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

Čabart, Pavel; Murphy, Shona

doi:10.1074/jbc.m108515200

Cited by 26 publications

(40 citation statements)

References 45 publications

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“…As observed previously, the addition of both TBP and Brf2 resulted in the formation of a prominent complex (henceforth referred to as the "two-factor complex," labeled 2 in lane 5; see also Fig. 2E, which summarizes the nomenclature used for some of the complexes), reflecting the cooperative binding of these two factors (6,27,43). With TBP and Bdp1, a weak complex migrating much more slowly than the TBP complex was obtained (lane 6, complex labeled TBP/Bdp1).…”

Section: Resultssupporting

confidence: 63%

Structure-Function Analysis of the Human TFIIB-Related Factor II Protein Reveals an Essential Role for the C-Terminal Domain in RNA Polymerase III Transcription

Saxena

Schramm

et al. 2005

Molecular and Cellular Biology

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The transcription factors TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound preinitiation complex, whereas Brf1 and Brf2 are involved, as part of activities also containing TBP and Bdp1 and referred to here as Brf1-TFIIIB and Brf2-TFIIIB, in the recruitment of Pol III. Brf1-TFIIIB recruits Pol III to type 1 and 2 promoters and Brf2-TFIIIB to type 3 promoters such as the human U6 promoter. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1. Here we have tested truncated Brf2, as well as Brf2/TFIIB chimeric proteins for U6 transcription and for assembly of U6 preinitiation complexes. Our results characterize functions of various human Brf2 domains and reveal that the C-terminal domain is required for efficient association of the protein with U6 promoter-bound TBP and SNAP c , a type 3 promoter-specific transcription factor, and for efficient recruitment of Bdp1. This in turn suggests that the C-terminal extensions in Brf1 and Brf2 are crucial to specific recruitment of Pol III over Pol II.In eukaryotes, the job of transcribing nuclear genes is divided among three different RNA polymerases: RNA polymerase I (Pol I), RNA Pol II, and RNA Pol III. A common step in transcription initiation by all three eukaryotic RNA polymerases is the recruitment of the polymerase to the proper promoters by a specific factor or complex. This transcription factor serves as a bridge between promoter-bound factors that nucleate preinitiation complex assembly and the RNA polymerase enzyme itself. For Pol II and Pol III transcription, the factors that accomplish this task are TFIIB and TFIIIB, respectively.Although TFIIB is a single polypeptide, the TFIIIB activity is minimally composed of three polypeptides (see references 11 and 33 for reviews). In human cells, two forms of the TFIIIB complex have been characterized thus far: Brf1-TFIIIB, which functions on type 1 and 2 Pol III promoters, and Brf2-TFIIIB, which functions on type 3 Pol III promoters such as the human U6 small nuclear RNA (snRNA) promoter. Brf1-TFIIIB and Brf2-TFIIIB both contain the TATA-box binding protein TBP and the SANT domain protein Bdp1. They differ by the presence of different members of a family of TFIIB-related factors: Brf1 in Brf1-TFIIIB and Brf2 in Brf2-TFIIIB.TFIIB, Brf1, and Brf2 each contain a Zn ribbon domain at their N terminus, followed by a core domain consisting of two imperfect repeats. In this region, human Brf2 is 20% identical with human TFIIB and 18% identical with human Brf1. In addition, Brf1 and Brf2 contain a C-terminal extension. In Brf1, this C-terminal segment contains two regions called homology domains II and III, which are conserved among yeast and human proteins. Moreover, a third region called homology domain I is conserved among several different yeast species (25...

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Section: Resultssupporting

confidence: 63%

Structure-Function Analysis of the Human TFIIB-Related Factor II Protein Reveals an Essential Role for the C-Terminal Domain in RNA Polymerase III Transcription

Saxena

Schramm

et al. 2005

Molecular and Cellular Biology

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“…For example, TBP and Brf2 bind cooperatively to a TATA box (1), and SNAP c and TBP bind cooperatively to probes containing both a PSE and a TATA box (18). We have shown that mini-SNAP c , although unable to bind cooperatively with the Oct-1 POU domain, can bind cooperatively with TBP (19).…”

mentioning

confidence: 82%

Redundant Cooperative Interactions for Assembly of a Human U6 Transcription Initiation Complex

