Alternative titles; symbols
HGNC Approved Gene Symbol: ARID1A
Cytogenetic location: 1p36.11 Genomic coordinates (GRCh38) : 1:26,696,015-26,782,104 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 1p36.11 | Coffin-Siris syndrome 2 | 614607 | Autosomal dominant | 3 |
ARID1A is a unique component of the BRG1 (SMARCA4; 603254)-associated factor (BAF) chromatin remodeling complex that facilitates gene activation by assisting transcription machinery to gain access to gene targets (Nie et al., 2000).
Takeuchi et al. (1997) reported a novel human cDNA encoding ARID1A, which they designated B120. B120 contains many repeat units, loosely identified as YXQQP, present in several human RNA-binding proteins. The B120 gene product is a 120-kD cytoplasmic protein expressed in various tissues including skeletal muscle, brain, and spleen. B120 has a CAG repeat length polymorphism, usually 7 repeats, encoding polyglutamine amino acids.
Using antibody against human p270 to screen a HeLa cell expression cDNA library, followed by screening a second HeLa cell library and 5-prime RACE of a WI-38 human fibroblast library, Dallas et al. (2000) obtained a partial cDNA encoding about 95% of the ARID1A protein, which they called p270. The deduced protein, which is N-terminally truncated, has a glutamine (Q)-rich N-terminal region, followed by an ARID domain, a second Q-rich region, and multiple copies of an LxxLL motif near the C terminus. Northern blot analysis revealed variable expression of an approximately 8.0-kb transcript in all tissues examined.
By sequencing peptides immunoaffinity purified with BRG1 from human cell line nuclear extracts, followed by EST database analysis and screening a Jurkat T-cell cDNA library, Nie et al. (2000) cloned full-length ARID1A, which they called BAF250. They noted that the B120 cDNA reported by Takeuchi et al. (1997) contains an unspliced intron at its 5-prime end and a sequencing error, resulting in a frameshift at its 3-prime end. The deduced 2,285-amino acid full-length BAF250 protein is rich in glutamine, proline, and alanine, and it shares 3 regions of conservation with its yeast and fly orthologs, including the ARID domain and 2 C-terminal regions containing LxxLL motifs. Swi1 is the closest ortholog of BAF250 in yeast. Northern blot analysis revealed wide expression of a 9.5-kb BAF250 transcript.
To examine the function of B120, Takeuchi et al. (1998) introduced B120 cDNA with an expression vector into various cell lines, including COS-1, C3H/10T1/2, and NIH 3T3 cells. These transfected cells exhibited small cytoplasmic spherical bodies. The cytoplasmic bodies appeared to be fat droplets on electron microscopy and histochemical staining. These findings suggested that B120 gene expression is associated with lipid metabolism and that overexpression of B120 may result in lipid deposition in various cells, including those of fibroblastic cell lines.
Dallas et al. (2000) showed that in vitro-translated human p270 bound immobilized native DNA. Deletion and mutation analysis revealed that DNA binding was confined to the ARID region and required conserved trp and tyr residues. Cloning and sequencing of DNA oligomers bound by the ARID region of p270 revealed no common motifs or sequence preferences.
By sequencing peptides that immunopurified with BAF and PBAF (see PBRM1; 606083) chromatin remodeling complexes, Nie et al. (2000) identified BAF250 as a component of the BAF complex only. The BAF complex possessed ATP-dependent mononucleosome disruption activity against a 176-bp fragment of 5S ribosomal DNA containing a nucleosome-positioning sequence. The intact BAF complex or a chimeric protein that included only the ARID domain of BAF250 bound a fragment containing the pyrimidine-rich element of the delta-globin (HBD;142000) gene. BAF250 also enhanced glucocorticoid receptor (GR, or GCCR; 138040)-mediated transcriptional activation following transfection of BAF250 into BAF250-negative human T47D breast cancer cells. The amount of BAF250 that associated with GR increased in the presence of glucocorticoid. Deletion of the conserved C-terminal region of BAF250 decreased its GR-dependent activation about 70%, and deletion of the ARID domain of BAF250 had a lesser effect.
