Alternative titles; symbols
HGNC Approved Gene Symbol: RBFOX1
Cytogenetic location: 16p13.3 Genomic coordinates (GRCh38): 16:5,239,721-7,713,340 (from NCBI)
RBFOX1 regulates tissue-specific splicing by binding to the element (U)GCAUG in mRNA precursors. Depending on where it binds relative to the regulated exon, RBFOX1 can regulate splicing positively or negatively (Fukumura et al., 2007).
By yeast 2-hybrid analysis, Shibata et al. (2000) identified A2BP1, which binds to the C terminus of ataxin-2 (ATXN2; 601517). The 377-amino acid coding sequence contains an RNP motif that is highly conserved among RNA-binding proteins. Northern blot analysis showed that A2BP1 was predominantly expressed in muscle and brain. Evidence for at least 3 isoforms was detected. By immunofluorescent staining, A2BP1 and ataxin-2 were both localized to the trans-Golgi network. Immunocytochemistry showed that A2BP1 was expressed in the cytoplasm of Purkinje cells and dentate neurons in a punctate pattern similar to that seen for ataxin-2 labeling. Western blot analysis of subcellular fractions indicated enrichment of A2BP1 in the same fractions as ataxin-2. Shibata et al. (2000) concluded that A2BP1 and related proteins form a novel gene family sharing RNA-binding motifs.
Martin et al. (2007) noted that there are 4 A2BP1 isoforms.
Jin et al. (2003) cloned mouse and zebrafish A2bp1, which they called Fox1. Northern blot analysis of mouse tissues detected Fox1 in heart, skeletal muscle, and brain. Whole-mount in situ hybridization of developing zebrafish showed that Fox1 expression was restricted to muscle.
Using immunofluorescence analysis, Underwood et al. (2005) showed that both Fox1 and Fox2 (RBM9; 612149) were highly expressed in mouse brain, with strong staining of neurons of the dentate gyrus and CA3 region of the hippocampus. Neurons in both the cerebellum and olfactory bulb expressed either Fox1 or Fox2, but not both. Both Fox1 and Fox2 were predominantly nuclear, but Fox2 also showed some cytoplasmic expression.
Underwood et al. (2005) determined that the A2BP1 gene contains 25 exons; 5 are alternative first exons that introduce alternative promoters.
Martin et al. (2007) noted that the A2BP1 gene contains 16 exons and spans about 1.7 Mb of genomic DNA. The first 3 exons and part of the fourth exon contain the 5-prime untranslated region. Isoform 4 spans the entire 1.7 Mb, while isoforms 1, 2, and 3 cover only 380 kb at the 3-prime end of the gene.
The A2BP1 gene maps to chromosome 16p13 (Martin et al., 2007).
The A2BP1 protein was first identified as a binding protein of ATXN2 (Shibata et al., 2000). Expansion of a polyglutamine tract in ATXN2 results in spinocerebellar ataxia-2 (SCA2; 183090), suggesting that A2BP1 is also involved in neurologic function.
Jin et al. (2003) found that zebrafish Fox1 promoted muscle-specific skipping of exon 9 in the human mitochondrial ATP synthase gamma subunit (ATP5C1; 108729) by binding to GCAUG sequences in intron 8. Conversely, Fox1 promoted inclusion of exon EIIIB in the fibronectin (FN1; 135600) transcript. Jin et al. (2003) concluded that FOX1 has both positive and negative roles in tissue-specific splicing via GCAUG.
Using yeast 2-hybrid screens, coaffinity purification analysis of transfected HEK293 cells, and bioinformatic analysis, Lim et al. (2006) developed an interaction network for 54 human proteins involved in 23 inherited ataxias. By database analysis, they expanded the core network to include more distantly related interacting proteins that could function as genetic modifiers. RBM9, A2BP1, and RBPMS (601558) formed a main hub in the network and interacted with several ataxia-causing proteins, including ATXN1 (601556).
Fukumura et al. (2007) examined the mechanism of exon skipping by mouse Fox1 using human ATP5C1 pre-mRNA, which contains 4 copies of GCAUG in intron 8, as substrate. Fox1 overexpression repressed intron 9 splicing and induced exon 9 skipping via binding to the GCAUG element. Splicing of intron 8 was unaffected. By binding to intron 8, Fox1 prevented formation of the pre-spliceosomal early (E) complex on intron 9. Mutation analysis showed that the C-terminal region of Fox1 was involved in repressing intron 9 splicing.
