| 1994 |
Yeast BRF (BRF1 ortholog) binds the 135-kD subunit of TFIIIC and also binds TBP; TBP interacts with both the TFIIB-homologous N-terminal half and the C-terminal half of BRF, with two conserved C-terminal regions required for the TBP–BRF C-terminal interaction. BRF also binds RNA Pol III subunit C34, and a region of C34 necessary for this interaction was defined. |
Protein–protein interaction assays (binding assays between BRF fragments and TFIIIC subunit, TBP, and Pol III subunit C34); functional analysis of deletion mutants; TBP mutants that selectively inhibit Pol III transcription in vivo impair the BRF C-terminal–TBP interaction |
Genes & development |
High |
7995525
|
| 1996 |
Human BRF1 (TFIIIB90/hBRF, 88 kDa) was purified as a TBP-associated complex and identified as the human homolog of yeast BRF. Immunodepletion of hBRF severely debilitates transcription from the tRNA-type VAI promoter but does not affect transcription from the TATA box-containing human U6 promoter, indicating promoter-type-specific requirement for hBRF. |
Biochemical purification; cDNA cloning; immunodepletion of hBRF from transcription extracts followed by in vitro transcription from VAI and U6 promoters |
Molecular and cellular biology |
High |
8943358
|
| 1996 |
Yeast TFIIIB90 (Bdp1/B") interacts weakly with TBP alone but this interaction is enhanced at least 25-fold by BRF1. TFIIIB was reconstituted from recombinant subunits (TBP, BRF1, TFIIIB90). Binding sites for BRF1 and TFIIIB90 on TBP-DNA overlap with binding sites for TFIIA and TFIIB, indicating shared TBP interface. |
Recombinant protein reconstitution; in vitro binding assays; competition with Pol II factors TFIIA and TFIIB |
The Journal of biological chemistry |
High |
8662956
|
| 1997 |
N-terminal deletion analysis of yeast Brf1 showed that the C-terminal half (residues 317–596) lacking the entire TFIIB-homologous domain can still interact with DNA-bound TBP and with B"/Bdp1. Brf1(165–596) lacking 164 N-proximal TFIIB-homologous residues is competent for TFIIIB-DNA complex assembly and TFIIIC-independent transcription, revealing functional complementarity and reciprocity between Brf1 and B" subunits. |
N-terminal deletion series of Brf1 tested in TFIIIB-DNA complex assembly and in vitro transcription; genetic complementation assays |
Molecular and cellular biology |
High |
9271407
|
| 1998 |
TBP surface residues on the top and side of the first TBP repeat (K181, L185, R186, E206, R231, L232, R235, K236, R239, Q242, K243, K249, F250) are required for interaction with yeast Pol III TAF Brf. The Brf C-terminal fragment (lacking TFIIB-homology region) retains TBP-DNA binding via this same surface. Brf and TFIIB interact differently with TBP; the Brf-binding surface on TBP overlaps with surfaces required for activated Pol II transcription. |
91 human TBP surface mutants analyzed in gel-shift assays with purified Brf and B"; in vitro U6 snRNA transcription; equivalent yeast TBP mutations tested |
Molecular and cellular biology |
High |
9488486
|
| 1998 |
Systematic analysis of Brf fragments defined that the principal TFIIIB-assembly function maps to a C-proximal segment (aa 435–545), while the principal transcription-directing function resides in the N-proximal TFIIB-homologous half. Split Brf fragments (aa 1–282 + 284–596) reconstitute fully active TFIIIB-DNA complexes. Photochemical cross-linking mapped proximities of each Brf half to DNA, providing a global model of Brf domain organization in the TFIIIB-DNA complex. |
Systematic Brf fragment analysis; in vitro transcription reconstitution; in vitro footprinting; photochemical protein-DNA cross-linking; TBP interaction mapping |
Molecular and cellular biology |
High |
9710642
|
| 2000 |
In Drosophila, TRF1 (rather than TBP) forms a complex with BRF to direct RNA polymerase III transcription. Immunoprecipitation showed TRF1:BRF complex in vivo; immunodepleted extracts supplemented with recombinant TRF1 and BRF reconstitute transcription of tRNA, 5S, and U6 RNA genes. In vivo, the majority of TRF1 is complexed with BRF and the two proteins colocalize at many polytene chromosome sites containing RNA Pol III genes. |
Immunoprecipitation; immunodepletion followed by in vitro transcription reconstitution with recombinant proteins; immunofluorescence colocalization on polytene chromosomes |
Cell |
High |
10850489
|