By gel filtration, mass spectrometry, and Western blot analysis of human cell lines, Nie et al. (2003) identified unique low-abundance SWI/SWF complexes that contained ENL (MLLT1; 159556), several common SWI/SNF subunits, and either BAF250A or BAF250B (ARID1B; 614556). Both BAF250A- and BAF250B-containing complexes displayed ATP-dependent mononucleosome disruption activity in vitro.
To explore the genetic origin of ovarian clear-cell carcinoma (167000), Jones et al. (2010) determined the exomic sequences of 8 tumors after immunoaffinity purification of cancer cells. Through comparative analyses of normal cells from the same patients, Jones et al. (2010) identified 4 genes that were mutated in at least 2 tumors. Two of these genes, ARID1A and PPP2R1A (605983), which encodes a regulatory subunit of serine/threonine phosphatase-2, were not known to be involved in ovarian clear-cell carcinoma. The other 2 genes, previously implicated in ovarian clear-cell carcinoma, were PIK3CA (171834) and KRAS (190070). The nature and pattern of the mutations suggest that PPP2R1A functions as an oncogene and ARID1A as a tumor-suppressor gene. In a total of 42 ovarian clear-cell carcinomas, 7% had mutations in PPP2R1A and 57% had mutations in ARID1A. Jones et al. (2010) concluded that their results suggested that aberrant chromatin remodeling contributes to the pathogenesis of ovarian clear-cell carcinoma.
Dykhuizen et al. (2013) showed that BAF complexes decatenate newly replicated sister chromatids, a requirement for proper chromosome segregation during mitosis. Dykhuizen et al. (2013) found that deletion of Brg1 (603254) in mouse cells, as well as the expression of BRG1 point mutations identified in human tumors, leads to anaphase bridge formation (in which sister chromatids are linked by catenated strands of DNA) and a G2/M-phase block characteristic of the decatenation checkpoint. Endogenous BAF complexes interact directly with endogenous topoisomerase II-alpha (TOP2A; 126430) through BAF250a and are required for the binding of TOP2A to approximately 12,000 sites across the genome. Dykhuizen et al. (2013) concluded that TOP2A chromatin binding is dependent on the ATPase activity of BRG1, which is compromised in oncogenic BRG1 mutants. They further concluded that the ability of TOP2A to prevent DNA entanglement at mitosis requires BAF complexes and suggested that this activity contributes to the role of BAF subunits as tumor suppressors.
By comparing Arid1a -/- mice and ARID1A -/- HC116 human colon cancer cell lines with normal controls, Mathur et al. (2017) found that ARID1A was required to target SWI/SNF complexes to enhancers, but not promoters, in chromatin. Loss of ARID1A did not effect SWI/SNF complexes containing ARID1B. ARID1A -/- cells showed loss of acetylated histone H3 (see 602810) at enhancers distal to transcriptional start sites, and this correlated with loss of transcription at the nearest genes. Mathur et al. (2017) concluded that ARID1A is required for SWI/SNF-dependent and enhancer-mediated gene regulation.
