RNA polymerase switch in transcription of yeast rDNA: Role of transcription factor UAF (upstream activation factor) in silencing rDNA transcription by RNA polymerase II

ABSTRACT Strains of the yeast Saccharomyces cerevisiae defective in transcription factor UAF give rise to variants able to grow by transcribing endogenous ribosomal DNA (rDNA) by RNA polymerase II (Pol II). We have demonstrated that the switch to growth using the Pol II system consists of two steps: a mutational alteration in UAF and an expansion of chromosomal rDNA repeats. The first step, a single mutation in UAF, is sufficient to allow Pol II transcription of rDNA. In contrast to UAF mutations, mutations in Pol I or other Pol I transcription factors can not independently lead to Pol II transcription of rDNA, suggesting a specific role of UAF in preventing polymerase switch. The second step, expansion of chromosomal rDNA repeats to levels severalfold higher than the wild type, is required for efficient cell growth. Mutations in genes that affect recombination within the rDNA repeats, fob1 and sir2, decrease and increase, respectively, the frequency of switching to growth using Pol II, indicating that increased rDNA copy number is a cause rather than a consequence of the switch. Finally, we show that the switch to the Pol II system is accompanied by a striking alteration in the localization and morphology of the nucleolus. The altered state that uses Pol II for rDNA transcription is semistable and heritable through mitosis and meiosis. We discuss the significance of these observations in relation to the plasticity of rDNA tandem repeats and nucleolar structures as well as evolution of the Pol I machinery.

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Probing Zn2+-binding effects on the zinc-ribbon domain of human general transcription factor TFIIB

Biochemical Journal ◽

10.1042/bj20031706 ◽

2004 ◽

Vol 378 (2) ◽

pp. 317-324 ◽

Cited By ~ 12

Author(s):

Mahua GHOSH ◽

Laura M. ELSBY ◽

Tapas K. MAL ◽

Jane M. GOODING ◽

Stefan G. E. ROBERTS ◽

...

Keyword(s):

Transcription Factor ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Structural Changes ◽

Core Promoter ◽

Critical Role ◽

General Transcription Factor ◽

Structural Rigidity ◽

Zinc Ribbon

The general transcription factor, TFIIB, plays an important role in the assembly of the pre-initiation complex. The N-terminal domain (NTD) of TFIIB contains a zinc-ribbon motif, which is responsible for the recruitment of RNA polymerase II and TFIIF to the core promoter region. Although zinc-ribbon motif structures of eukaryotic and archaeal TFIIBs have been reported previously, the structural role of Zn2+ binding to TFIIB remains to be determined. In the present paper, we report NMR and biochemical studies of human TFIIB NTD, which characterize the structure and dynamics of the TFIIB Zn2+-binding domain in both Zn2+-bound and -free states. The NMR data show that, whereas the backbone fold of NTD is pre-formed in the apo state, Zn2+ binding reduces backbone mobility in the β-turn (Arg28–Gly30), induces enhanced structural rigidity of the charged-cluster domain in the central linker region of TFIIB and appends a positive surface charge within the Zn2+-binding site. V8 protease-sensitivity assays of full-length TFIIB support the Zn2+-dependent structural changes. These structural effects of Zn2+ binding on TFIIB may have a critical role in interactions with its binding partners, such as the Rpb1 subunit of RNA polymerase II.

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The role of TBP in rDNA transcription by RNA polymerase I in Saccharomyces cerevisiae: TBP is required for upstream activation factor-dependent recruitment of core factor.

Genes & Development ◽

10.1101/gad.10.20.2551 ◽

1996 ◽

Vol 10 (20) ◽

pp. 2551-2563 ◽

Cited By ~ 68

Author(s):

J S Steffan ◽

D A Keys ◽

J A Dodd ◽

M Nomura

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Polymerase ◽

Rna Polymerase I ◽

Rdna Transcription ◽

Activation Factor ◽

Polymerase I

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ZFP281 Recruits MYC to Active Promoters in Regulating Transcriptional Initiation and Elongation

Molecular and Cellular Biology ◽

10.1128/mcb.00329-19 ◽

2019 ◽

Vol 39 (24) ◽

Cited By ~ 1

Author(s):

Zhuojuan Luo ◽

Xiaoxu Liu ◽

Hao Xie ◽

Yan Wang ◽

Chengqi Lin

Keyword(s):

Stem Cells ◽

Transcription Factor ◽

Transcriptional Regulation ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Embryonic Stem ◽

General Mechanism ◽

Transcriptional Initiation ◽

Genome Scale

ABSTRACT The roles of the MYC transcription factor in transcriptional regulation have been studied intensively. However, the general mechanism underlying the recruitment of MYC to chromatin is less clear. Here, we found that the Krüppel-like transcription factor ZFP281 plays important roles in recruiting MYC to active promoters in mouse embryonic stem cells. At the genome scale, ZFP281 is broadly associated with MYC, and the depletion of ZFP281 significantly reduces the levels of MYC and RNA polymerase II at the ZFP281- and MYC-cobound genes. Specially, we found that recruitment is required for the regulation of the Lin28a oncogene and pri-let-7 transcription. Our results therefore suggest a major role of ZFP281 in recruiting MYC to chromatin and the integration of ZFP281 and the MYC/LIN28A/Let-7 loop into a multilevel circuit.

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The role of TFIIB conformation in transcriptional regulation

Biochemical Society Transactions ◽

10.1042/bst0321098 ◽

2004 ◽

Vol 32 (6) ◽

pp. 1098-1099 ◽

Cited By ~ 6

Author(s):

L.M. Elsby ◽

S.G.E. Roberts

Keyword(s):

Transcription Factor ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Intramolecular Interaction ◽

Transcription Control ◽

Activator Proteins ◽

General Transcription Factors ◽

Transcription Factor Iib ◽

General Transcription Factor

Transcription by RNA polymerase II requires the assembly of the general transcription factors at the promoter to form a preinitiaiton complex. TFIIB (transcription factor IIB) plays a central role in this process, mediating the recruitment of RNA polymerase II and positioning it over the transcription start site. The assembly of TFIIB at the promoter can be a limiting event and several activator proteins have been shown to target TFIIB recruitment in the process of transcriptional stimulation. TFIIB is composed of two domains that engage in an intramolecular interaction. Indeed, the conformation of TFIIB has been found to underpin the function of this general transcription factor. Here we discuss our current understanding of TFIIB conformation and its role in transcription control.

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