Alternative titles; symbols
HGNC Approved Gene Symbol: BRF1
SNOMEDCT: 1237475006;
Cytogenetic location: 14q32.33 Genomic coordinates (GRCh38) : 14:105,209,286-105,315,589 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 14q32.33 | Cerebellofaciodental syndrome | 616202 | Autosomal recessive | 3 |
The BRF1 gene encodes a protein that, together with TBP (600075) and BDP1 (607012), forms the transcription factor IIIB, which recruits RNA polymerase III (Pol III) to target genes. Pol III synthesizes a variety of noncoding RNAs with structural and catalytic functions (summary by Borck et al., 2015).
By screening a Burkitt lymphoma and other human cDNA cell libraries using degenerate PCR primers corresponding to peptide sequences of the 90-kD subunit of TFIIIB, Wang and Roeder (1995) obtained a cDNA encoding TAF3B2, which they called TFIIIB90. Sequence analysis revealed that the 675-amino acid TAF3B2 protein contains a high mobility group protein-2 (HMG2; 163906)-related region in the highly charged C-terminal half of the protein and a sequence related to TFIIB (GTF2B; 189963) in the N terminus. Western blot analysis showed that TAF3B2 is expressed as a 92-kD protein, the C terminus of which binds TBP. Recombinant TAF3B2 together with TBP, but neither alone, could replace purified natural TFIIIB. Deletion of either the N-terminal TFIIB-related or the C-terminal HMG2-related half of the protein abolished activity.
Mital et al. (1996) cloned a cDNA identical to the TAF3B2 cDNA obtained by Wang and Roeder (1995) except for scattered nucleotide differences and the presence of 6 additional nucleotides. These last differences change the open reading frame, predicting a different sequence over 67 amino acids of the TAF3B2 protein, which Mital et al. (1996) called BRF due to its homology with the S. cerevisiae BRF protein. Mital et al. (1996) confirmed the association of TAF3B2 with TBP reported by Wang and Roeder (1995).
RNA polymerases are unable to initiate RNA synthesis in the absence of additional proteins that assemble in a complex on the DNA promoter and recruit the RNA polymerase. TFIII is essential for RNA polymerase III to make a number of small nuclear and cytoplasmic RNAs, including 5S RNA (180420), tRNA, and virus-associated (VA) RNA. Transcription of these RNAs begins with TFIIIC (see GTF3C1, 603246) recognition of internal promoter elements (A and B boxes), followed by sequential binding of TFIIIB and RNA polymerase III. 5S RNA transcription is similar, except that the binding of TFIIIA (GTF3A; 600860) to a distinct set of internal promoter elements is required for GTF3C recruitment. An essential component of TFIIIB, TATA box-binding protein (TBP), is required by all 3 classes of eukaryotic RNA polymerases (summary by Wang and Roeder, 1995).
The International Radiation Hybrid Mapping Consortium mapped the TAF3B2 gene to the telomeric end of 14q (stSG45294).
Crystal Structure
Juo et al. (2003) reported a 2.95-angstrom resolution crystal structure of the ternary complex containing BRF1 homology domain II, the conserved region of TBP, and 19 basepairs of U6 (180692) promoter DNA. The structure revealed the core interface for assembly of transcription factor IIIB and demonstrated how the loosely packed BRF1 domain achieves remarkable binding specificity with the convex and lateral surfaces of TBP.
In 6 patients from 3 unrelated families with cerebellofaciodental syndrome (CFDS; 616202), Borck et al. (2015) identified homozygous or compound heterozygous mutations in the BRF1 gene (604902.0001-604902.0004). The mutations, which were found by whole-exome sequencing, segregated with the disorder in each family. In vitro functional assays in yeast showed that at least 1 mutation (T259M; 604902.0002) reduced Brf1 occupancy at tRNA target genes, and that some mutations (R223W, 604902.0003 and P292H, 604902.0004) impaired cell growth. In yeast, all mutations showed some evidence of impaired Pol III-dependent transcriptional activity compared to wildtype. The mutations were either completely or partially unable to rescue the neurodevelopmental defects in a zebrafish knockout model. The effects of the variants appeared to be restricted to isoform 2. These findings suggested that BRF1-mediated Pol III transcription, representing basal cellular function, is required for normal cerebellar and cognitive development.
Borck et al. (2015) found that morpholino knockdown of the brf1b gene in zebrafish embryos resulted in microcephaly, significant reduction in size of the optic tectum, and cerebellar hypoplasia. Human BRF1 was able to rescue the phenotype.
