Alternative titles; symbols
HGNC Approved Gene Symbol: ADARB1
Cytogenetic location: 21q22.3 Genomic coordinates (GRCh38): 21:45,074,578-45,226,563 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 21q22.3 | Neurodevelopmental disorder with hypotonia, microcephaly, and seizures | 618862 | Autosomal recessive | 3 |
ADAR enzymes, such as ADARB1, bind to double-stranded RNA and catalyze A-to-I RNA editing. A-to-I editing in 3-prime UTRs can affect RNA abundance, whereas editing in coding regions can cause amino acid substitutions because the translational machinery recognizes inosine as guanosine (summary by Terajima et al., 2017).
RNA editing involves the deamination of adenosines at specific sites, the result of which can be a change in the amino acid sequence of the protein so that it differs from that predicted by the sequence of the DNA. Editing of the glutamate receptor B (GluRB, or GRIA2; 138247) pre-mRNA has been shown to alter a codon (referred to as the Q/R site) for a channel determinant that controls the calcium permeability of the AMPA glutamate receptors. Melcher et al. (1996) tested the candidate dsRNA adenosine deaminase Drada (ADAR; 146920) and showed that when coexpressed with a GluRB minigene in HEK 293 cells, Drada produced low-level editing at the GluRB Q/R site. The authors then screened a rat brain cDNA library with the predicted catalytic domain of rat DRADA to identify other potential editing enzymes. A cDNA encoding a predicted 711-amino acid protein was isolated that gave about 90% of the expected activity in their editing assay. Melcher et al. (1996) designated this novel mammalian RNA editing protein RNA-editing enzyme-1 (Red1). Rat Red1 and Drada share about 31% overall identity primarily due to their conservation in the C-terminal catalytic domain. Northern blot analysis showed highest expression of Red1 in rat brain. Melcher et al. (1996) further observed that while Red1 was more efficient at deaminating some sites, Drada had stronger activity at others. They speculated that a combination of these and perhaps other editing enzymes may be involved in determining the overall editing process for a given transcript.
Mittaz et al. (1997) also cloned a human gene homologous to rat Red1. The human gene, ADARB1, comprises 741 amino acids and contains 2 double-stranded RNA-binding domains in its N-terminal region. The authors detected 2 transcripts of 8.8 and 4.2 kb that were strongly expressed in brain and in many human adult and fetal tissues.
By searching for ESTs related to DRADA, Lai et al. (1997) also isolated human cDNAs encoding ADARB1, which they designated DRADA2. The DRADA2 gene was expressed ubiquitously in human adult and fetal tissues. It had a complex transcription pattern, with 1 major 8.6-kb mRNA and several minor shorter mRNAs, some of which showed tissue specificity. Four DRADA2 isoforms, ranging in predicted size from 674 to 741 amino acids, result from alternative splicing and differ in their RNA editing capabilities in vitro.
The glutamate receptor subunit B pre-mRNA is edited at 2 adenosine residues, resulting in amino acid changes that alter the electrophysiologic properties of the glutamate receptor. These amino acid changes are due to adenosine-to-inosine conversions in 2 codons resulting from adenosine deamination. Yang et al. (1997) described the purification and characterization of a human RNA adenosine deaminase from HeLa cells that efficiently and accurately edits glutamate receptor subunit B pre-mRNA at both of these sites. They concluded that the activity reflects the human homolog of the RED1 protein, a member of the family of double-stranded RNA-dependent deaminase proteins. O'Connell et al. (1997) described the purification of a 90-kD protein identified as human RED1. They showed that it edits the glutamine codon at position 586 in the pre-mRNA of the glutamate receptor B subunit.
Using mouse liver for chromatin immunoprecipitation and RNA sequencing, Terajima et al. (2017) found circadian expression of Adarb1, which has 2 Clock (601851)-binding sites in its first intron. Adarb1 caused circadian A-to-I RNA editing in various transcripts, including self-editing of its own pre-RNA, which caused expression of a long Adarb1 splice variant. Most of the rhythmic editing sites were found in 3-prime UTRs of transcripts, with much less found within coding regions.
Tan et al. (2017) reported dynamic spatiotemporal patterns and novel regulators of RNA editing, discovered through an extensive profiling of adenosine-to-inosine RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. Tan et al. (2017) showed that editing levels in nonrepetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 (146920) is the primary editor of repetitive sites and ADAR2 is the primary editor of nonrepetitive coding sites, whereas the catalytically inactive ADAR3 (602065) predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. Tan et al. (2017) curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. The authors also found that AIMP2 (600859), a component of the aminoacyl-tRNA synthetase complex, interacts with both ADAR1 and ADAR2 and reduces editing by enhancing their degradation.