Hernandez

2002

Molecular and Cellular Biology

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The core human U6 promoter consists of a proximal sequence element (PSE) located upstream of a TATA box. The PSE is recognized by the snRNA-activating protein complex (SNAP c ), which consists of five types of subunits, SNAP190, SNAP50, SNAP45, SNAP43, and SNAP19. The TATA box is recognized by TATA box binding protein (TBP). In addition, basal U6 transcription requires the SANT domain protein Bdp1 and the transcription factor IIB-related factor Brf2. SNAP c and mini-SNAP c , which consists of just SNAP43, SNAP50, and the N-terminal third of SNAP190, bind cooperatively with TBP to the core U6 promoter. By generating complexes smaller than mini-SNAP c , we have identified a 50-amino-acid region within SNAP190 that is (i) required for cooperative binding with TBP in the context of mini-SNAP c and (ii) sufficient for cooperative binding with TBP when fused to a heterologous DNA binding domain. We show that derivatives of mini-SNAP c lacking this region are active for transcription and that with such complexes, TBP can still be recruited to the U6 promoter through cooperative interactions with Brf2. Our results identify complexes smaller than mini-SNAP c that are transcriptionally active and show that there are at least two redundant mechanisms to stably recruit TBP to the U6 transcription initiation complex.An important event during activation of transcription is the establishment of a stable transcription initiation complex. For RNA polymerase II, transcription initiation complexes appear to be partially disassembled at each round of transcription, losing transcription factor IIB (TFIIB), RNA polymerase II, and TFIIF as well as, in some cases, TFIIE and TFIIH (23,24,33,34). Other factors including TFIIA, TATA box binding protein (TBP), some of the TFIID TBP-associated factors (TAFs), and, in a crude extract containing mediator, TFIIH, TFIIE, and mediator itself, are left behind and form a scaffold for reinitiation of transcription (33). In the case of RNA polymerase III transcription, initiation complexes preformed on 5S-and tRNA-type promoters can direct several rounds of transcription in the presence of concentrations of sarcosyl that inhibit formation of new initiation complexes, suggesting that the complexes are stable for several rounds of transcription (8,9).The human U6 snRNA promoter is a type 3 RNA polymerase III promoter characterized by gene-external promoter elements, which can be divided into enhancer and core regions. The enhancer region, referred to as the distal sequence element, is located about 200 bp upstream of the transcription start site and contains binding sites for the POU domain protein Oct-1 and the zinc finger protein STAF (see reference 7 for a review). Both of these factors can activate U6 transcription and can be localized to the U6 promoter region in vivo by chromatin immunoprecipitation experiments (14, 20-22, 26, 28, 35).The U6 core promoter region consists of a proximal sequence element (PSE) and a TATA box located about 50 and 25 bp, respectively, upstream of the transcription s...

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“…HsBrf2 resembles TFIIB in that it recognizes the TATA-box/TBP complex through its TFIIB-related core domain (Cabart and Murphy 2001). In contrast, for S. cerevisiae Brf1, the task of recognizing the TBP-TATAbox complex is performed by two regions of the protein, the TFIIB-related N-terminal half as well as the Brf1-specific C-terminal half, with the latter playing the major role.…”

Section: Binding Of Tfiiib To the Tata Boxmentioning

confidence: 99%

“…5; Cabart and Murphy 2002). Similarly, although HsBrf2 can be shown to associate with HsTBP in GST pull-downs (Cabart andMurphy 2001, 2002), it is not strongly associated with TBP in HeLa cell extracts (Schramm et al 2000). Thus, the TFIIIB components do not always form a stable complex off the DNA.…”

Section: Identification Of Human Bdp1mentioning

confidence: 99%

Recruitment of RNA polymerase III to its target promoters

Schramm¹,

Hernandez²

2002

Genes Dev.

544

601

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A key step in retrieving the information stored in the complex genomes of eukaryotes involves the identification of transcription units and, more specifically, the recognition of promoter sequences by RNA polymerase. In eukaryotes, the task of recognizing nuclear gene promoters and then transcribing the genes is divided among three highly related enzymes, RNA polymerases I, II, and III. Each of these RNA polymerases is dedicated to the transcription of specific sets of genes, and each depends on accessory factors, the so-called transcription factors, to recognize its cognate promoter sequences.RNA polymerase I is unique among the nuclear RNA polymerases in transcribing only one set of genes, the large, tandemly repeated, ribosomal RNA genes, and thus in having to recognize a single promoter structure. RNA polymerase II transcribes the protein-coding genes (mRNA genes) as well as some small nuclear RNA (snRNA) genes. The RNA polymerase II promoters can be divided into a core region, defined as the minimal region capable of directing transcription in vitro, and a regulatory region. The regulatory regions are highly varied in structure, reflecting the highly varied synthesis patterns of cellular proteins and the need for exquisite and complex regulation of these patterns. The core promoters themselves come in different types that, in mRNA-encoding genes, can contain a TATA box, an initiator, a downstream promoter element, or various combinations thereof. The assembly of a functional RNA polymerase II transcription complex on a promoter consisting of just a TATA box has been extensively studied. All the factors involved in the process have been identified, and much is known about how these factors interact with DNA and with each other to recruit, eventually, RNA polymerase II (for reviews, see Orphanides et al. 1996;Woychik and Hampsey 2002). How RNA polymerase II transcription complexes assemble on TATA-less promoters is, however, not as well understood.RNA polymerase III is dedicated to the transcription of an eclectic collection of genes whose main common features are that they encode structural or catalytic RNAs and that they are, as a rule, shorter than 400 base pairs (bp). This length limit is consistent with the elongation properties of RNA polymerase III, which recognizes a simple run of T residues as a termination signal. The genes transcribed by RNA polymerase III encode RNA molecules involved in fundamental metabolic processes, specifically components of the protein synthesis apparatus and components of the splicing and tRNA processing apparatus, as well as RNAs of unknown function. The RNA polymerase III promoters are more varied in structure than the uniform RNA polymerase I promoters, and yet not as diverse as the RNA polymerase II promoters. They have been divided into three main types, two of which are gene-internal and generally TATA-less, and one of which is gene-external and contains a TATA box. Remarkably, we have a good, and in some cases a very detailed, understanding of how RNA polymerase III ...

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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

Cited by 26 publications

References 45 publications

Structure-Function Analysis of the Human TFIIB-Related Factor II Protein Reveals an Essential Role for the C-Terminal Domain in RNA Polymerase III Transcription

Structure-Function Analysis of the Human TFIIB-Related Factor II Protein Reveals an Essential Role for the C-Terminal Domain in RNA Polymerase III Transcription

Redundant Cooperative Interactions for Assembly of a Human U6 Transcription Initiation Complex

Recruitment of RNA polymerase III to its target promoters

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