HGNC Approved Gene Symbol: BNC2
Cytogenetic location: 9p22.3-p22.2 Genomic coordinates (GRCh38): 9:16,409,503-16,870,670 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 9p22.3-p22.2 | Lower urinary tract obstruction, congenital | 618612 | Autosomal dominant | 3 |
The BNC2 gene encodes basonuclin-2, one of the most evolutionarily conserved DNA-binding zinc finger proteins expressed in many human tissues, including epithelial and germ cells (summary by Visser et al., 2014).
Romano et al. (2004) cloned mouse Bnc2. The deduced 1,049-amino acid protein has a calculated molecular mass of 116.5 kD. Bnc2 contains a pair of zinc fingers in its N-terminal half, followed by a central nuclear localization signal and 2 pairs of zinc fingers in its C-terminal half. By searching an EST database for sequences similar to mouse Bnc2, followed by RT-PCR of human skin RNA, Romano et al. (2004) cloned human BNC2. The deduced mouse and human proteins share 98% amino acid identity. Northern blot analysis of several mouse tissues detected 4 major transcripts expressed at highest levels in ovary, followed by kidney and skin. Bnc2 expression was also detected in whole mouse embryos. RT-PCR detected BNC2 expression in primary human keratinocytes and in a keratinocyte cell line, but not in a hepatoma cell line. Immunofluorescence microscopy localized mouse Bnc2 in the nucleus of transfected HeLa cells.
By EST database analysis and 5-prime RACE, Vanhoutteghem and Djian (2007) discovered that the BNC2 gene possesses 6 promoters, 4 polyadenylation sites, and 23 exons, all of which are alternatively spliced. Characterization of nearly 100 mRNA variants suggested that each promoter, splice site, and poly(A) addition site is used independently. The BNC2 gene therefore has the potential to generate up to 90,000 variants encoding more than 2,000 different proteins ranging in size from 43 to 1,211 amino acids. Some BNC2 proteins bear no sequence similarity to others. The longest deduced BNC2 protein has an N-terminal domain, followed by 2 zinc fingers, a nuclear localization signal (NLS), 2 more zinc fingers, a serine strip, and 2 C-terminal zinc fingers. Transcripts containing exon 3a, which includes a stop codon, encode proteins of 43 to 189 amino acids that lack all zinc fingers and the NLS. PCR analysis and transient expression in HeLa cells showed that the major BNC2 mRNA variants were stable and were translated into stable proteins. Immunofluorescence analysis revealed that all proteins containing the NLS were expressed in the nucleus, whereas the proteins lacking the NLS were expressed in both cytoplasm and nucleus. By EST database analysis, Vanhoutteghem and Djian (2007) determined that many exons used in BNC2 transcripts are specific to humans, and they found no evidence of alternative splicing in the related BNC1 gene (601930).
Using histologic analysis, Vanhoutteghem et al. (2016) showed that Bnc1 and Bnc2 had nearly identical expression patterns in mouse. Both were present in male and female germ cells, ovary, testis, connective cells of organ capsules, sensory neurons, hair follicles, and palate. Bnc2 was also expressed in perichondrium and growth plate of long bones, whereas Bnc1 was absent in perichondrium.
Legnini et al. (2017) identified a circular BNC2 transcript that was upregulated following differentiation of human and mouse myoblasts into myotubes. Circular BNC2 was detected predominantly in the cytoplasm of fractionated cells.
By immunohistochemical staining in human urethra from a 7-week embryo, Kolvenbach et al. (2019) detected BNC2 expression in the urogenital sinus and its outflow tract. The most prominent signal was in the primitive urothelium, with weaker immunoreactivity in the surrounding mesenchyme. Expression was also detected in the urothelium of the adult human male urethra. Using in situ hybridization in mouse embryos, the authors found Bnc2 expression in the developing lower urinary tract structures, primarily in the genital tubercle above the phallic urethra and below the pelvic urethra at embryonic day 13.5, which the authors noted is the critical time point for urethral development. Expression of Bnc2 was also visible in the brain, mandibular area, and in dorsal parts above the spinal cord. In situ hybridization in zebrafish larvae showed strong expression of bnc2 in the brain as well as in the pronephric ducts and the developing cloaca region at 33 hours postfertilization. Expression in the pronephric ducts was confirmed by immunohistochemistry. In addition, the authors demonstrated overlap of bnc2 expression with that of a marker for pronephric and cloacal tissue, pax2a, in zebrafish embryos.