| 2000 |
Recombinant Brf and TBP subunits of TFIIIB, interacting over the SNR6 TATA box, are sufficient to direct Ty3 retrotransposon integration at the SNR6 transcription initiation site in the absence of detectable TFIIIC or TFIIIB subunit B", establishing that the minimal requirements for Pol III transcription and Ty3 integration are very similar. |
In vitro integration assay with recombinant Brf and TBP; TFIIIC-independent system using U6/SNR6 gene with TATA box |
The Journal of biological chemistry |
High |
10882723
|
| 2000 |
Alternatively spliced human BRF variants have distinct promoter specificities: hBRF1 functions at the gene-internal 5S, VA1, 7SL and EBER2 promoters, while a different variant hBRF2 is required at the gene-external human U6 promoter, demonstrating that Pol III utilizes different TFIIIB complexes at structurally distinct promoters. |
Isolation of alternatively spliced cDNAs; immunopurification of hBRF-containing complexes; in vitro transcription from different Pol III promoter types |
The EMBO journal |
High |
10921893
|
| 2001 |
In human cells, a TFIIIB subcomponent containing TBP and TAF3B2 (human BRF1) is the target of repression during p53-mediated cell cycle arrest. TAF3B2 protein levels are markedly reduced in extracts from cell cycle-arrested cells due to decreased TAF3B2 protein stability, providing a mechanism for reducing Pol III transcriptional capacity. |
Cell-based complementation assays with in vitro transcription; protein stability analysis in p53-arrested cells; cell fractionation |
The Journal of biological chemistry |
Medium |
11283026
|
| 2002 |
BRF1 (butyrate response factor 1, ZFP36L1 family) was identified as an essential regulator of ARE-dependent mRNA decay: a mutagenized cell line (slowC) failing to degrade ARE-containing mRNA carries frameshift mutations in both BRF1 alleles; retroviral re-expression rescues rapid mRNA decay. siRNA knockdown independently confirms BRF1's active role. BRF1 accelerates mRNA decay and antagonizes PI3-kinase-mediated stabilization; zinc finger mutations abolish both ARE binding and mRNA decay activity. |
Functional genetic screen (retroviral cDNA library rescue of decay-deficient cells); flow cytometry-based reporter assay; siRNA knockdown; transfection of BRF1 zinc finger mutants |
The EMBO journal |
High |
12198173
|
| 2002 |
A gain-of-function mutation (PCF1-1, H190Y) in TPR2 of TFIIIC131 increases binding affinity of TFIIIC131 for Brf1 without affecting Bdp1 binding affinity, by overcoming autoinhibition of Brf1 binding—Brf1 does not interact directly at the mutation site, but the mutation stabilizes an alternative conformation of TFIIIC131 that promotes Brf1 interaction. |
Site-directed mutagenesis; structural modeling; binding affinity assays for Brf1 and Bdp1 with TFIIIC131 fragments; dominant mutation analysis |
Molecular and cellular biology |
Medium |
12167707
|
| 2003 |
The Brf1 and Bdp1 subunits of TFIIIB bind to overlapping sites in the tetratricopeptide repeats (TPRs) of Tfc4 (TFIIIC subunit). TPRs6–9 contain a binding site for Brf1; the L469K mutation in TPR7 reduces Brf1 recruitment into TFIIIB-TFIIIC-DNA complexes and reduces direct Tfc4–Brf1 interaction, and also decreases Bdp1 incorporation, indicating both subunits compete for overlapping Tfc4 sites. |
Site-directed mutagenesis of Tfc4 TPR residues; biochemical assembly assays for TFIIIB-TFIIIC-DNA complexes; direct binding assays; multicopy suppression analysis |
The Journal of biological chemistry |
High |
12930823
|
| 2004 |
Protein kinase B (PKB/Akt) phosphorylates BRF1 (ARE-decay factor) at serine 92 (S92), which impairs BRF1 mRNA decay activity without affecting ARE binding, and induces complex formation of BRF1 with the scaffold protein 14-3-3, causing ARE-mRNA stabilization. |
Recombinant BRF1 in vitro mRNA decay assay; in vitro PKB kinase assay; phosphorylation-site mutagenesis (S92A); co-immunoprecipitation of BRF1 with 14-3-3; ARE-mRNA stability measurements in vivo |
The EMBO journal |
High |
15538381
|
| 2004 |
Brf1 (yeast) induces dissociation of TBP dimers, requiring both its high-affinity TBP-binding C-terminal domain and its TFIIB homology domain working in concert; the C-terminal TBP-binding domain alone is insufficient to promote TBP dimer dissociation. |
In vitro TBP dimerization and dissociation assays with Brf1 domain fragments; functional domain analysis |
