Affinage

BRF2

Transcription factor IIIB 50 kDa subunit · UniProt Q9HAW0

Round 2 corrected
Length
419 aa
Mass
46.5 kDa
Annotated
2026-04-28
53 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

BRF2 is a vertebrate-specific subunit of the TFIIIB-α complex that, together with TBP and BDP1, directs RNA Polymerase III to gene-external (type III) promoters including U6 snRNA and selenocysteine tRNA genes, thereby controlling the synthesis of essential small non-coding RNAs (PMID:11121026, PMID:11564744). BRF2 binds DNA-bound TBP in a TATA-box-dependent manner, extending the TBP footprint to stabilize the pre-initiation complex, and harbors a redox-sensing disulfide module whose oxidation-state switch specifically upregulates Pol III transcriptional output under oxidative stress, functionally linking it to the Nrf2/Keap1 pathway (PMID:26638071). Focal amplification of BRF2 at 8p12 acts as a lineage-specific oncogene in lung squamous cell carcinoma by increasing Pol III-dependent snRNA synthesis, and BRF2 overexpression promotes proliferation and metastasis in additional cancer types through MAPK/ERK and other signaling axes (PMID:20668658, PMID:34012797). Biallelic loss-of-function BRF2 variants cause a neurodevelopmental syndrome with craniofacial anomalies, immunodeficiency, and impaired transcription of redox-protective genes GPX1 and GPX4 (PMID:40229899, PMID:40781771).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2000 High

    Identification of BRF2 as a second TFIIB-related factor in humans resolved how vertebrate RNA Pol III discriminates between gene-internal and gene-external promoter architectures, establishing that two distinct TFIIIB complexes exist.

    Evidence Cloning and biochemical reconstitution of TFIIIB-α activity with purified BRF2, TBP, and BDP1 in vitro

    PMID:11121026

    Open questions at the time
    • No structural information on how BRF2 differs from BRF1 at the atomic level
    • In vivo promoter occupancy not yet demonstrated
  2. 2001 High

    Demonstration that BRF2 is recruited to the TATA-box via TBP and stabilizes TBP on DNA defined the minimal assembly pathway of the TFIIIB-α complex on type III promoters.

    Evidence DNase I footprinting, gel mobility shift assays, truncation/mutagenesis, and in vitro transcription

    PMID:11564744

    Open questions at the time
    • Role of BDP1 in the ternary complex not structurally resolved
    • No information on how SNAPc coordinates with BRF2-TBP
  3. 2007 Medium

    Showing that Maf1 represses Pol III transcription through both BRF1 and BRF2 established a conserved negative regulatory mechanism acting at the TFIIIB level.

    Evidence RNA Pol III luciferase reporter assays, in vivo transcription assays, co-immunoprecipitation

    PMID:17505538

    Open questions at the time
    • Direct physical interaction between Maf1 and BRF2 not mapped at residue level
    • Single-lab finding without independent replication
  4. 2010 High

    Identification of BRF2 as a lineage-specific oncogene amplified in lung squamous cell carcinoma established that deregulated Pol III transcription of small RNAs is sufficient to drive cellular transformation.

    Evidence Array CGH across >330 clinical samples, ectopic BRF2 expression inducing transformation of bronchial epithelial cells, RNAi knockdown suppressing growth of SqCC cells

    PMID:20668658

    Open questions at the time
    • Specific Pol III transcript repertoire mediating transformation not defined
    • Whether BRF2 amplification cooperates with other 8p12 co-amplified genes unclear
  5. 2015 High

    Crystal structures of the BRF2–TBP complex on natural Pol III promoters revealed a redox-sensing disulfide module within BRF2 that regulates Pol III output under oxidative stress, establishing BRF2 as the first transcription factor integrating redox signals directly into Pol III activity.

    Evidence X-ray crystallography, cysteine mutagenesis, in vitro transcription, and cell-based oxidative stress assays

    PMID:26638071

    Open questions at the time
    • Identity of the upstream oxidant or reductant that modulates the disulfide in vivo not determined
    • Whether the redox switch operates at all BRF2-dependent promoters or selectively is unknown
  6. 2015 Medium

    Demonstration that daidzein induces BRF2 expression through mRNA stabilization and promoter demethylation in ER-positive breast cancer cells revealed an estrogen receptor-dependent epigenetic axis controlling BRF2 levels.