Underwood et al. (2005) found the expression of Fox1 was upregulated during differentiation in mouse neuroblastoma cell line. Differentiation of a mouse myoblast cell line into myotubes was associated with increased Fox1 expression and decreased Fox2 expression. Both Fox1 and Fox2 activated splicing of neuron-specific exons by binding to a downstream UGCAUG element.
Ponthier et al. (2006) stated that the red cell membrane protein 4.1R (EPB41; 130500) in early erythroid progenitors is derived from transcripts in which exon 16 is skipped, and this isoform exhibits low affinity for spectrin (see SPTA1, 182860) and actin (see ACTG1; 102560). In contrast, late-stage erythroblasts include exon 16 and express a high-affinity isoform. Ponthier et al. (2006) found that FOX1 and FOX2 stimulate exon 16 splicing into a 4.1R pre-mRNA minigene via specific binding to UGCAUG splicing enhancer motifs downstream of exon 16.
Voineagu et al. (2011) analyzed postmortem brain tissue samples from 19 autism cases and 17 controls from the Autism Tissue Project and the Harvard brain bank using Illumina microarrays. For each individual, they profiled 3 regions previously implicated in autism: superior temporal gyrus, prefrontal cortex, and cerebellar vermis. Voineagu et al. (2011) demonstrated consistent differences in transcriptome organization between autistic and normal brain by gene coexpression network analysis. Remarkably, regional patterns of gene expression that typically distinguish frontal and temporal cortex are significantly attenuated in the autism spectrum disorder (ASD) brain, suggesting abnormalities in cortical patterning. Voineagu et al. (2011) further identified discrete modules of coexpressed genes associated with autism: a neuronal module enriched for known autism susceptibility genes, including the neuronal-specific splicing factor A2BP1 (also known as FOX1), and a module enriched for immune genes and glial markers. Using high-throughput RNA sequencing, they demonstrated dysregulated splicing of A2BP1-dependent alternative exons in the ASD brain. Moreover, using a published autism genomewide association study (GWAS) data set, Voineagu et al. (2011) showed that the neuronal module is enriched for genetically associated variants, providing independent support for the causal involvement of those genes in autism. The top module for differential expression between autism control groups was highly enriched for neuronal markers. The hubs of this group, called M12 in this study, which represented the genes with the highest rank of M12 membership, were A2BP1 but also APBA2 (602712), SCAMP5 (613766), CNTNAP1 (602346), KLC2 (611729), and CHRM1 (118510). In contrast, the immune-glial module showed no enrichment for autism GWAS signals, indicating a nongenetic etiology for this process. Voineagu et al. (2011) concluded that their results provided strong evidence for convergent molecular abnormalities in ASD, and implicated transcriptional and splicing dysregulation as underlying mechanisms of neuronal dysfunction in this disorder.
Hamada et al. (2016) found that knockdown of the dominant neuronal nuclear isoform of Rbfox1 (isoform-1) in primary cultured mouse hippocampal neurons caused migration delay and abnormal positioning of neurons during corticogenesis, with many knockdown cells failing to reach their target destination. Imaging analysis of Rbfox1 isoform-1-deficient neurons showed that isoform-1 likely regulated 2 steps of cortical neuron migration: smooth crossing of the border between intermediate zone and cortical plate, and subsequent radial migration in the cortical plate. Further examination of radial migration of isoform-1-deficient neurons revealed normal leading process extension but defects in nucleokinesis that advanced the centrosome and translocated the nucleus toward the centrosome. Analysis of cortical neurons showed that functional loss of Rbfox1 isoform-1 impaired synaptic connectivity through defects in axon and dendrite network formation. Assessment of dendritic spine morphology in cultured mouse hippocampal Rbfox1 isoform-1-deficient neurons showed defects in formation of synaptic structures, resulting in functional defects in synapses, as demonstrated by electrophysiologic analysis.
A typical RNA-binding domain folds into an alpha-beta sandwich in which a 4-stranded antiparallel beta sheet is packed against 2 alpha helices. Using NMR spectroscopy and surface plasmon resonance analysis, Auweter et al. (2006) examined the RNA-binding domain of human FOX1 in complex with UGCAUGU. They found that the last 3 nucleotides, UGU, were recognized in a canonical way by the 4-stranded beta sheet. In contrast, the first 4 nucleotides, UGCA, were bound by 2 loops of the protein in an unprecedented manner. Nucleotides U, G, and C wrapped around a single phenylalanine, while G and A formed a basepair. This novel RNA-binding site was independent from the beta sheet binding interface.