The Journal of biological chemistry |
Medium |
15190063
|
| 2005 |
TTP and BRF-1 (ARE-decay factors) each contain two activation domains that recruit mRNA decay enzymes involved in deadenylation, decapping, 3'-to-5' exonucleolytic decay, and 5'-to-3' exonucleolytic decay. The N-terminal activation domain of BRF-1 functions as a binding platform for mRNA decay enzymes. Both activation domains can activate mRNA decay when fused to a heterologous RNA-binding protein and inhibit ARE-mediated mRNA decay when overexpressed. |
Co-immunoprecipitation of mRNA decay enzymes with TTP/BRF-1; tethering assays (fusion to heterologous RNA-binding protein); dominant-negative overexpression; two activation domain mapping |
Genes & development |
High |
15687258
|
| 2005 |
A Brf1-TBP triple fusion protein (TBP core placed between N- and C-proximal domains of Brf1) effectively replaces both Brf1 and TBP in TFIIIC-dependent and -independent transcription in vitro, forms extremely stable TFIIIB-DNA complexes, and can recruit Pol III for TATA box-directed transcription in the absence of Bdp1, confirming the modular architecture of Brf1 and its bipartite TBP interaction mode. |
Structure-informed protein engineering (triple fusion); in vitro transcription reconstitution; chemical nuclease footprinting; in vivo complementation in yeast |
Proceedings of the National Academy of Sciences of the United States of America |
High |
16227432
|
| 2006 |
PKB phosphorylates BRF1 (ARE-decay factor) at a second regulatory site, S203, which cooperates with S92 in vivo. Double alanine mutation of both S92 and S203 uncouples BRF1 from PKB regulation, leading to constitutive mRNA decay. Phosphorylation-dependent 14-3-3 binding requires phosphorylation at both sites. BRF1 is subject to proteasomal degradation (half-life <3 h) but phosphorylation stabilizes it; cell compartment fractionation showed that 14-3-3 binding sequesters BRF1 through relocalization, preventing mRNA decay activity and protecting from proteasomal degradation. |
In vitro kinase assay; site-directed mutagenesis (S92A, S203A, double mutant); mRNA decay assays; co-immunoprecipitation with 14-3-3; protein stability assays in PKBα−/− cells; cell fractionation |
Molecular and cellular biology |
High |
17030608
|
| 2006 |
The principal attachment site of Brf1 for Bdp1 in TFIIIB was mapped: a 66-amino acid segment of Brf1's C-terminal half serves as a two-sided adhesive surface with one face interacting with TBP and the other anchoring Bdp1. The interacting Bdp1 domain was demarcated to a 66-amino acid segment including the SANT domain, which is the most phylogenetically conserved region of Bdp1. |
Structure-informed site-directed mutagenesis; photochemical protein-DNA cross-linking; deletion series of Brf1 and Bdp1 fragments in binding assays |
The Journal of biological chemistry |
High |
16551611
|
| 2006 |
Brf1 peptides from three distinct regions interact with the TPR-containing Tfc4 subunit of TFIIIC. A peptide binding specifically to TPR6-9 of Tfc4 promotes formation of TFIIIC-DNA and Brf1-TFIIIC-DNA complexes and causes a conformational change in TFIIIC that overcomes Tfc4 autoinhibition of Brf1 binding, suggesting repositioning of Brf1 is required during TFIIIB assembly. |
Yeast two-hybrid screen of Brf1 peptide libraries against Tfc4 fragments; native gel mobility shift assays; biochemical binding studies |
Molecular and cellular biology |
Medium |
16880507
|
| 2006 |
In Drosophila, genome-wide ChIP analysis identified 354 TRF1-binding sites, ~78% of which colocalize with BRF. The TRF1/BRF complex is functionally required for transcription of novel targets including 7SL RNA and small nucleolar RNAs, indicating TRF1/BRF is responsible for all known classes of Pol III transcription in Drosophila. |
Genome-wide ChIP with tiling microarrays; functional transcription assays for novel targets |
The EMBO journal |
Medium |
17170711
|
| 2007 |
Human Maf1 represses RNA Pol III transcription via direct interaction with TFIIIB, specifically through the TFIIB family members Brf1 and Brf2 (not through other components). This was demonstrated in vivo with a Pol III luciferase reporter assay. |
RNA Pol III luciferase reporter assay in vivo; epistasis analysis showing Maf1 repression acts through Brf1 and Brf2 subunits of TFIIIB |
International journal of biological sciences |
