Complete sequence of a eukaryotic regulatory gene.

Hubert, J.; Guyonvarch, Armel; Kammerer, B.; Exinger, Françoise; Liljelund, Patricia; Lacroute, François

doi:10.1002/j.1460-2075.1983.tb01702.x

Cited by 63 publications

(39 citation statements)

References 13 publications

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“…TFIIS localizes to the coding regions of genes as shown by ChIP and physically interacts with the Spt5 subunit of DSIF (Pokholok et al 2002;Lindstrom et al 2003). Yeast TFIIS, termed PPR2, was initially cloned as a gene that regulated the pyrimidine biosynthesis pathway and, although it is not an essential gene, ppr2 mutants display sensitivity to 6-azauracil (Hubert et al 1983;Nakanishi et al 1995). Numerous biochemical studies use stalled RNAP II complexes formed during low NTP concentrations.…”

Section: Factors That Influence Transcriptional Arrest: Tfiismentioning

confidence: 99%

Elongation by RNA polymerase II: the short and long of it

Sims¹,

Belotserkovskaya²,

Reinberg³

2004

Genes Dev.

617

586

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Appreciable advances into the process of transcript elongation by RNA polymerase II (RNAP II) have identified this stage as a dynamic and highly regulated step of the transcription cycle. Here, we discuss the many factors that regulate the elongation stage of transcription. Our discussion includes the classical elongation factors that modulate the activity of RNAP II, and the more recently identified factors that facilitate elongation on chromatin templates. Additionally, we discuss the factors that associate with RNAP II, but do not modulate its catalytic activity. Elongation is highlighted as a central process that coordinates multiple stages in mRNA biogenesis and maturation.The regulation of gene expression is one of the most intensely studied areas in all of science. Differential gene expression in multicellular organisms forms the foundation of cell-type specificity. Deregulation of the appropriate pattern of gene expression has profound effects on cellular function and underlies many diseases. Although there are many cellular processes that control gene expression, the most direct regulation occurs during transcription. The transcription of protein-coding genes in eukaryotes is performed by RNA polymerase II (RNAP II). Up until recently, the vast majority of studies aimed at elucidating the molecular mechanisms of transcription regulation have focused on early stages, such as the formation of a transcription initiation complex (preinitiation) and initiation (see below). For many years, transcript elongation has been thought of as the trivial addition of ribonucleoside triphosphates to the growing mRNA chain. It is now apparent that this process is a dynamic and highly regulated stage of the transcription cycle capable of coordinating downstream events. Numerous factors have been identified that specifically target the elongation stage of transcription. Importantly, multiple steps in mRNA maturation, including premRNA capping, splicing, 3Ј-end processing, surveillance, and export, are modulated through interactions with the RNAP II transcript elongation complex (TEC). It also appears that distinct elongation factors function in specific transcriptional contexts; the requirements for these specialized factors are largely unknown and highlight the need to better understand elongation in vivo. Many molecular and biochemical approaches have been used to quantify the different aspects of elongation, many of which are discussed below. It remains important to assimilate both in vitro and in vivo experimental systems when discussing what constitutes an elongation factor. An elongation factor can be defined as any molecule that affects the activities of or is associated with the TEC. We suggest that there are at least two major types of transcript elongation factors: one family, referred to as active elongation factors, and a second family, denoted as passive elongation factors. The difference resides in whether the factor affects the catalytic activity of RNAP II, regardless of whether the factor remains associate...

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Section: Factors That Influence Transcriptional Arrest: Tfiismentioning

confidence: 99%

Elongation by RNA polymerase II: the short and long of it

Sims¹,

Belotserkovskaya²,

Reinberg³

2004

Genes Dev.

617

586

View full text Add to dashboard Cite

show abstract

“…The present study deals with the Rpb9 subunit, belonging to a conserved family of eukaryotic and archeal zinc-binding polypeptides that also includes the yeast Pol I (Rpa12 (6)) and Pol III (Rpc11 (7)) subunits and the TFIIS elongation factor (8 -10) encoded by PPR2 in Saccharomyces cerevisiae (11,12). There is ample evidence that Rpb9 (9), Rpc11 (7), and TFIIS (9, 13) control transcription elongation by activating the RNA cleavage activity inherent to all RNA polymerases.…”

mentioning

confidence: 99%

The Rpb9 Subunit of RNA Polymerase II Binds Transcription Factor TFIIE and Interferes with the SAGA and Elongator Histone Acetyltransferases