Villard et al. (1997) found that the ADARB1 gene spans approximately 25 kb and comprises 10 exons of coding sequence. The 2 RNA binding domains are located within the 935-bp exon 2. An alternatively processed exon 6 potentially interrupts the catalytic domain. A survey of expression patterns revealed differential processing of the 5- and 8.5-kb transcripts in all sources examined. The difference in transcript size appeared to result from alternative processing in the 3-prime untranslated portion.
Mittaz et al. (1997) mapped the ADARB1 gene to chromosome 21q22.3 by YAC contig analysis. See also ADARB2 (602065).
Using a cDNA fragment containing sequences homologous to the rat RED1 RNA editase gene, Villard et al. (1997) localized the human ADARB1 gene to chromosome 21 by hybridization to a panel of somatic cell hybrids containing subregions of 21q. This confirmed the location of RED1 in distal 21q22.3.
Crystal Structure
Macbeth et al. (2005) reported the crystal structure of human ADAR2 at 1.7-angstrom resolution. The structure revealed a zinc ion in the active site and suggested how the substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP6) is buried within the enzyme core, contributing to the protein fold. Although there are no reports that adenosine deaminases that act on RNA (ADARs) require a cofactor, Macbeth et al. (2005) showed that IP6 is required for activity. Amino acids that coordinate IP6 in the crystal structure are conserved in some adenosine deaminases that act on transfer RNA, (ADATs), related enzymes that edit tRNA. Macbeth et al. (2005) showed that IP6 is also essential for in vivo and in vitro deamination of adenosine-37 of tRNA(alanine) (601431) by ADAT1 (604230).
In 4 unrelated patients with neurodevelopmental disorder with hypotonia, microcephaly, and seizures (NEDHYMS; 618862), Tan et al. (2020) identified homozygous or compound heterozygous missense mutations in the ADARB1 gene (601218.0001-601218.0005). The patients were evaluated by exome sequencing at different centers and ascertained through the GeneMatcher or Matchmaker Exchange programs. The mutations occurred throughout the gene, and molecular modeling showed that they were situated in or around the deaminase domain or the dsRBD1 domain. In vitro functional expression assays in HEK293 cells showed that 4 of the 5 variants caused variable decreases in the RNA editing activity of ADARB1 compared to controls. Some of the variants also impaired ADARB1 RNA editing of the mouse Gria2 (138247) Q/R site. The authors hypothesized that the mutations had adverse effects on RNA editing of target substrates, although the precise molecular effects remained to be clarified.
In 3 children from 2 unrelated consanguineous families with NEDHYMS, Maroofian et al. (2021) identified homozygous mutations in the ADARB1 gene (R630Q, 601218.0006; c.1245_1247+1del, 601218.0007). The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Expression of the R630Q mutation in HEK293 cells resulted in decreased RNA editing activity compared to controls. Expression of the c.1245_1247+1del mutation in a minigene assay resulted in abnormal splicing, with skipping of exon 4, and was predicted to result in nonsense-mediated decay.
Higuchi et al. (2000) studied ADAR2-mediated RNA editing by generating mice that were homozygous for a targeted functional null allele. Editing in Adar2 -/- mice was substantially reduced at most of 25 positions in diverse transcripts; the mutant mice became prone to seizures and died young. The impaired phenotype appeared to result entirely from a single underedited position, since it reverted to normal when both alleles for the underedited transcript were substituted with alleles encoding the edited version exonically. The critical position specifies an ion channel determinant, the Q/R site, in AMPA receptor GluRB premessenger RNA. Higuchi et al. (2000) concluded that this transcript is physiologically the most important substrate of ADAR2.
Terajima et al. (2017) found that Adarb1 -/- mice with rescued Gria2 expression showed attenuated rhythms in large populations of mRNAs compared with wildtype. Furthermore, rescued Adarb1 -/- mice exhibited short-period rhythms in locomotor activity and gene expression and loss of day/night variation in plasma free fatty acid levels. Terajima et al. (2017) concluded that ADARB1 plays a key role in generating cyclic editing and mRNA rhythms and that these rhythms are important in diverse aspects of physiology, including control of circadian oscillation speed.