Medium |
17505538
|
| 2007 |
TTP and BRF-1 (ARE-binding proteins) deliver ARE-mRNAs to processing bodies (PBs). Depletion of endogenous TTP and BRF proteins or dominant-negative TTP impairs ARE-mRNA localization to PBs. TTP and BRF-1 can tether mRNAs to PBs and TTP can nucleate PB formation on untranslated mRNAs. ARE-mRNA PB localization is mediated by TTP N- and C-terminal domains and occurs downstream from polysome release. |
siRNA depletion of TTP and BRF proteins; dominant-negative overexpression; tethering assays; fluorescence microscopy/live imaging of reporter ARE-mRNAs in PBs; cycloheximide treatment to trap polysomes |
Genes & development |
High |
17369404
|
| 2008 |
MAPK-activated protein kinase 2 (MK2) phosphorylates BRF1 (ARE-decay factor) at S54, S92, S203, and an unidentified C-terminal site, inhibiting BRF1's ARE mRNA decay activity. MK2-mediated inhibition requires phosphorylation at S54, S92, and S203. Phosphorylation by MK2 does not alter BRF1's ability to bind AREs or associate with mRNA decay enzymes, suggesting inhibition occurs downstream of RNA binding and decay enzyme recruitment. |
In vitro kinase assays with MK2 and BRF1 fragments; site-directed mutagenesis (S54, S92, S203); ARE-mRNA decay assays in cells with active MK2; ARE-binding and co-immunoprecipitation of decay enzymes |
RNA (New York, N.Y.) |
High |
18326031
|
| 2008 |
NMR mapping of the Brf1–Bdp1 interaction at single-amino acid resolution showed that the principal anchorage site of Brf1 is on a convex surface of Bdp1 encompassing helix 1 and helix 3 of its conserved SANT domain, with the main Bdp1 anchorage provided by residues 470–495 of Brf1. |
NMR chemical shift perturbation mapping using minimal functional segments of Brf1 and Bdp1; NMR-derived structural model |
Biochemistry |
High |
19086269
|
| 2010 |
Ethanol induces RNA Pol III-dependent transcription in HepG2 cells and primary mouse hepatocytes by upregulating BRF1 and TBP expression (TFIIIB components) through JNK1 activation and enhanced c-Jun expression. c-Jun is directly recruited to TBP, BRF1, and tRNA gene promoters. Chronic alcohol administration in mice increases BRF1, TBP, tRNA, and 5S rRNA transcription in liver. |
Chromatin immunoprecipitation (ChIP); luciferase reporter assays; siRNA knockdown; in vivo mouse alcohol feeding model; quantitative RT-PCR |
The Journal of biological chemistry |
Medium |
21106530
|
| 2011 |
Tis11b/BRF1 (ARE-decay factor) binds to endogenous Dll4 mRNA and represses its expression without affecting mRNA stability, through a novel mechanism involving mRNA 3'-end processing. One AUUUA motif in a weak noncanonical polyadenylation signal in the Dll4 3'-UTR is the major Tis11b-binding site. Inhibition of Tis11b expression changes the ratio between mRNAs cleaved or read-through at the poly(A) signal, indicating Tis11b interferes with mRNA cleavage and polyadenylation efficiency. |
siRNA knockdown of Tis11b in endothelial cells; RNA immunoprecipitation of endogenous Dll4 mRNA; 3'-UTR reporter assays; poly(A) site usage analysis; hypoxia treatment |
Molecular biology of the cell |
Medium |
21832157
|
| 2013 |
Site-specific non-natural amino acid cross-linking mapped Brf1's protein interaction network in the Pol III preinitiation complex: the N-terminal domain of Brf1 shows multiple protein interactions in the Pol III active-site cleft reminiscent of TFIIB, with the cyclin repeat subdomain additionally contacting C34 at its WH2–WH3 connecting region. The C-terminal domain of Brf1 contains extensive binding sites for TBP and Bdp1 to hold TFIIIB together on the promoter. |
Site-specific non-natural amino acid incorporation for cross-linking; site-directed hydroxyl radical probing; protein interaction mapping in the preinitiation complex |
Molecular and cellular biology |
High |
24277937
|
| 2014 |
Brf1 (ZFP36L1/mRNA decay factor) operates downstream of FGF/ERK MAP kinase signaling in mouse embryonic stem cells: ERK signaling upregulates Brf1, which directly destabilizes target mRNAs including Nanog mRNA to disrupt pluripotency-associated gene expression and attenuate mESC self-renewal. Enhanced Brf1 expression preferentially regulates mesendoderm commitment during differentiation, accelerating primitive streak marker expression. |
FGF/ERK pathway manipulation; Brf1 gain-of-function and loss-of-function in mESCs; mRNA stability assays for Nanog and other targets; differentiation assays |