Vanhoutteghem and Djian (2007) determined that the BNC2 gene spans 461 kb and contains 23 exons, all of which are alternatively spliced. BNC2 transcripts are initiated from 1 major and 5 minor promoters. The 5-prime flanking region of the major promoter in exon 1 lacks a TATA box, but it contains 2 overlapping SP1 (189906) sites within a GC-rich region. Two other GC-rich regions are located upstream and downstream of exon 1. The minor downstream promoters are TATA-less and lack SP1 sites and CpG islands.
By genomic sequence analysis, Romano et al. (2004) mapped the BNC2 gene to chromosome 9p22.1. They mapped the mouse Bnc2 gene to chromosome 4.
Using recombinant mouse Bnc2, Romano et al. (2004) determined that a Bnc2 fragment containing only the first zinc finger pair bound a DNA sequence containing a BNC1-binding site. In vitro translated full-length Bnc2 and a truncated Bnc2 protein containing only the zinc finger domains bound this DNA sequence.
BNC1 and BNC2 share only about 40% amino acid identity, but they share similar protein characteristics. Using antibodies specific for BNC1 or BNC2, Vanhoutteghem and Djian (2006) found that in keratinocytes, the only cell type expressing both proteins, BNC1 was expressed relatively uniformly in the nucleoplasm, whereas BNC2 was concentrated in nuclear aggregates. BNC2, but not BNC1, colocalized with splicing factor SC35 (SFRS2; 600813) in nuclear speckles. Actinomycin D treatment caused redistribution of SC35 and BNC2, but not BNC1, suggesting that BNC2 participates in mRNA processing.
Congenital Lower Urinary Tract Obstruction
In affected members of 2 unrelated families with congenital lower urinary tract obstruction (LUTO; 618612), Kolvenbach et al. (2019) identified heterozygous mutations in the BNC2 gene. In the first family, in which the obstruction was due to distal urethral stenosis, affected individuals were heterozygous for a nonsense mutation (R853X; 608669.0001). In the second family, a father and son with obstruction caused by posterior urethral valve were heterozygous for a missense mutation (H888R; 608669.0002).
Associations Pending Confirmation
Jacobs et al. (2013) found an association between a SNP (rs10756819) in the first intron of the BNC2 gene and color saturation of skin pigment among 5,860 Dutch individuals whose skin color variation was ascertained from digital photographs. The gene was chosen for study because of its association with mouse coat color (Smyth et al., 2006).
Visser et al. (2014) determined that the intergenic SNP rs12350739 (A/G) is in high linkage disequilibrium with rs10756819 and is likely the causal DNA variant for the observed BNC2 skin color association. The A allele is most common in Europeans (57%), rare in sub-Saharan Africans (1%), and absent in East Asians. A study of 29 skin epidermal samples from donors with different pigmentation showed higher BNC2 expression in dark skin compared to light skin, and BNC2 was expressed within melanocytes. A highly conserved region surrounding rs12350739 was found to function as an enhancer element regulating BNC2 transcription in human melanocytes, and the activity of this enhancer depended on the allelic status of the SNP. The A/A allele rendered the chromatin inaccessible, and the enhancer element was only slightly active, resulting in low expression of BNC2 and thus light skin pigmentation. In contrast, the chromatin was open and more accessible in cell lines harboring G/A or G/G alleles, resulting in a higher expression of BNC2, corresponding with dark skin pigmentation. Visser et al. (2014) emphasized that this finding is an example of how an intergenic noncoding DNA variant can modulate the regulatory potential of the enhancer element it is located within, which in turn results in allele-dependent differential gene expression affecting variation in common human traits.
For a discussion of a possible association between variation in the BNC2 gene and susceptibility to adolescent idiopathic scoliosis, see IS1 (181800).
Smyth et al. (2006) analyzed the genomic sequence of the mouse Tyrp1 (115501) deletion complex on mouse chromosome 4 that determines brown coat color. Misexpression of the Bnc2 gene was associated with a Tyrp1 inversion-mediated coat color mutant named 'white-based brown,' or B(w). The findings suggested that overexpression of Bnc2 resulted from a Tyrp1-Bnc2 fusion transcript that caused a dominant loss of pigment in hair follicle melanocytes.