    Evidence mRNA stability assays, promoter methylation analysis, 5-azacytidine rescue in ER-positive vs. ER-negative cell lines

    PMID:26573593

    Open questions at the time
    • Direct ER binding to the BRF2 promoter not demonstrated
    • In vivo relevance of dietary isoflavone exposure to BRF2 regulation not established
  7. 2021 Medium

    Identification of miRNA-mediated post-transcriptional regulation of BRF2 (let-7b-3p in LUAD, miR-1-3p via MALAT1 ceRNA in HCC) and downstream signaling through MAPK/ERK and LKB1/AMPK pathways extended the oncogenic role of BRF2 beyond Pol III transcription to broader proliferative and metastatic signaling networks.

    Evidence Dual-luciferase target validation, transcriptome sequencing, xenograft models, pathway rescue experiments

    PMID:34012797 PMID:37653482

    Open questions at the time
    • Whether MAPK/ERK activation is a direct or indirect consequence of BRF2-driven Pol III transcript changes is unresolved
    • The specific Pol III transcripts mediating these signaling effects remain unidentified
  8. 2025 High

    Discovery that biallelic BRF2 loss-of-function variants cause a neurodevelopmental syndrome with craniofacial anomalies, immunodeficiency, and impaired transcription of GPX1/GPX4 established BRF2 as a Mendelian disease gene and linked its redox-sensing function to human developmental biology.

    Evidence Whole-exome sequencing in independent families, ChIP/occupancy assays in patient cells, zebrafish morpholino knockdown rescued by wild-type but not mutant human BRF2 mRNA, single-cell RNA-seq identifying GPX1/GPX4 as affected targets

    PMID:40229899 PMID:40781771

    Open questions at the time
    • Full spectrum of BRF2-dependent Pol III transcripts disrupted in patient cells not catalogued
    • Whether immunodeficiency is driven by GPX-dependent redox failure or broader Pol III transcript deficiency is unclear
    • No mouse model yet reported

Open questions

Synthesis pass · forward-looking unresolved questions
  • Major open questions include the complete repertoire of BRF2-dependent Pol III transcripts in different tissues, the identity of the physiological redox regulators controlling the BRF2 disulfide switch in vivo, and the structural basis of the full human SNAPc–TFIIIB–Pol III pre-initiation complex at atomic resolution.
  • No published high-resolution structure of the complete human BRF2-containing PIC from a peer-reviewed journal
  • Tissue-specific BRF2-dependent transcriptome not mapped
  • Mechanism connecting BRF2 redox state to specific downstream transcript selectivity unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 4 GO:0140223 general transcription initiation factor activity 3 GO:0003677 DNA binding 2 GO:0140299 molecular sensor activity 1
Localization
GO:0005634 nucleus 4
Pathway
R-HSA-74160 Gene expression (Transcription) 5 R-HSA-1643685 Disease 3 R-HSA-8953897 Cellular responses to stimuli 2
Partners
BDP1MAF1SNAPC1SNAPC2SNAPC5TBP
Complex memberships
TFIIIB-α (BRF2–TBP–BDP1)