Bhalla et al. (2004) described 2 patients with abnormal phenotypes, characterized predominantly by epilepsy in one and by mental retardation in the other, who carried de novo translocations of chromosome 16: t(14;16) and t(1;16), respectively. The mapping was confirmed by FISH of clones that spanned the breakpoints to metaphase spreads derived from the patients. The authors found that the 16p13.3 breakpoints of the 2 translocations disrupted the A2BP1 gene, which encompasses a large genomic region of 1.7 Mb. Bhalla et al. (2004) proposed that disruption of the A2BP1 gene was a cause of the abnormal phenotypes of the 2 patients. No mutations were found in the A2BP1 gene in 96 patients with sporadic epilepsy and 96 female patients with mental retardation screened by SSCP, suggesting that disruption of the A2BP1 gene is not a common cause of sporadic epilepsy or mental retardation.
Martin et al. (2007) reported a girl with mental retardation, seizures, hypotonia, uneven gait, mild facial dysmorphism, fluctuating liver enzymes, and features of autism. Cytogenetic and FISH analysis identified a de novo translocation of chromosomes 15 and 16 with a 160-kb deletion of chromosome 16. QT-PCR analysis confirmed the 160-kb deletion, resulting in loss of exon 1 in the 5-prime promoter region of the A2BP1 gene, and showed decreased mRNA expression in the patient's lymphocytes. The deletion was present in the paternal chromosome. No pathogenic abnormalities in the A2BP1 gene were identified in 88 additional patients with autism.
Gehman et al. (2011) targeted deletion of mouse Rbfox1 to central nervous system (CNS) stem and neural progenitor cells. CNS-specific Rbfox1 -/- mice were viable, but they were slightly smaller and had reduced fertility compared with Rbfox1 +/- and wildtype littermates. Histologic analysis revealed that CNS-specific Rbfox1 -/- brain had normal gross morphology, cellular architecture, and synapse number. However, CNS-specific Rbfox1 -/- mice were prone to infrequent, spontaneous seizures, which were accompanied by upregulation of Fos (164810), an indirect marker for neuronal activity. In addition, all CNS-specific Rbfox1 -/- and Rbfox1 +/- mice tested showed an abnormally elevated response to intraperitoneal kainic acid administration and developed status epilepticus culminating in death. Electrophysiologic recording of CNS-specific Rbfox1 -/- dentate gyrus revealed increased synaptic function. Whole-transcriptome analysis identified multiple splicing changes in CNS-specific Rbfox1 -/- brain, the majority of which were predicted to alter proteins mediating synaptic transmission and membrane excitation, such as Grin1 (138249), Gabrg2 (137164), Kcnd3 (605411), Cacna1d (114206), and Stx3 (600876).
Wamsley et al. (2018) found that mice with cortical interneuron-specific deletion of Rbfox1 were born at the expected mendelian ratios but had increased lethality beginning at postnatal day-18 (P18) and were all dead by P45. Mutant mice had increased seizure susceptibility, likely caused by impairments in inhibitory function in cortex. Immunofluorescence analysis and genetic fate mapping showed that Rbfox1 was expressed in both parvalbumin (PV, or PVALB; 168890)-positive and somatostatin (SST; 182450)-positive cortical interneurons in mouse brain. Analysis of Sst-positive and Pv-positive cortical interneurons from mutant mice revealed that Rbfox1 inactivation impaired efferent connectivity in both cell types. Conditional removal of Rbfox1 within either Sst-positive or Pv-positive cortical interneurons had opposite effects on efferent connectivity, as Pv-positive cortical interneurons showed a reduced number of efferent synapses, and Sst-positive cortical interneurons formed supernumerary but nonfunctional inhibitory efferent synapses. Further examination revealed that Rbfox1 mediated alternative splicing of transcripts encoding presynaptic proteins, and these alternative splicing events were altered in a cell-specific manner in Sst-positive and Pv-positive cortical interneurons.