Vanhoutteghem et al. (2009) found that Bnc2 -/- mice were born at the expected mendelian ratio, but they were abnormally small and died within 24 hours of birth. Bnc2 -/- mice showed aerial distention of the digestive tract associated with clefting of the secondary palate and abnormalities of craniofacial bones and tongue. Other skeletal structures appeared normal. In wildtype embryonic head, Bnc2 expression was restricted to mesenchymal cells in the palate, at the periphery of the tongue, and in the mesenchymal sheaths that surround the brain and osteocartilaginous structures. In late Bnc2 -/- embryos, the rate of multiplication of these mesenchymal cells was greatly diminished. Vanhoutteghem et al. (2009) noted that, similar to Bnc2 -/- mice, loss of the insect disco proteins, which are orthologous to Bnc2, results in growth failure that affects the head segment. They concluded that BNC2 is essential for the multiplication of craniofacial mesenchymal cells during embryogenesis.
By examining the small number of Bnc2 -/- mice that survived neonatal lethality, Vanhoutteghem et al. (2016) observed disrupted oocyte maturation, dwarfism, infertility, and abnormalities of palatal rugae and molar teeth. In hair follicles, Bnc2 was specific to germ cells and was required for progression of the first hair cycle and initiation of the second. As a result, hair follicles of Bnc2 -/- mice tended to be shorter and the hypodermis was thinner compared with wildtype, and they displayed abnormal morphology. Knockin expression of Bnc1 in Bnc2 -/- mice did not rescue them from neonatal lethality.
Lang et al. (2009) reported the recessive zebrafish mutant bonaparte, which was characterized by female infertility and severe disruption of adult stripe pattern. The authors identified bnc2 mutations as the underlying cause of the bonaparte mutant. Bnc2 acted nonautonomously to metamorphic melanophores, was expressed by hypodermal cells in contact with melanophores, xanthophores, and iridophores, and was required for survival of all 3 chromatophores. Despite normal differentiation, all 3 chromatophores were ultimately lost in bonaparte mutants, resulting in gross defects in adult stripe formation. Bnc2 was also expressed in somatic cells of ovary, and bonaparte mutant females were infertile and exhibited excess somatic tissue within ovaries.
In approximately 21% of 399 zebrafish embryos with targeted knockdown of Bnc2, Kolvenbach et al. (2019) detected a vesicle in the cloacal region, representing distal pronephric outlet obstruction; none of 500 controls showed such a vesicle. The morphants also showed abnormal body curvature (9%) and hydrocephalus (5%), as well as pericardial effusion (44%). The authors noted that pericardial effusion has been considered to be a nonspecific phenotype and is also seen in wildtype fish, but they suggested that here it might represent a secondary effect of kidney impairment. A probe against a marker for pronephric and cloacal tissue (pax2a) demonstrated the close proximity of the pronephric outlet obstruction to the distal pronephric duct at the cloacal opening.
In 4 affected members over 3 generations of a family with congenital lower urinary tract obstruction (LUTO; 618612), Kolvenbach et al. (2019) identified heterozygosity for a c.2557C-T transition (c.2557C-T, NM_017637.6) in the BNC2 gene, resulting in an arg853-to-ter (R853X) substitution. The variant was present in heterozygosity in 5 of 175,684 alleles in the gnomAD database (minor allele frequency, 0.000028). In zebrafish with pronephric outlet obstruction after knockdown of bcn2, wildtype BNC2 significantly rescued the obstruction phenotype, whereas there was no reduction with the R853X mutant.
In a father and son with lower urinary tract obstruction (LUTO; 618612) due to posterior urethral valves, Kolvenbach et al. (2019) identified heterozygosity for a c.2663A-G transition (c.2663A-G, NM_017637.6) in the BNC2 gene, resulting in a his888-to-arg (H888R) substitution at a highly conserved residue within the fourth C2H2 zinc finger domain. The proband's paternal grandmother was an unaffected carrier of the mutation. In zebrafish with pronephric outlet obstruction after knockdown of bcn2, wildtype BNC2 significantly rescued the obstruction phenotype, whereas there was no reduction with the H888R mutant.