Using a combination of gain- and loss-of-function approaches in several cellular contexts, Chang et al. (2018) showed that YAP (606608) and TAZ (607392) are necessary to induce the effects of the inactivation of the SWI/SNF complex, such as cell proliferation, acquisition of stem cell-like traits, and liver tumorigenesis. Chang et al. (2018) found that YAP/TAZ form a complex with SWI/SNF; this interaction is mediated by ARID1A and is alternative to the association of YAP/TAZ with the DNA-binding platform TEAD. Cellular mechanotransduction regulates the association between ARID1A-SWI/SNF and YAP/TAZ. The inhibitory interaction of ARID1A-SWI/SNF and YAP/TAZ is predominant in cells that experience low mechanical signaling, in which loss of ARID1A rescues the association between YAP/TAZ and TEAD. At high mechanical stress, nuclear F-actin binds to ARID1A-SWI/SNF, thereby preventing the formation of the ARID1A-SWI/SNF-YAP/TAZ complex, in favor of an association between TEAD and YAP/TAZ. Chang et al. (2018) proposed that a dual requirement must be met to fully enable the YAP/TAZ responses: promotion of nuclear accumulation of YAP/TAZ, for example, by loss of Hippo signaling, and inhibition of ARID1A-SWI/SNF, which can occur either through genetic inactivation or because of increased cell mechanics. Chang et al. (2018) concluded that their study offered a molecular framework in which mechanical signals that emerge at the tissue level together with genetic lesions activate YAP/TAZ to induce cell plasticity and tumorigenesis.
Cryoelectron Microscopy
He et al. (2020) reported the 3.7-angstrom resolution cryoelectron microscopy structure of the human BRG1/BRM-associated factor (BAF) complex, consisting of the catalytic subunit SMARCA4 (BRG1) and 9 auxiliary subunits, including ARID1A, bound to the nucleosome. The structure revealed that the nucleosome is sandwiched by the base and the ATPase modules, which are bridged by the actin-related protein (ARP) module, composed of an ACTL6A (604958)-ACTB (102630) heterodimer and the long alpha helix of the helicase-SANT-associated region (HSA) of SMARCA4. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal alpha helix of SMARCB1 (601607), enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. ARID1A and the SWI/SNF complex subunit SMARCC (601732) serve as a structural core and scaffold in the base module organization, respectively.
Takeuchi et al. (1998) mapped the ARID1A gene to chromosome 1p36.1-p35 by fluorescence in situ hybridization. Several human disorders, including Schnyder crystalline corneal dystrophy (121800), map to the 1p36.1-p35 region by genetic linkage. Since the cornea is composed of fibroblastic cells, Takeuchi et al. (1998) suggested that overfunction of ARID1A may be related to the pathogenesis of Schnyder crystalline corneal dystrophy.
Coffin-Siris Syndrome 2
In 3 patients with Coffin-Siris syndrome-2 (CSS2; 614607), Tsurusaki et al. (2012) identified heterozygous mutations in the ARID1A gene (603024.0001-603024.0003).
Using a combination of whole-exome sequencing, next-generation sequencing of 23 SWI/SNF complex genes, and molecular karyotyping, Wieczorek et al. (2013) identified mutations in 28 (60%) of 46 patients with a clinical phenotype consistent with Coffin-Siris syndrome or Nicolaides-Baraitser syndrome (NCBRS; 601358), which shows similar features. Only 1 patient had a heterozygous truncating mutation in the ARID1A gene, which was likely somatic mosaic (R1989X; 603024.0004). Functional studies of the variant were not performed.
In 4 unrelated patients with CSS2, Santen et al. (2013) identified 4 different de novo heterozygous pathogenic mutations in the ARID1A gene (see, e.g., 603024.0005-603024.0006). The mutations were all shown to be somatic mosaic, although to different extents. Santen et al. (2013) noted that homozygous loss of the Arid1a gene is embryonic lethal in mice, and suggested that truncating germline variants in the ARID1A gene may be embryonic lethal in humans as well. The patients were ascertained from a large cohort of 63 patients with a clinical diagnosis of CSS who were screened for mutations in the 6 genes of the BAF complex. Functional studies of the variants were not performed.
