Intramolecular interaction of yeast TFIIB in transcription control

Zhang, Dong Yi; Dorsey, Michael J.; Voth, Warren P.; Carson, Daniel J.; Zeng, Xiao; Stillman, David J.; Ma, Jun

doi:10.1093/nar/28.9.1913

Cited by 12 publications

(5 citation statements)

References 38 publications

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“…This involves the B-finger region and the second direct repeat of TFIIB (see Fig. 2) and has been demonstrated by protein interaction assays, limited proteolysis, and direct effects of the TFIIB N terminus on TFIIBc in NMR Hayashi et al 1998;Bangur et al 1999;Wu and Hampsey 1999;Hawkes et al 2000;Zhang et al 2000;Glossop et al 2004). Small angle-X-ray scattering of TFIIB derived a shape for intact TFIIB in solution, into which the solved structures of the TFIIB core domain and zinc ribbon could be placed (Grossmann et al 2001).…”

Section: Tfiib Conformationmentioning

confidence: 77%

TFIIB and the regulation of transcription by RNA polymerase II

Deng

Roberts

2007

Chromosoma

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Accurate transcription of a gene by RNA polymerase II requires the assembly of a group of general transcription factors at the promoter. The general transcription factor TFIIB plays a central role in preinitiation complex assembly, providing a bridge between promoter-bound TFIID and RNA polymerase II. TFIIB makes extensive contact with the core promoter via two independent DNA-recognition modules. In addition to interacting with other general transcription factors, TFIIB directly modulates the catalytic center of RNA polymerase II in the transcription complex. Moreover, TFIIB has been proposed as a target of transcriptional activator proteins that act to stimulate preinitiation complex assembly. In this review, we will discuss our current understanding of these activities of TFIIB.

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Section: Tfiib Conformationmentioning

confidence: 77%

TFIIB and the regulation of transcription by RNA polymerase II

Deng

Roberts

2007

Chromosoma

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“…These TFIIB mutant effects are made all the more evident by the analysis conducted in the presence of TFIIF, in which there was more robust pol IIcontaining AdML promoter complex formation but the pattern remained the same (lanes 15 to 18). Interestingly, this species-specific difference in TFIIB function differs from that discovered in the TFIIB CORE by Ma and colleagues (51,52,60). These results suggest that multiple surfaces of TFIIB may be involved in the direct or indirect recruitment of pol II.…”

Section: Resultsmentioning

confidence: 58%

A Nonconserved Surface of the TFIIB Zinc Ribbon Domain Plays a Direct Role in RNA Polymerase II Recruitment

Tubon

Tansey

Herr

2004

Molecular and Cellular Biology

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The general transcription factor TFIIB is a highly conserved and essential component of the eukaryotic RNA polymerase II (pol II) transcription initiation machinery. It consists of a single polypeptide with two conserved structural domains: an amino-terminal zinc ribbon structure (TFIIB ZR ) and a carboxy-terminal core (TFIIB CORE ). We have analyzed the role of the amino-terminal region of human TFIIB in transcription in vivo and in vitro. We identified a small nonconserved surface of the TFIIB ZR that is required for pol II transcription in vivo and for different types of basal pol II transcription in vitro. Consistent with a general role in transcription, this TFIIB ZR surface is directly involved in the recruitment of pol II to a TATA box-containing promoter. Curiously, although the amino-terminal human TFIIB ZR domain can recruit both human pol II and yeast (Saccharomyces cerevisiae) pol II, the yeast TFIIB amino-terminal region recruits yeast pol II but not human pol II. Thus, a critical process in transcription from many different promoters-pol II recruitmenthas changed in sequence specificity during eukaryotic evolution.Regulated gene transcription requires the coordinated temporal and spatial recruitment of an appropriate RNA polymerase to specific promoters. In eukaryotes, one of three nuclear RNA polymerases, RNA polymerase II (pol II), transcribes the large number of protein-encoding genes as well as selected small nuclear RNA (snRNA) genes. A major challenge in the regulation of transcription by pol II is the recruitment of an enzyme with little inherent promoter selectivity to specific pol II promoters in response to transcriptional activators.A major aspect of this selectivity process is the association of pol II with general transcription factors (GTFs), particularly TFIIA, TFIIB, and TFIID, which recognize specific promoter DNA sequences and can nucleate the assembly of a preinitiation complex with pol II and other GTFs (e.g., TFIIE, TFIIF, and TFIIH). For mRNA-type promoters, the binding of TATA-binding protein (TBP) to the TATA box can nucleate the assembly of the preinitiation complex. This complex can then either be completed directly by the recruitment of a pol II-and GTF-containing holoenzyme (42, 45) or proceed stepwise by the sequential incorporation of single GTFs or combinations of GTFs (44). A central player in both processes is TFIIB (20), which interacts with the TATA box-bound TBP (6,21,27,39,59) and directs the assembly of the other GTFs to form an active transcription initiation complex (3,4,6,21,48).TBP contains a conserved carboxy-terminal core domain (TBP CORE ), which is responsible for binding to the TATA box. TFIIB also contains a conserved carboxy-terminal core domain (TFIIB CORE ), which, when it binds to the TATA box-bound TBP CORE , contacts the surfaces of TBP and a DNA sequence upstream of the TATA box called the B recognition element (BRE) (34). This TFIIB-TBP-TATA box interaction greatly stabilizes TBP on the DNA (3,21,23,27,31,61). In addition to the TFIIB CORE , T...

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“…It can control the progress of cell cycle by phosphorylate different transcription factor. In our case, CDC28 phosphorylate ACE2 [ 32 ] which can increase the activity of transcription factor, SUA7 [ 33 ]. SUA7 is the transcription factor of TGL4, which is a lipase in linoleic acid metabolism pathway.…”

Section: Resultsmentioning

confidence: 99%

A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae

Yuan

Tang

et al. 2016

BMC Syst Biol

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BackgroundExpression quantitative trait locus (eQTL) analysis has been widely used to understand how genetic variations affect gene expressions in the biological systems. Traditional eQTL is investigated in a pair-wise manner in which one SNP affects the expression of one gene. In this way, some associated markers found in GWAS have been related to disease mechanism by eQTL study. However, in real life, biological process is usually performed by a group of genes. Although some methods have been proposed to identify a group of SNPs that affect the mean of gene expressions in the network, the change of co-expression pattern has not been considered. So we propose a process and algorithm to identify the marker which affects the co-expression pattern of a pathway. Considering two genes may have different correlations under different isoforms which is hard to detect by the linear test, we also consider the nonlinear test.ResultsWhen we applied our method to yeast eQTL dataset profiled under both the glucose and ethanol conditions, we identified a total of 166 modules, with each module consisting of a group of genes and one eQTL where the eQTL regulate the co-expression patterns of the group of genes. We found that many of these modules have biological significance.ConclusionsWe propose a network based covariance test to identify the SNP which affects the structure of a pathway. We also consider the nonlinear test as considering two genes may have different correlations under different isoforms which is hard to detect by linear test.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-015-0245-0) contains supplementary material, which is available to authorized users.

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Intramolecular interaction of yeast TFIIB in transcription control

Cited by 12 publications

References 38 publications

TFIIB and the regulation of transcription by RNA polymerase II

TFIIB and the regulation of transcription by RNA polymerase II

A Nonconserved Surface of the TFIIB Zinc Ribbon Domain Plays a Direct Role in RNA Polymerase II Recruitment

A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae

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