Differential Utilization of TATA Box-binding Protein (TBP) and TBP-related Factor 1 (TRF1) at Different Classes of RNA Polymerase III Promoters

Verma, Neha; Hung, Ko-Hsuan; Kang, Jaw Jou; Barakat, Nermeen H.; Stumph, William E.

doi:10.1074/jbc.c113.503094

Cited by 10 publications

(9 citation statements)

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“…Recent work in our lab confirmed that TRF1 replaced TBP as a subunit of TFIIIB for tRNA gene transcription in fruit flies. Interestingly, however, we also found that transcription of U6 snRNA genes by Pol III instead utilized TBP rather than TRF1 . Thus, different types of Pol III promoters in insects can differentially utilize either TBP (at Type III promoters) or TRF1 (at Type I and Type II promoters) as a component of TFIIIB.…”

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confidence: 70%

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TFIIIB subunit locations on U6 gene promoter DNA mapped by site‐specific protein–DNA photo‐cross‐linking

Kang

Stumph

2016

FEBS Letters

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Edited by Ivan SadowskiRNA polymerase III-transcribed U6 snRNA genes have gene-external promoters that contain TATA boxes. U6 TATA sequences are bound by TFIIIB that in Drosophila contains the three subunits TBP, Brf1, and Bdp1. The overall structure of TFIIIB is still not well understood. We have therefore studied the mode of TFIIIB binding to DNA by site-specific protein-DNA photo-cross-linking. The results indicate that a portion of Brf1 is sandwiched between Bdp1 and TBP upstream of the TATA box. Furthermore, Bdp1 traverses the DNA under the N-terminal stirrup of TBP to interact with the DNA (and very likely Brf1) downstream of the TATA sequence.Keywords: Bdp1; Brf1; Protein-DNA photo-cross-linking; RNA polymerase III transcription; TATA box-binding protein; TFIIIB Eukaryotic RNA polymerase III (Pol III) synthesizes a wide variety of small RNA molecules involved in diverse metabolic processes, including components of the protein synthesis apparatus (tRNA and 5S rRNA) and the spliceosome (U6 snRNA). The Pol III promoters can be divided into three distinct types: Type I (5S rRNA) and Type II (e.g. tRNA) promoters are gene-internal and usually are TATA-less [1][2][3]. Type III promoters (e.g., U6) on the other hand are geneexternal and inevitably contain a TATA sequence [1][2][3][4][5][6][7]. The only general transcription factor that is required at all three types of Pol III promoters is TFIIIB. TFIIIB is considered to be the Pol III initiation factor per se because once bound to the DNA, TFIIIB is able to recruit Pol III for multiple rounds of transcription initiation [8].TFIIIB is composed of three subunits, normally the TATA box-binding protein (TBP), Brf1, and Bdp1 [3]. However, heterogeneity can exist in TFIIIB at different Pol III promoters. For example, in Drosophila melanogaster, the TBP-related factor TRF1 was found to be utilized for Pol III transcription in place of TBP [9]. Recent work in our lab confirmed that TRF1 replaced TBP as a subunit of TFIIIB for tRNA gene transcription in fruit flies. Interestingly, however, we also found that transcription of U6 snRNA genes by Pol III instead utilized TBP rather than TRF1 [10]. Thus, different types of Pol III promoters in insects can differentially utilize either TBP (at Type III promoters) or TRF1 (at Type I and Type II promoters) as a component of TFIIIB.Brf1, another subunit of TFIIIB, is related to the Pol II general transcription factor TFIIB. The N-terminal half of Brf1 is homologous to the zinc ribbon domain and the two cyclin-fold repeats of TFIIB, but Brf1 has an extended C-terminus that averages over 360 amino acid residues in length among yeast, fruit flies, and humans [3].Interestingly, U6 transcription in mammals requires a unique and distinct form of Brf known as Brf2 [11,12]. Human Brf2 contains an N-terminal domain homologous to those found in TFIIB and Brf1, and it Abbreviations TFIIIB, transcription factor IIIB; TBP, TATA box binding protein; TRF1; TBP-related factor 1; TFIIB, transcription factor IIB; Brf1, TFIIB-related factor 1; Brf...

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“…The TFIIIB subunits were overexpressed or co‐overexpressed in stably transfected S2 cells under the control of the copper‐inducible metallothionein promoter as previously described . Proteins were partially purified or copurified by nickel chelate affinity chromatography also as previously described .…”

Section: Methodsmentioning

confidence: 99%

TFIIIB subunit locations on U6 gene promoter DNA mapped by site‐specific protein–DNA photo‐cross‐linking

Kang

Stumph

2016

FEBS Letters

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“…It can bind to the TATA box along with TFIIA and TFIIB and substitute for TBP in the transcription of some Pol II promoters in vitro (Hansen et al 1997;Holmes and Tjian 2000). Moreover, TRF1 associates with BRF1 (an RNA Pol III transcription factor) and mediates tRNA gene transcription from Pol III promoters (Takada et al 2000;Isogai et al 2007a;Verma et al 2013). Thus, TRF1 participates in both Pol II and Pol III transcription.…”

Section: Trf1mentioning

confidence: 99%

The punctilious RNA polymerase II core promoter

et al. 2017

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The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.

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“…Likewise, the transcription initiation factors for Pol I and Pol III (SL1/Tif-1B and TFIIIB, respectively) contain a TFIIB-related protein and TBP (or a TBP-related protein (Trf1) in Drosophila) counterparts (7)(8)(9)20).…”

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RNA Polymerase III Accurately Initiates Transcription from RNA Polymerase II Promoters in Vitro

Duttke

2014

Journal of Biological Chemistry

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Background: RNA polymerase II (Pol II) and III (Pol III) transcription systems are reported to regulate non-overlapping sets of genes. Results: Pol III can initiate transcription from Pol II promoters with AT-rich sequence. The DNA template to nuclear extract ratio determines the predominant polymerase. Conclusion: Pol II and Pol III transcription initiation can overlap. Significance: RNA polymerase specificity is variable and depends on the transcription conditions.

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Differential Utilization of TATA Box-binding Protein (TBP) and TBP-related Factor 1 (TRF1) at Different Classes of RNA Polymerase III Promoters

Cited by 10 publications

References 40 publications

TFIIIB subunit locations on U6 gene promoter DNA mapped by site‐specific protein–DNA photo‐cross‐linking

TFIIIB subunit locations on U6 gene promoter DNA mapped by site‐specific protein–DNA photo‐cross‐linking

The punctilious RNA polymerase II core promoter

RNA Polymerase III Accurately Initiates Transcription from RNA Polymerase II Promoters in Vitro

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