In a 5.9-year-old boy (patient 1) with neurodevelopmental disorder with hypotonia, microcephaly, and seizures (NEDHYMS; 618862), Tan et al. (2020) identified compound heterozygous missense mutations in the ADARB1 gene: a c.1101G-C transversion (c.1101G-C, NM_001112.4), resulting in a lys367-to-asn (K367N) substitution, and a c.1492A-G transition, predicted to result in a thr498-to-ala (T498A) substitution close to the deaminase domain. The mutations, which were found by exome sequencing, segregated with the disorder in the family. Both variants were found in the heterozygous state in the gnomAD database at low frequencies (8.5 x 10(-6) and 5.3 x 10(-4), respectively). The mutant proteins localized normally to the nucleus in transfected HeLa cells. Transfection of the K367N mutation into HEK293 cells showed that it caused a 10.9% decrease in RNA editing compared to controls; the effect was more pronounced in the S isoform. However, expression of both the K367N and T498A mutations together did not decrease the RNA editing activity. In vitro cellular expression studies in neuroblastoma cells, HeLa cells, and patient fibroblasts showed that the c.1492A-G variant altered the splicing of exon 5a.
For discussion of the c.1492A-G transition (c.1492A-G, NM_001112.4) in the ADARB1 gene, resulting in a thr498-to-ala (T498A) substitution, that was found in compound heterozygous state in a patient with neurodevelopmental disorder with hypotonia, microcephaly, and seizures (NEDHYMS; 618862) by Tan et al. (2020), see 601218.0001.
In a 2-year-old boy (patient 2) of Hispanic descent with neurodevelopmental disorder with hypotonia, microcephaly, and seizures (NEDHYMS; 618862), Tan et al. (2020) identified a homozygous c.379A-G transition (c.379A-G, NM_001112.4) in the ADARB1 gene, resulting in a lys127-to-glu (K127E) substitution in the dsRBD1 domain. The mutation, which was found by exome sequencing, segregated with the disorder in the family and was not found in the gnomAD database. The mutant protein localized normally to the nucleus in transfected HeLa cells. Transfection of the mutation into HEK293 cells showed that the variant caused a 14.6% decrease in RNA editing activity compared to controls; the effect was more pronounced in the S isoform.
In a 2-year-old boy (patient 3), born of consanguineous Muslim parents, with neurodevelopmental disorder with hypotonia, microcephaly, and seizures (NEDHYMS; 618862), Tan et al. (2020) identified a homozygous c.1808G-A transition (c.1808G-A, NM_001112.4) in the ADARB1 gene, resulting in an arg603-to-gln (R603Q) substitution at a highly conserved residue in the deaminase domain. The mutation, which was found by exome sequencing, segregated with the disorder in the family. The variant was found at a low frequency (3.98 x 10(-6)) in the heterozygous state in the gnomAD database. Immunoblot analysis of cells transfected with the mutation showed low protein levels compared to controls, indicating that the mutation causes instability of the protein. However, the mutant protein localized normally to the nucleus in transfected HeLa cells. Transfection of the mutation into HEK293 cells showed that the variant caused a severe decrease (over 85% decrease) in RNA editing activity compared to controls.
In an 11-year-old boy (patient 4), born of consanguineous Azari parents, with neurodevelopmental disorder with hypotonia, microcephaly, and seizures (NEDHYMS; 618862), Tan et al. (2020) identified a homozygous c.2165C-T transition (c.2165C-T, NM_001112.4) in the ADARB1 gene, resulting in an ala722-to-val (A722V) substitution in the deaminase domain. The mutation, which was found by exome sequencing, segregated with the disorder in the family. The variant was found at a low frequency (4.08 x 10(-6)) in the heterozygous state in the gnomAD database. The mutant protein localized normally to the nucleus in transfected HeLa cells. Transfection of the mutation into HEK293 cells showed that the variant caused a 4.4% decrease in RNA editing activity compared to controls.
In a 5-year-old girl (patient 1), born to consanguineous Iraqi parents, with neurodevelopmental disorder with hypotonia, microcephaly, and seizures (NEDHYMS; 618862), Maroofian et al. (2021) identified homozygosity for a c.1889G-A transition (c.1889G-A, NM_015833.4) in exon 8 of the ADARB1 gene, resulting in an arg630-to-gln (R630Q) substitution at a conserved residue. The mutation, which was identified by whole-exome sequencing and confirmed by Sanger sequencing, was present in heterozygous state in the parents. Expression of R630Q in HEK293 cells resulted in decreased RNA editing activity compared to controls. The patient had 2 similarly affected deceased sibs who had not undergone genetic testing.
In 4.9- and 6-year-old sisters (patients 2 and 3), born to consanguineous Egyptian parents, with neurodevelopmental disorder with hypotonia, microcephaly, and seizures (NEDHYMS; 618862), Maroofian et al. (2021) identified homozygosity for a 4-bp deletion (c.1245_1247+1del, NM_015833.4) in exon 4 and the downstream intron of the ADARB1 gene, resulting in a frameshift and premature termination (Leu415PhefsTer14). The mutation, which was identified by whole-exome sequencing and confirmed by Sanger sequencing, was present in heterozygous state in the parents. A minigene assay to assess splicing in ADARB1 with the c.1245_1247+1del mutation resulted in abnormal splicing, including a major isoform with skipping of exon 4, and was predicted to result in nonsense-mediated decay.