Jacobs, L. C., Wollstein, A., Lao, O., Hofman, A., Klaver, C. C., Uitterlinden, A. G., Nijsten, T., Kayser, M., Liu, F. Comprehensive candidate gene study highlights UGT1A and BNC2 as new genes determining continuous skin color variation in Europeans. Hum. Genet. 132: 147-158, 2013. [PubMed: 23052946] [Full Text: https://doi.org/10.1007/s00439-012-1232-9]
Kolvenbach, C. M., Dworschak, G. C., Frese, S., Japp, A. S., Schuster, P., Wenzlitschke, N., Yilmaz, O., Lopes, F. M., Pryalukhin, A., Schierbaum, L., van der Zanden, L. F. M., Kause, F., and 28 others. Rare variants in BNC2 are implicated in autosomal-dominant congenital lower urinary-tract obstruction. Am. J. Hum. Genet. 104: 994-1006, 2019. [PubMed: 31051115] [Full Text: https://doi.org/10.1016/j.ajhg.2019.03.023]
Lang, M. R., Patterson, L. B., Gordon, T. N., Johnson, S. L., Parichy, D. M. Basonuclin-2 requirements for zebrafish adult pigment pattern development and female fertility. PLoS Genet. 5: e1000744, 2009. Note: Electronic Article. [PubMed: 19956727] [Full Text: https://doi.org/10.1371/journal.pgen.1000744]
Legnini, I., Di Timoteo, G., Rossi, F., Morlando, M., Briganti, F., Sthandier, O., Fatica, A., Santini, T., Andronache, A., Wade, M., Laneve, P., Rajewsky, N., Bozzoni, I. Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis. Molec. Cell 66: 22-37, 2017. [PubMed: 28344082] [Full Text: https://doi.org/10.1016/j.molcel.2017.02.017]
Romano, R.-A., Li, H., Tummala, R., Maul, R., Sinha, S. Identification of Basonuclin2, a DNA-binding zinc-finger protein expressed in germ tissues and skin keratinocytes. Genomics 83: 821-833, 2004. [PubMed: 15081112] [Full Text: https://doi.org/10.1016/j.ygeno.2003.11.009]
Smyth, I. M., Wilming, L., Lee, A. W., Taylor, M. S., Gautier, P., Barlow, K., Wallis, J., Martin, S., Glithero, R., Phillimore, B., Pelan, S., Andrew, R., and 48 others. Genomic anatomy of the Tyrp1 (brown) deletion complex. Proc. Nat. Acad. Sci. 103: 3704-3709, 2006. [PubMed: 16505357] [Full Text: https://doi.org/10.1073/pnas.0600199103]
Vanhoutteghem, A., Delhomme, B., Herve, F., Nondier, I., Petit, J.-M., Araki, M., Araki, K., Djian, P. The importance of basonuclin 3 in adult mice and its relation to basonuclin 1. Mech. Dev. 140: 53-73, 2016. [PubMed: 26923665] [Full Text: https://doi.org/10.1016/j.mod.2016.02.002]
Vanhoutteghem, A., Djian, P. Basonuclins 1 and 2, whose genes share a common origin, are proteins with widely different properties and functions. Proc. Nat. Acad. Sci. 103: 12423-12428, 2006. [PubMed: 16891417] [Full Text: https://doi.org/10.1073/pnas.0605086103]
Vanhoutteghem, A., Djian, P. The human basonuclin 2 gene has the potential to generate nearly 90,000 mRNA isoforms encoding over 2000 different proteins. Genomics 89: 44-58, 2007. [PubMed: 16942855] [Full Text: https://doi.org/10.1016/j.ygeno.2006.07.006]
Vanhoutteghem, A., Maciejewski-Duval, A., Bouche, C., Delhomme, B., Herve, F., Daubigney, F., Soubigou, G., Araki, M., Araki, K., Yamamura, K., Djian, P. Basonuclin 2 has a function in the multiplication of embryonic craniofacial mesenchymal cells and is orthologous to disco proteins. Proc. Nat. Acad. Sci. 106: 14432-14437, 2009. [PubMed: 19706529] [Full Text: https://doi.org/10.1073/pnas.0905840106]
Visser, M., Palstra, R.-J., Kayser, M. Human skin color is influenced by an intergenic DNA polymorphism regulating transcription of the nearby BNC2 pigmentation gene. Hum. Molec. Genet. 23: 5750-5762, 2014. [PubMed: 24916375] [Full Text: https://doi.org/10.1093/hmg/ddu289]