Somatic ARID1A Mutations in Cancer
Wiegand et al. (2010) sequenced the whole transcriptomes of 18 ovarian clear-cell carcinomas and 1 ovarian clear-cell carcinoma cell line and found somatic mutations in ARID1A in 6 of the samples. ARID1A encodes BAF250a, a key component of the SWI-SNF chromatin remodeling complex. Wiegand et al. (2010) then sequenced ARID1A in an additional 210 ovarian carcinomas and a second ovarian clear-cell carcinoma cell line and measured BAF250a expression by means of immunohistochemical analysis in an additional 455 ovarian carcinomas. ARID1A mutations were seen in 55 of 119 ovarian clear-cell carcinomas (46%), 10 of 33 endometrioid carcinomas (30%), and none of the 76 high-grade serous ovarian carcinomas. Seventeen of the carcinomas had 2 somatic mutations each. Loss of the BAF250a protein correlated strongly with the ovarian clear-cell carcinoma and endometrioid carcinoma subtypes and the presence of ARID1A mutations. In 2 patients, ARIDIA mutations and loss of BAF250a expression were evident in the tumor and contiguous atypical endometriosis but not in distal endometriotic lesions. Wiegand et al. (2010) concluded that these data implicated ARID1A in as a tumor suppressor gene frequently disrupted in ovarian clear-cell and endometrioid carcinoma. Since ARID1A mutation and loss of BAF250a can be seen in preneoplastic lesions, Wiegand et al. (2010) speculated that mutation of ARID1A is an early event in the transformation of endometriosis into cancer.
The finding of frequent ARID1A mutations in ovarian clear-cell and endometrioid carcinomas by Wiegand et al. (2010) suggested to Nissenblatt (2011) that such tumors may be of mullerian rather than coelomic derivation. Nissenblatt (2011) noted that the 3 most common types of ovarian carcinoma, i.e., serous, endometrioid, and mucinous, are histologically identical to tumors of the fallopian tube, endometrium, and endocervix, tumors known to arise from the embryonic mullerian duct. In a reply to the comments of Nissenblatt (2011), Huntsman et al. (2011) suggested that endometrioid carcinomas of the ovary and clear-cell carcinomas should be included with similar uterine cancers in clinical trials.
Birnbaum et al. (2011) profiled pancreatic carcinoma samples from 39 patients and 8 cell lines using high-resolution array comparative genomic hybridization and found a heterozygous deletion of the 1p35 chromosomal region in 56.4% of tumors and 5 cell lines. This region, which is commonly deleted in human cancers, includes ARID1A, which is involved in chromatin remodeling and is suspected to be a tumor suppressor gene. Sequencing of ARID1A exons detected 2 acquired heterozygous mutations (1 nonsense and 1 missense) in tumors. These mutations were different from those reported in ovarian cancer. Birnbaum et al. (2011) concluded that their results suggested a potential role of ARID1A and aberrant chromatin remodeling in pancreatic carcinoma and showed that the spectrum of ARID1A alterations, including deletions, may be large. Huntsman et al. (2011) stated that the findings of Birnbaum et al. (2011) added to a body of evidence implicating abnormalities in chromatin-remodeling complexes, and in particular the BAF250a-containing SWI/SNF nucleosome remodeling complex, as key events in many cancers.
Le Gallo et al. (2012) used whole-exome sequencing to comprehensively search for somatic mutations in 13 primary serous endometrial tumors (see 608089), and subsequently resequenced 18 genes that were mutated in more than 1 tumor and/or were components of an enriched functional grouping from 40 additional serous tumors. Le Gallo et al. (2012) identified a high frequency of somatic mutation (6%) in the ARID1A gene.
Jiao et al. (2013) detected somatic ARID1A mutations in 6 of 32 (19%) intrahepatic cholangiocarcinomas (615619) in a discovery screen and in 3 of 32 (9%) independent intrahepatic cholangiocarcinomas in the prevalence screen. Chan-on et al. (2013) identified somatic ARID1A mutations in 9 of 86 (10.5%) non-O.viverrini cholangiocarcinomas and in 19 of 108 (17.6%) O. viverrini-related cholangiocarcinomas.
