367085852023Association of two ARID5B gene variant single nucleotide polymorphisms with acute lymphoblastic leukemia in the Egyptian population.0
369524662023Contributions of ARID5B, IKZF1, PIP4K2A, and GATA3 Gene Polymorphisms to Childhood Acute Lymphoblastic Leukemia in a Chinese Population.0
370965022023[Correlation between ARID5B Gene SNP and MTX Resistance in Children with ALL].0
374836042023ARID5B regulates fatty acid metabolism and proliferation at the Pre-B cell stage during B cell development.0

Citation

Heng Xu ; Jun J Yang

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

Atlas Genet Cytogenet Oncol Haematol. 2013-08-01

Online version: http://atlasgeneticsoncology.org/gene/51529/css/gene-fusions-explorer/