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 TFIIIB50 (BRF2) was identified and cloned as a novel TFIIB homologue that, together with TBP and TFIIIB150 (BDP1), reconstitutes human TFIIIB-alpha activity required for transcription of RNA Pol III genes with upstream (gene-external) promoter elements. This established that higher eukaryotes evolved two distinct TFIIB-related factors (BRF1 and BRF2) that mediate promoter selectivity by RNA Pol III. Cloning, biochemical reconstitution of TFIIIB-alpha activity in vitro, in vitro transcription assays Proceedings of the National Academy of Sciences of the United States of America High 11121026
2001 BRFU (BRF2) is directly recruited to the TATA-box of Pol III-type snRNA gene promoters in a TBP-dependent manner. BRF2 in turn stabilizes TBP on TATA-containing template and extends the TBP footprint both upstream and downstream of the TATA element. The core domain of TBP is sufficient for BRF2·TBP·DNA complex formation. BRF2 has no intrinsic specificity for sequences flanking the TATA-box, indicating polymerase recruitment is not determined solely by TATA-box sequence context. DNase I footprinting, gel mobility shift assays, in vitro transcription, domain mapping by truncation/mutagenesis The Journal of biological chemistry High 11564744
2007 Human Maf1 negatively regulates RNA Pol III transcription via both TFIIB family members BRF1 and BRF2. Maf1 repression of Pol III transcription occurs through TFIIIB, specifically targeting BRF1 and BRF2. RNA Pol III luciferase reporter assay, in vivo transcription assays, co-immunoprecipitation International journal of biological sciences Medium 17505538
2008 BRF2 and BRF1 are differentially expressed in cancer cell lines. BRF2 protein expression levels correlate with U6 promoter activity (BRF2-dependent Pol III transcription), while BRF1 protein levels did not correlate with BRF1-dependent transcription. The BRF2 promoter is more active than the BRF1 promoter across all cancer cell lines tested, suggesting deregulation of BRF2 expression is a key mechanism for observed upregulation of Pol III transcription in cancer. Quantitative RT-PCR, western blotting, promoter-reporter assays, in vitro transcription BMC molecular biology Medium 18700021
2010 BRF2 was identified as a lineage-specific oncogene in lung squamous cell carcinoma. Focal amplification of BRF2 at chromosome 8p12 drives increased Pol III-mediated transcription of snRNAs. Ectopic BRF2 expression in human bronchial epithelial cells induced cellular transformation, while RNAi-mediated BRF2 knockdown suppressed growth and colony formation of SqCC cells overexpressing BRF2 but not adenocarcinoma cells. Comparative genomic hybridization, gene expression microarrays, RNAi knockdown, ectopic overexpression with colony formation assays, integrative genomics PLoS medicine High 20668658
2015 Crystal structures of a human BRF2–TBP complex bound to natural Pol III promoters (U6 snRNA and selenocysteine tRNA genes) revealed a detailed molecular view of interactions at BRF2-dependent Pol III promoters and showed general structural and functional conservation between human Pol II and Pol III pre-initiation complexes. Crucially, BRF2 harbors a redox-sensing module: under oxidative stress conditions, a disulfide bond forms within BRF2 that specifically regulates Pol III transcriptional output in living cells, establishing BRF2 as a central redox-sensing transcription factor involved in the oxidative stress pathway. X-ray crystallography, in vitro transcription assays, mutagenesis of redox-sensing cysteines, cell-based oxidative stress assays Cell High 26638071
2015 The soy isoflavone daidzein specifically stimulates BRF2 expression in ER-positive breast cancer cells through two mechanisms: stabilization of BRF2 mRNA and selective demethylation of the BRF2 promoter. BRF2 induction is accompanied by increased levels of BRF2-regulated non-coding RNAs. These effects are ER-dependent, as they are absent in ER-negative breast cancer cells. qRT-PCR, western blotting, mRNA stability assays, promoter methylation analysis, 5-azacytidine demethylation experiments BMC cancer Medium 26573593