Gao et al. (2008) found that complete absence of Baf250a in mice was embryonic lethal, resulting in developmental arrest around day E6.5 without formation of a primitive streak or mesoderm, indicating its critical role in early germ-layer formation at gastrulation. Cellular studies showed that Baf250a deficiency in embryonic stem cells compromised embryonic cell pluripotency, inhibited self-renewal, and promoted differentiation into primitive endoderm-like cells.
Krosl et al. (2010) generated a mutant mouse strain harboring a Baf250a allele lacking exons 2 and 3. Transcripts from this allele were expressed at normal levels and encoded a Baf250 protein lacking 150 amino acids within the N-terminal region. Heterozygous mutant mice were healthy for over 12 months, but no homozygous mutant offspring were obtained. Krosl et al. (2010) examined hemopoiesis in homozygous mutant fetal liver and found that Baf250a was not required for hemopoietic stem cell specification, onset of definitive hemopoiesis, or differentiation of blood cells. However, stromal cell layers established from homozygous mutant fetal liver cells were more efficient than wildtype fetal liver cells in in vitro maintenance and expansion of primitive hemopoietic cells. This advantage was associated with enhanced expression of transcripts encoding soluble factors associated with hematopoietic stem cell growth and reduced expression of transcripts associated with cell senescence or oxidative stress-induced apoptosis. Krosl et al. (2010) hypothesized that BAF250A controls the size of the fetal liver hematopoietic stem cell pool through regulation of the fetal liver microenvironment.
In Patient 3 with Coffin-Siris syndrome (CSS2; 614607), Tsurusaki et al. (2012) detected a heterozygous 26-bp deletion (31_56del) in the ARID1A gene, resulting in frameshift and premature termination 91 amino acids downstream (Ser11AlafsTer91). The patient presented with hepatoblastoma as well as multiple congenital anomalies. This mutation was not identified in 330 control chromosomes or in the dbSNP (build 132), 1000 Genomes Project, or Exome Sequencing Project databases. The parents were unavailable for testing.
In Patient 6 with Coffin-Siris syndrome (CSS2; 614607), Tsurusaki et al. (2012) detected a heterozygous C-to-T transition at nucleotide 2758 of the ARID1A gene that resulted in a gln-to-ter substitution at codon 920 (Q920X). This mutation was not identified in 376 control chromosomes or in the dbSNP (build 132), 1000 Genomes Project, or Exome Sequencing Project databases. The parents were unavailable for testing.
In Patient 8 with Coffin-Siris syndrome (CSS2; 614607), Tsurusaki et al. (2012) detected a heterozygous C-to-T transition at nucleotide 4003 of the ARID1A gene, resulting in an arg-to-ter substitution at codon 1335 (R1335X). The mutation occurred as a de novo event.
In a patient (K2435) with Coffin-Siris syndrome-2 (CSS2; 614607), Wieczorek et al. (2013) identified a de novo heterozygous c.5965C-T transition in exon 20 of the ARID1A gene, resulting in an arg1989-to-ter (R1989X) substitution. The mutant allele was detected at a lower proportion than the wildtype allele, indicating the presence of somatic mosaicism in the individual. The patient was 1 of 46 patients with a clinical phenotype consistent with Coffin-Siris syndrome who underwent sequencing of 23 SWI/SNF complex genes. Functional studies of the variant were not performed.
In a patient (patient 48) with Coffin-Siris syndrome-2 (CSS2; 614607), Santen et al. (2013) identified a de novo heterozygous 1-bp deletion (c.1113del, NM_006015.4) in exon 1 of the ARID1A gene, resulting in a frameshift and premature termination (Gln372SerfsTer19). The mutant peak was lower than the wildtype peak, suggesting somatic mosaicism.
In a patient (patient 26) with Coffin-Siris syndrome-2 (CSS2; 614607), Santen et al. (2013) identified a de novo heterozygous c.3679G-T transversion (c.3679G-T, NM_006015.4) in exon 14 of the ARID1A gene, resulting in a glu1227-to-ter (E1227X) substitution. The mutant peak was lower than the wildtype peak, suggesting somatic mosaicism.
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