Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock

Zanton, Sara J.; Pugh, B. Franklin

doi:10.1101/gad.1437506

Cited by 105 publications

(122 citation statements)

References 81 publications

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“…A similar role has been suggested for TFE, the archaeal analog of TFIIE, which is essential for initiation by archaeal RNA polymerase (8). It has been reported that potential promoters in yeast can recruit most of the general transcript initiation factors, including TFIIE, but these promoters remain inactive because they fail to recruit both pol II and TFIIH (9). Some yeast genes apparently do not require TFIIE for expression.…”

mentioning

confidence: 61%

Inactivated RNA Polymerase II Open Complexes Can Be Reactivated with TFIIE

Čabart

Luse

2012

Journal of Biological Chemistry

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mentioning

confidence: 61%

Inactivated RNA Polymerase II Open Complexes Can Be Reactivated with TFIIE

Čabart

Luse

2012

Journal of Biological Chemistry

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“…Although the addition of TFIIE to a PIC in vitro is generally thought to require the prior addition of TBP, TFIIB, TFIIF, and Pol II (14,23), TFIIE can maintain its DNA template association in extracts in the absence of TFIIB, TFIIF, and Pol II as a component of the stable reinitiation ''scaffold'' (21). Moreover, TFIIE maintains genome contacts in vivo in the apparent absence of Pol II and some of the other general transcription factors (24). The effects of AptTBP-101 on the different equilibrium distributions of promoter-associated and free TFIIB and TFIIE could be a consequence of assembly of a transient preinitiation complex in which TFIIE is recruited and stably maintained even after TFIIB leaves the complex.…”

Section: Discussionmentioning

confidence: 99%

RNA aptamers directed to discrete functional sites on a single protein structural domain

Shi

Xiu

Sevilimedu

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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Cellular regulatory networks are organized such that many proteins have few interactions, whereas a few proteins have many. These densely connected protein ''hubs'' are critical for the systemwide behavior of cells, and the capability of selectively perturbing a subset of interactions at these hubs is invaluable in deciphering and manipulating regulatory mechanisms. SELEX-generated RNA aptamers are proving to be highly effective reagents for inhibiting targeted proteins, but conventional methods generate one or several aptamer clones that usually bind to a single target site most preferred by a nucleic acid ligand. We advance a generalized scheme for isolating aptamers to multiple sites on a target molecule by reducing the ability of the preferred site to select its cognate aptamer. We demonstrate the use of this scheme by generating aptamers directed to discrete functional surfaces of the yeast TATA-binding protein (TBP). Previously we selected ''class 1'' RNA aptamers that interfere with the TBP's binding to TATA-DNA. By masking TBP with TATA-DNA or an unamplifiable class 1 aptamer, we isolated a new aptamer class, ''class 2,'' that can bind a TBP⅐DNA complex and is in competition with binding another general transcription factor, TFIIA. Moreover, we show that both of these aptamers inhibit RNA polymerase II-dependent transcription, but analysis of template-bound factors shows they do so in mechanistically distinct and unexpected ways that can be attributed to binding either the DNA or TFIIA recognition sites. These results should spur innovative approaches to modulating other highly connected regulatory proteins.hubs ͉ SELEX ͉ TATA-binding protein ͉ transcription factor TFIIA

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“…During PIC formation, interactions between gene-specific activator proteins, chromatin remodeling complexes, coactivator complexes, and general transcription factors (GTFs) result in the recruitment of an initiation-competent Pol II to the promoter (2,3). Importantly, both the exact composition and the order of factor recruitment at specific promoters are still unresolved questions (4,5).…”

mentioning

confidence: 99%

The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes

Kim

Nesvizhskii²,

Rani

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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In this article, we provide direct evidence that the evolutionarily conserved transcription elongation factor TFIIS functions during preinitiation complex assembly. First, we identified TFIIS in a mass spectrometric screen of RNA polymerase II (Pol II) preinitiation complexes (PICs). Second, we show that the association of TFIIS with a promoter depends on functional PIC components including Mediator and the SAGA complex. Third, we demonstrate that TFIIS is required for efficient formation of active PICs. Using truncation mutants of TFIIS, we find that the Pol II-binding domain is the minimal domain necessary to stimulate PIC assembly. However, efficient formation of active PICs requires both the Pol II-binding domain and the poorly understood N-terminal domain. Importantly, Domain III, which is required for the elongation function of TFIIS, is dispensable during PIC assembly. The results demonstrate that TFIIS is a PIC component that is required for efficient formation and/or stability of the complex.isotope-coded affinity tagging ͉ quantitative mass spectrometry ͉ Saccharomyces cerevisiae ͉ stable isotopes T ranscription of protein-coding genes by RNA polymerase II (Pol II) is a dynamic process that begins with the formation of a preinitiation complex (PIC) at the promoter and proceeds through initiation, elongation, termination, and, finally, reinitiation (1). Proper regulation of transcription during this cycle involves interactions between a number of factors with Pol II and chromatin. During PIC formation, interactions between gene-specific activator proteins, chromatin remodeling complexes, coactivator complexes, and general transcription factors (GTFs) result in the recruitment of an initiation-competent Pol II to the promoter (2, 3). Importantly, both the exact composition and the order of factor recruitment at specific promoters are still unresolved questions (4, 5).During the transition from initiation to elongation, promoterspecific contacts between Pol II and the PIC are disrupted as the polymerase begins messenger RNA synthesis and traverses into the ORF (1, 6). The efficiency of elongation by Pol II is regulated by a number of additional factors such as TFIIS, Spt4-Spt5, FACT, and Paf (6). At least one PIC component, TFIIF, stimulates elongation in vitro. The elongation factors can exert their effects through a number of distinct mechanisms, which include controlling the rate of elongation or the processivity of Pol II, facilitating transcription through nucleosomes, or by reactivating Pol II that has become arrested (6).TFIIS is perhaps the best characterized elongation factor (7). In vitro, TFIIS stimulates arrested Pol II to cleave the nascent transcript that has fallen out of register with template DNA (7,8). This generates a new 3Ј end in the nascent mRNA that is used by Pol II to resume transcription. The recently solved structure of a TFIISPol II complex has provided important details regarding TFIIS function that are consistent with many of the known biochemical activities of TFIIS (9).Cons...

show abstract

Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock

Cited by 105 publications

References 81 publications

Inactivated RNA Polymerase II Open Complexes Can Be Reactivated with TFIIE

Inactivated RNA Polymerase II Open Complexes Can Be Reactivated with TFIIE

RNA aptamers directed to discrete functional sites on a single protein structural domain

The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes

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