2017 BRF2 acts as a master switch of the oxidative stress response and interplays with the Nrf2/Keap1 pathway. The redox-sensing module of BRF2 integrates oxidative stress signals to regulate Pol III transcription, placing BRF2 downstream of or in parallel with Nrf2/Keap1 signaling. Review/synthesis of structural and functional data (based on prior experimental work from PMID:26638071) Transcription Medium 28854119
2021 BRF2 promotes LUAD cell proliferation and metastasis via the MAPK/ERK signaling pathway. Let-7b-3p directly targets the 3' UTR of BRF2 mRNA to suppress its expression, and BRF2 knockdown phenocopies let-7b-3p overexpression. Transcriptome sequencing and western blot analyses confirmed BRF2-mediated activation of MAPK/ERK signaling. Dual-luciferase reporter assay (miRNA target validation), transcriptome sequencing, western blotting, MTT/colony formation/Transwell assays, in vivo xenograft Translational lung cancer research Medium 34012797
2021 BRF2 is a novel player in the DNA damage response pathway. BRF2 overexpression promotes cancer cell survival under oxidative stress, and treatment with bexarotene reduces oxidative stress-induced BRF2 levels, decreasing cellular proliferation. BRF2 binds the TBP-DNA complex, and virtual screening identified compounds disrupting the BRF2-TBP-DNA interface. Virtual screening, molecular dynamics simulation, cell viability assays, western blotting with oxidative stress induction (tBHQ) Cancers Low 34359683
2023 MALAT1 acts as a competitive endogenous RNA (ceRNA) to sponge miR-1-3p, thereby upregulating BRF2 expression in HCC. BRF2 knockdown inhibits HCC progression by activating the LKB1/AMPK signaling pathway, and BRF2 overexpression reverses the inhibitory effects of MALAT1 knockdown. Dual-luciferase reporter assay, qRT-PCR, western blotting, CCK-8/colony formation/Transwell assays, flow cytometry, xenograft tumor model Cancer cell international Medium 37653482
2023 BRF2 promotes HCC invasion and metastasis through the Wnt/β-catenin signaling pathway. miR-409-3p was identified as binding to the 3' UTR of BRF2 and downregulating its expression. BRF2 depletion suppressed HCC metastasis and invasion. Luciferase activity assay (miRNA target validation), bioinformatic pathway analysis, siRNA knockdown, invasion/migration assays Cancer cell international Low 36927769
2025 Biallelic loss-of-function variants in BRF2 cause a novel neurodevelopmental syndrome with craniofacial anomalies and perinatal death. In silico 3D modeling and functional analyses showed that patient variants impair BRF2-dependent RNA Pol III transcription (altered target loci occupancy). Zebrafish brf2 knockdown recapitulated craniofacial malformations and behavioral deficits, which were rescued by wild-type human BRF2 mRNA but not mutant mRNA. Whole-exome sequencing, in silico 3D structural modeling, ChIP/occupancy assays (target loci), zebrafish morpholino knockdown with mRNA rescue Genome medicine High 40229899
2025 Biallelic BRF2 variants causing multisystem anomalies and primary immunodeficiency disrupt BRF2-dependent RNA Pol III transcription of redox-regulating genes GPX1 and GPX4 (glutathione peroxidases), establishing a pathogenic link between BRF2 dysfunction and disrupted redox homeostasis. Compound heterozygous variants are predicted to disrupt BRF2 interaction with TBP. Whole-exome sequencing, single-cell RNA sequencing, functional analysis of BRF2-dependent Pol III transcription in patient cells, western blotting Molecular therapy : the journal of the American Society of Gene Therapy Medium 40781771
2024 Cryo-EM structures of the full-length SNAPc-containing RNA Pol III pre-initiation complex (PIC) assembled on the U6 snRNA promoter in open and melting states (3.2–4.2 Å resolution) revealed the molecular architecture of the Brf2-containing TFIIIB complex within the PIC. Comparative analysis revealed unexpected structural differences from the yeast PIC and defined the molecular basis of selective, structurally distinct SNAPc engagement within Pol III versus Pol II PICs. Crosslinking mass spectrometry localized SNAPC2 and SNAPC5 subunits in proximity to the promoter DNA. Cryo-EM structure determination, crosslinking mass spectrometry, comparative structural analysis bioRxivpreprint High bio_10.1101_2024.09.10.612236