Proceedings of the National Academy of Sciences of the United States of America |
Medium |
24733888
|
| 2015 |
Biallelic missense mutations in BRF1 reduce Brf1 occupancy at tRNA target genes in S. cerevisiae, impair yeast cell growth, and reduce Pol III-related transcription activity in vitro. CRISPR-mediated deletion of brf1 in zebrafish recapitulates neurodevelopmental phenotypes. In vivo complementation showed all four candidate disease mutations to be pathogenic in an isoform-specific context, confirming BRF1 mutations that reduce protein activity cause cerebellar hypoplasia and intellectual disability. |
Whole-exome sequencing; yeast complementation with human BRF1 disease alleles; ChIP for Brf1 occupancy at tRNA genes in yeast; in vitro Pol III transcription assay; CRISPR deletion and morpholino knockdown in zebrafish |
Genome research |
High |
25561519
|
| 2016 |
TIS11b/BRF1 (ARE-decay factor) is phosphorylated by PKA at S54 and S334. Phosphomimetic mutation at C-terminal S334 markedly increases TIS11b half-life and enhances mRNA decay activity; this is accompanied by enhanced interaction with the decapping coactivator Dcp1a. Prevention of phosphorylation at S334 potentiates interaction with the Ccr4-Not deadenylase complex subunit Cnot1, revealing that differential phosphorylation at S334 switches TIS11b's association between distinct decay pathway components. |
Site-directed mutagenesis; in vitro kinase assays; phosphosite-specific immunodetection; protein half-life measurements; co-immunoprecipitation with Dcp1a and Cnot1; mRNA decay assays |
Molecular biology of the cell |
High |
27708140
|
| 2017 |
BRF1 (TFIIIB subunit) physically interacts with estrogen receptor alpha (ERα) in breast cancer cells, as shown by co-immunoprecipitation and colocalization in the nucleus. ERα mediates BRF1 expression, and BRF1 and ERα synergistically regulate transcription of Pol III genes. Inhibition of ERα by siRNA or tamoxifen reduces BRF1 levels and Pol III gene expression. |
Co-immunoprecipitation; immunofluorescence colocalization; ChIP; siRNA knockdown of ERα; tamoxifen treatment; Pol III gene expression analysis |
Molecular oncology |
Medium |
28972307
|
| 2018 |
RNF12, a RING domain-containing ubiquitin E3 ligase, physically interacts with BRF1 (TFIIIB subunit) and catalyzes Lys27- and Lys33-linked polyubiquitination of BRF1. RNF12 negatively regulates Pol III-dependent transcription and cell proliferation via BRF1. |
Co-immunoprecipitation; in vitro ubiquitination assay; linkage-specific ubiquitin chain analysis; Pol III transcription assays; cell proliferation assays with RNF12 overexpression/knockdown |
The Journal of biological chemistry |
Medium |
30413534
|
| 2018 |
The WH3 insertion domain of Rpc82 (TFIIE-related Pol III subunit) interacts with BRF1 within the preinitiation complex, as revealed by site-specific photo-crosslinking. Rpc82 also contacts upstream DNA and the protrusion and wall domains of the Pol III cleft, with the WH3 insertion important for cell growth and in vitro transcription activity. |
Site-specific photo-crosslinking with non-natural amino acid; hydroxyl radical probing; in vitro transcription assays; genetic growth assays |
Nucleic acids research |
Medium |
29177422
|
| 2019 |
Brf1 knockout in mice leads to embryonic lethality at the blastocyst stage. Conditional deletion of Brf1 in gastrointestinal epithelial tissues (intestine, liver, pancreas) is incompatible with organ homeostasis and induces apoptosis. Overexpression of BRF1 rescues the phenotypes of Brf1 deletion in intestine and liver, confirming BRF1 is essential for normal tissue homeostasis. |
Conditional knockout mouse models; genetic rescue by BRF1 overexpression; histological analysis; apoptosis assays |
Cell death and differentiation |
High |
30858608
|
| 2020 |
Sp1 controls BRF1 expression by binding to the BRF1 promoter 4 (BRF1P4) and promoting occupancy of TBP, TFIIAα, and p300 at this promoter, thereby modulating Pol III gene transcription. Sp1 knockdown inhibits BRF1 expression and Pol III transcription; Sp1 overexpression enhances these activities. |
Reporter gene assays; ChIP for Sp1, TBP, TFIIAα, p300 at BRF1 promoter; siRNA knockdown and overexpression of Sp1; Pol III transcription assays |
The Journal of biological chemistry |
Medium |
32115405
|