Higuchi, M., Maas, S., Single, F. N., Hartner, J., Rozov, A., Burnashev, N., Feldmeyer, D., Sprengel, R., Seeburg, P. H. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406: 78-81, 2000. [PubMed: 10894545] [Full Text: https://doi.org/10.1038/35017558]
Lai, F., Chen, C.-X., Carter, K. C., Nishikura, K. Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases. Molec. Cell. Biol. 17: 2413-2424, 1997. [PubMed: 9111310] [Full Text: https://doi.org/10.1128/MCB.17.5.2413]
Macbeth, M. R., Schubert, H. L., VanDemark, A. P., Lingam, A. T., Hill, C. P., Bass, B. L. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science 309: 1534-1539, 2005. [PubMed: 16141067] [Full Text: https://doi.org/10.1126/science.1113150]
Maroofian, R., Sedmik, J., Mazaheri, N., Scala, M., Zaki, M. S., Keegan, L. P., Azizimalamiri, R., Issa, M., Shariati, G., Sedaghat, A., Beetz, C., Bauer, P., Galehdari, H., O'Connell, M. A., Houlden, H. Biallelic variants in ADARB1, encoding a dsRNA-specific adenosine deaminase, cause a severe developmental and epileptic encephalopathy. J. Med. Genet. 58: 495-504, 2021. [PubMed: 32719099] [Full Text: https://doi.org/10.1136/jmedgenet-2020-107048]
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Mittaz, L., Scott, H. S., Rossier, C., Seeburg, P. H., Higuchi, M., Antonarakis, S. E. Cloning of a human RNA editing deaminase (ADARB1) of glutamate receptors that maps to chromosome 21q22.3. Genomics 41: 210-217, 1997. [PubMed: 9143496] [Full Text: https://doi.org/10.1006/geno.1997.4655]
O'Connell, M. A., Gerber, A., Keller, W. Purification of human double-stranded RNA-specific editase 1 (hRED1) involved in editing of brain glutamate receptor B pre-mRNA. J. Biol. Chem. 272: 473-478, 1997. [PubMed: 8995285] [Full Text: https://doi.org/10.1074/jbc.272.1.473]
Tan, M. H., Li, Q., Shanmugam, R., Piskol, R., Kohler, J., Young, A. N., Liu, K. I., Zhang, R., Ramaswami, G., Ariyoshi, K., Gupte, A., Keegan, L. P., and 18 others. Dynamic landscape and regulation of RNA editing in mammals. Nature 550: 249-254, 2017. [PubMed: 29022589] [Full Text: https://doi.org/10.1038/nature24041]
Tan, T. Y., Sedmik, J., Fitzgerald, M. P., Halevy, R. S., Keegan, L. P., Helbig, I., Basel-Salmon, L., Cohen, L., Straussberg, R., Chung, W. K., Helal, M., Maroofian, R., Houlden, H., Juusola, J., Sadedin, S., Pais, L., Howell, K. B., White, S. M., Christodoulou, J., O'Connell, M. A. Bi-allelic ADARB1 variants associated with microcephaly, intellectual disability, and seizures. Am. J. Hum. Genet. 106: 467-483, 2020. [PubMed: 32220291] [Full Text: https://doi.org/10.1016/j.ajhg.2020.02.015]
Terajima, H., Yoshitane, H., Ozaki, H., Suzuki, Y., Shimba, S., Kuroda, S., Iwasaki, W., Fukada, Y. ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm. Nature Genet. 49: 146-151, 2017. [PubMed: 27893733] [Full Text: https://doi.org/10.1038/ng.3731]
Villard, L., Tassone, F., Haymowicz, M., Welborn, R., Gardiner, K. Map location, genomic organization and expression patterns of the human RED1 RNA editase. Somat. Cell Molec. Genet. 23: 135-145, 1997. [PubMed: 9330641] [Full Text: https://doi.org/10.1007/BF02679972]
Yang, J.-H., Sklar, P., Axel, R., Maniatis, T. Purification and characterization of a human RNA adenosine deaminase for glutamate receptor B pre-mRNA editing. Proc. Nat. Acad. Sci. 94: 4354-4359, 1997. [PubMed: 9113993] [Full Text: https://doi.org/10.1073/pnas.94.9.4354]