Source papers

Stage 0 corpus · 53 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2009 A census of human transcription factors: function, expression and evolution. Nature reviews. Genetics 1191 19274049
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2016 An improved smaller biotin ligase for BioID proximity labeling. Molecular biology of the cell 665 26912792
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2010 Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromosome 2p16.3, 2p21 and 9q33.3. Nature genetics 555 21151128
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2013 Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions. Science signaling 383 24255178
1996 Generation and analysis of 280,000 human expressed sequence tags. Genome research 376 8889549
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2010 Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell 318 21145461
2004 Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d. Nature structural & molecular biology 302 14981510
2016 An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nature communications 211 27173435
2015 A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. eLife 198 26673895
2007 A novel tandem affinity purification strategy for the efficient isolation and characterisation of native protein complexes. Proteomics 183 17979178
2008 Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PloS one 148 18461144
2011 The roles of TTP and BRF proteins in regulated mRNA decay. Wiley interdisciplinary reviews. RNA 132 21278925
2017 Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas. Gut 98 28860350
2020 Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Nature metabolism 92 32694731
2015 Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2. Cell 85 26638071
2010 Integrative genomic analyses identify BRF2 as a novel lineage-specific oncogene in lung squamous cell carcinoma. PLoS medicine 84 20668658
2014 ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK-RSK pathway. Nucleic acids research 78 25106868
2016 Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signaling Pathways. Cell reports 77 26972000
2019 Whole-genome sequencing reveals novel tandem-duplication hotspots and a prognostic mutational signature in gastric cancer. Nature communications 76 31048690
2000 A stable complex of a novel transcription factor IIB- related factor, human TFIIIB50, and associated proteins mediate selective transcription by RNA polymerase III of genes with upstream promoter elements. Proceedings of the National Academy of Sciences of the United States of America 70 11121026
2021 Genomic evolution and diverse models of systemic metastases in colorectal cancer. Gut 68 33632712
2017 Assembly of the WHIP-TRIM14-PPP6C Mitochondrial Complex Promotes RIG-I-Mediated Antiviral Signaling. Molecular cell 68 29053956
2018 ZFP36L1 and ZFP36L2 inhibit cell proliferation in a cyclin D-dependent and p53-independent manner. Scientific reports 62 29426877
2011 RNA polymerase III transcription in cancer: the BRF2 connection. Molecular cancer 61 21518452
2019 Long noncoding RNA MNX1-AS1 contributes to lung cancer progression through the miR-527/BRF2 pathway. Journal of cellular physiology 54 30618167
2007 Human Maf1 negatively regulates RNA polymerase III transcription via the TFIIB family members Brf1 and Brf2. International journal of biological sciences 54 17505538
2015 Induction of proto-oncogene BRF2 in breast cancer cells by the dietary soybean isoflavone daidzein. BMC cancer 31 26573593
2017 MicroRNA-373 Inhibits Cell Proliferation and Invasion via Targeting BRF2 in Human Non-small Cell Lung Cancer A549 Cell Line. Cancer research and treatment 29 29025258
2021 Let-7b-3p inhibits tumor growth and metastasis by targeting the BRF2-mediated MAPK/ERK pathway in human lung adenocarcinoma. Translational lung cancer research 25 34012797
2008 Differential expression of the TFIIIB subunits Brf1 and Brf2 in cancer cells. BMC molecular biology 25 18700021
2001 BRFU, a TFIIB-like factor, is directly recruited to the TATA-box of polymerase III small nuclear RNA gene promoters through its interaction with TATA-binding protein. The Journal of biological chemistry 25 11564744
1997 Apolipoprotein B gene regulatory factor-2 (BRF-2) is structurally and immunologically highly related to hepatitis B virus X associated protein-1 (XAP-1). Biochemistry 25 9020796
2023 MALAT1/ mir-1-3p mediated BRF2 expression promotes HCC progression via inhibiting the LKB1/AMPK signaling pathway. Cancer cell international 17 37653482
2023 BRF2 is mediated by microRNA-409-3p and promotes invasion and metastasis of HCC through the Wnt/β-catenin pathway. Cancer cell international 10 36927769
2021 Targeting BRF2 in Cancer Using Repurposed Drugs. Cancers 10 34359683
2020 Silencing of BRF2 inhibits the growth and metastasis of lung cancer cells. Molecular medicine reports 9 32705258
2018 BRF2 as a promising indicator for radical lymph-node dissection surgery in patients with cN0 squamous cell carcinoma of the middle thoracic esophagus. Surgery today 8 30182305
2017 New tricks for an old dog: Brf2-dependent RNA Polymerase III transcription in oxidative stress and cancer. Transcription 8 28854119
1992 Transcriptional regulation of the apolipoprotein B100 gene: purification and characterization of trans-acting factor BRF-2. Molecular and cellular biology 8 1620125
2019 Double mutation of BRF1 and BRF2 leads to sterility in Arabidopsis thaliana. Biochemical and biophysical research communications 5 31277948
2025 Bi-allelic variants in BRF2 are associated with perinatal death and craniofacial anomalies. Genome medicine 1 40229899
2025 Biallelic BRF2 mutations disrupt redox homeostasis as etiological factors in syndromic immunodeficiency and developmental disorders. Molecular therapy : the journal of the American Society of Gene Therapy 0 40781771
2023 Targeting BRF2: insights from in silico screening and molecular dynamic simulations. Journal of biomolecular structure & dynamics 0 37705251