Auweter, S. D., Fasan, R., Reymond, L., Underwood, J. G., Black, D. L., Pitsch, S., Allain, F. H.-T. Molecular basis of RNA recognition by the human alternative splicing factor Fox-1. EMBO J. 25: 163-173, 2006. [PubMed: 16362037] [Full Text: https://doi.org/10.1038/sj.emboj.7600918]
Bhalla, K., Phillips, H. A., Crawford, J., McKenzie, O. L. D., Mulley, J. C., Eyre, H., Gardner, A. E., Kremmidiotis, G., Callen, D. F. The de novo chromosome 16 translocations of two patients with abnormal phenotypes (mental retardation and epilepsy) disrupt the A2BP1 gene. J. Hum. Genet. 49: 308-311, 2004. [PubMed: 15148587] [Full Text: https://doi.org/10.1007/s10038-004-0145-4]
Fukumura, K., Kato, A., Jin, Y., Ideue, T., Hirose, T., Kataoka, N., Fujiwara, T., Sakamoto, H., Inoue, K. Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1-gamma gene. Nucleic Acids Res. 35: 5303-5311, 2007. [PubMed: 17686786] [Full Text: https://doi.org/10.1093/nar/gkm569]
Gehman, L. T., Stoilov, P., Maguire, J., Damianov, A., Lin, C.-H., Shiue, L., Ares, M., Jr., Mody, I., Black, D. L. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nature Genet. 43: 706-711, 2011. [PubMed: 21623373] [Full Text: https://doi.org/10.1038/ng.841]
Hamada, N., Ito, H., Nishijo, T., Iwamoto, I., Morishita, R., Tabata, H., Momiyama, T., Nagata, K.-I. Essential role of the nuclear isoform of RBFOX1, a candidate gene for autism spectrum disorders, in the brain development. Sci. Rep. 6: 30805, 2016. Note: Electronic Article. [PubMed: 27481563] [Full Text: https://doi.org/10.1038/srep30805]
Jin, Y., Suzuki, H., Maegawa, S., Endo, H., Sugano, S., Hashimoto, K., Yasuda, K., Inoue, K. A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. EMBO J. 22: 905-912, 2003. [PubMed: 12574126] [Full Text: https://doi.org/10.1093/emboj/cdg089]
Lim, J., Hao, T., Shaw, C., Patel, A. J., Szabo, G., Rual, J.-F., Fisk, C. J., Li, N., Smolyar, A., Hill, D. E., Barabasi, A.-L., Vidal, M., Zoghbi, H. Y. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125: 801-814, 2006. [PubMed: 16713569] [Full Text: https://doi.org/10.1016/j.cell.2006.03.032]
Martin, C. L., Duvall, J. A., Ilkin, Y., Simon, J. S., Arreaza, M. G., Wilkes, K., Alvarez-Retuerto, A., Whichello, A., Powell, C. M., Rao, K., Cook, E., Geschwind, D. H. Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism. Am. J. Med. Genet. 144B: 869-876, 2007. [PubMed: 17503474] [Full Text: https://doi.org/10.1002/ajmg.b.30530]
Ponthier, J. L., Schluepen, C., Chen, W., Lersch, R. A., Gee, S. L., Hou, V. C., Lo, A. J., Short, S. A., Chasis, J. A., Winkelmann, J. C., Conboy, J. G. Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16. J. Biol. Chem. 281: 12468-12474, 2006. [PubMed: 16537540] [Full Text: https://doi.org/10.1074/jbc.M511556200]
Shibata, H., Huynh, D. P., Pulst, S.-M. A novel protein with RNA-binding motifs interacts with ataxin-2. Hum. Molec. Genet. 9: 1303-1313, 2000. Note: Erratum: Hum. Molec. Genet. 9: 1903 only, 2000. [PubMed: 10814712] [Full Text: https://doi.org/10.1093/hmg/9.9.1303]
Underwood, J. G., Boutz, P. L., Dougherty, J. D., Stoilov, P., Black, D. L. Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Molec. Cell. Biol. 25: 10005-10016, 2005. [PubMed: 16260614] [Full Text: https://doi.org/10.1128/MCB.25.22.10005-10016.2005]
Voineagu, I., Wang, X., Johnston, P., Lowe, J. K., Tian, Y., Horvath, S., Mill, J., Cantor, R. M., Blencowe, B. J., Geschwind, D. H. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474: 380-384, 2011. [PubMed: 21614001] [Full Text: https://doi.org/10.1038/nature10110]
Wamsley, B., Jaglin, X. H., Favuzzi, E., Quattrocolo, G., Nigro, M. J., Yusuf, N., Khodadadi-Jamayran, A., Rudy, B., Fishell, G. Rbfox1 mediates cell-type-specific splicing in cortical interneurons. Neuron 100: 846-859, 2018. [PubMed: 30318414] [Full Text: https://doi.org/10.1016/j.neuron.2018.09.026]