In 2 brothers, born of consanguineous Italian parents, with cerebellofaciodental syndrome (CFDS; 616202), Borck et al. (2015) identified a homozygous c.677C-T transition in the BRF1 gene, resulting in a ser226-to-leu (S226L) substitution. Two sibs from another Italian family with a similar disorder were compound heterozygous for the S226L mutation and a c.776C-T transition, resulting in a thr259-to-met (T259M; 604902.0002) substitution. Both mutations affected conserved residues in the cyclin 2 domain. The mutations, which were identified by whole-exome sequencing in both families, were confirmed by Sanger sequencing and segregated with the disorder in the families. Neither mutation was found in 200 ethnically matched control chromosomes; in the Exome Variant Server database, the c.677C-T was absent, whereas c.776C-T was found in 1 of 13,006 chromosomes. In the context of BRF1 isoform 2, the S226L and T259M mutants were scored as hypomorphic in rescue experiments in zebrafish with morpholino knockdown of the orthologous brf1b gene, as these mutations only partially rescued the reduction in head size and cerebellar hypoplasia observed in the mutant animals. Yeast cells transformed with S226L and/or T259M showed normal growth. ChIP assays in yeast demonstrated that the T259M variant had strongly decreased promoter occupancy at 4 tRNA loci that are Pol III gene targets, whereas the S226L variant was similar to wildtype. In vitro assays in yeast showed that both mutations impaired Pol III-dependent transcriptional activity compared to wildtype.
For discussion of the thr259-to-met (T259M; rs373957300) mutation in the BRF1 gene that was found in compound heterozygous state in 2 sibs with cerebellofaciodental syndrome (CFDS; 616202) by Borck et al. (2015), see 604902.0001.
In 2 Portuguese sisters with cerebellofaciodental syndrome (CFDS; 616202), Borck et al. (2015) identified compound heterozygous mutations in the BRF1 gene: a c.667C-T transition, resulting in an arg223-to-trp (R223W) substitution inherited from the unaffected mother, and a c.875C-A transversion, resulting in a pro292-to-his (P292H; 604902.0004) substitution likely inherited from the unaffected father (paternal DNA was not available for analysis). The R223W substitution occurred at a conserved residue in the cyclin-2 domain. Neither mutation was found in 100 control chromosomes. The mutations were found by whole-exome sequencing and confirmed by Sanger sequencing. In the Exome Variant Server database, c.875C-A mutation was absent, whereas the c.667C-T mutation was found in 2 of 12,996 chromosomes. In the context of BRF1 isoform 2, both the R223W and P292H mutants were scored as functionally null in rescue experiments in zebrafish with morpholino knockdown of the orthologous brf1b gene, as these mutations were unable to rescue the reduction in head size and cerebellar hypoplasia observed in the mutant fish. Yeast transfected with the R223W and/or P292H mutations failed to grow, further corroborating the lack of function of these 2 alleles. In vitro assays in yeast showed that both mutations impaired Pol III-dependent transcriptional activity compared to wildtype.
For discussion of the pro292-to-his (P292H) mutation in the BRF1 gene that was found in compound heterozygous state in 2 sisters with cerebellofaciodental syndrome (CFDS; 616202) by Borck et al. (2015), see 604902.0003.
Borck, G., Hog, F., Dentici, M. L., Tan, P. L., Sowada, N., Medeira, A., Gueneau, L., Thiele, H., Kousi, M., Lepri, F., Wenzeck, L., Blumenthal, I., and 13 others. BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies. Genome Res. 25: 155-166, 2015. Note: Erratum: Genome Res. 25: 609 only, 2015. [PubMed: 25561519] [Full Text: https://doi.org/10.1101/gr.176925.114]
Juo, Z. S., Kassavetis, G. A., Wang, J., Geiduschek, E. P., Sigler, P. B. Crystal structure of a transcription factor IIIB core interface ternary complex. Nature 422: 534-539, 2003. [PubMed: 12660736] [Full Text: https://doi.org/10.1038/nature01534]
Mital, R., Kobayashi, R., Hernandez, N. RNA polymerase III transcription from the human U6 and adenovirus type 2 VAI promoters has different requirements for human BRF, a subunit of human TFIIIB. Molec. Cell. Biol. 16: 7031-7042, 1996. [PubMed: 8943358] [Full Text: https://doi.org/10.1128/MCB.16.12.7031]
Wang, Z., Roeder, R. G. Structure and function of a human transcription factor TFIIIB subunit that is evolutionarily conserved and contains both TFIIB- and high-mobility-group protein 2-related domains. Proc. Nat. Acad. Sci. 92: 7026-7030, 1995. [PubMed: 7624363] [Full Text: https://doi.org/10.1073/pnas.92.15.7026]