Mullem

Wéry

Werner³

et al. 2002

Journal of Biological Chemistry

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Rpb9 is a small subunit of yeast RNA polymerase II participating in elongation and formed of two conserved zinc domains. rpb9 mutants are viable, with a strong sensitivity to nucleotide-depleting drugs. Deleting the C-terminal domain down to the first 57 amino acids has no detectable growth defect. Thus, the critical part of Rpb9 is limited to a N-terminal half that contacts the lobe of the second largest subunit (Rpb2) and forms a ␤-addition motif with the "jaw" of the largest subunit (Rpb1). Rpb9 has homology to the TFIIS elongation factor, but mutants inactivated for both proteins are indistinguishable from rpb9 single mutants. In contrast, rpb9 mutants are lethal in cells lacking the histone acetyltransferase activity of the RNA polymerase II Elongator and SAGA factors. In a two-hybrid test, Rpb9 physically interacts with Tfa1, the largest subunit of TFIIE. The interacting fragment, comprising amino acids 62-164 of Tfa1, belongs to a conserved zinc motif. Tfa1 is immunoprecipitated by RNA polymerase II. This co-purification is strongly reduced in rpb9-⌬, suggesting that Rpb9 contributes to the recruitment of TFIIE on RNA polymerase II.The recent determination of the bacterial RNA polymerase (1) and yeast RNA polymerase II (Pol II) 1 (2) core structures has opened a new chapter in transcription studies. The remarkably similar organization of these two enzymes leaves no doubt as to the strong mechanistic conservation of the transcription process. This similarity was anticipated from the sequence homology existing between the ␤Ј␤␣ 2 bacterial core enzyme and 5 of the 10 core subunits of Pol II. Rpb1 and Rpb2 are homologues of ␤Ј and ␤, the Rpb3/Rpb11 heterodimer corresponding to the bacterial ␣2 dimer, and is distantly related to Rpb6 (3). On the other hand, Pol II contains five small subunits (Rpb5, Rpb8, Rpb9, Rpb10, Rpb12) not found in the bacterial enzyme. These subunits also belong to the core structure of Pol I and Pol III or are related to it, in the case of Rpb9. Except for Rpb8, they are also akin to archaeal polypeptides (4, 5).The present study deals with the Rpb9 subunit, belonging to a conserved family of eukaryotic and archeal zinc-binding polypeptides that also includes the yeast Pol I (Rpa12 (6)) and Pol III (Rpc11 (7)) subunits and the TFIIS elongation factor (8 -10) encoded by PPR2 in Saccharomyces cerevisiae (11,12). There is ample evidence that Rpb9 (9), Rpc11 (7), and TFIIS (9, 13) control transcription elongation by activating the RNA cleavage activity inherent to all RNA polymerases. The fact that yeast ppr2 (14), rpb9 (15), and rpa12 (16) mutants are strongly sensitive to nucleotide-depleting drugs is also consistent with a major elongation defect. Rpb9 is highly conserved in evolution, and the yeast subunit can be replaced in vivo by its human counterpart (17). However, animal mutants (Drosophila melanogaster) are lethal (18), whereas yeast null mutants have only a limited growth defect (19).Rpa12, Rpb9, and Rpc11 have a related organization in Pol I, Pol II, and Pol III, respectively. ...

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“…In yeast, mutation or disruption of the gene encoding SII, DST1 (gene names in this study are those designated in the Saccharomyces Genome Database; DST1 is also known as PPR2), renders cells sensitive to the base analog 6-azauracil (6AU) (19,23,24). 6AU depletes cellular levels of the RNA precursors UTP and GTP (12).…”

mentioning

confidence: 99%

Mutations in RNA Polymerase II and Elongation Factor SII Severely Reduce mRNA Levels in Saccharomyces cerevisiae

Lennon

Wind

Saunders

et al. 1998

Molecular and Cellular Biology

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Elongation factor SII interacts with RNA polymerase II and enables it to transcribe through arrest sites in vitro. The set of genes dependent upon SII function in vivo and the effects on RNA levels of mutations in different components of the elongation machinery are poorly understood. Using yeast lacking SII and bearing a conditional allele of RPB2, the gene encoding the second largest subunit of RNA polymerase II, we describe a genetic interaction between SII and RPB2. An SII gene disruption or the rpb2-10 mutation, which yields an arrest-prone enzyme in vitro, confers sensitivity to 6-azauracil (6AU), a drug that depresses cellular nucleoside triphosphates. Cells with both mutations had reduced levels of total poly(A) ؉ RNA and specific mRNAs and displayed a synergistic level of drug hypersensitivity. In cells in which the SII gene was inactivated, rpb2-10 became dominant, as if template-associated mutant RNA polymerase II hindered the ability of wild-type polymerase to transcribe. Interestingly, while 6AU depressed RNA levels in both wild-type and mutant cells, wild-type cells reestablished normal RNA levels, whereas double-mutant cells could not. This work shows the importance of an optimally functioning elongation machinery for in vivo RNA synthesis and identifies an initial set of candidate genes with which SII-dependent transcription can be studied.The elongation phase of transcription is an important control point for the regulation of gene expression (reviewed in references 4, 29, and 41). Several general elongation factors, including TFIIF, ELL, and elongin (SIII), are able to increase the overall rate of transcription elongation of RNA polymerase II (PolII) in vitro (7,13,26,37). SII enables PolII to transcribe through a variety of transcriptional blockages, including intrinsic arrest sites and nucleoprotein complexes (reviewed in references 29 and 41). SII reactivates arrested PolII complexes by binding to the enzyme and activating a nascent RNA cleavage activity, which eventually results in polymerase escape (reviewed in reference 28). It has been hypothesized that elongation factors such as TFIIF reduce the frequency of arrest by reducing the dwell time of PolII at arrest sites (6,15).Little is known about gene sequences that block transcription and the interaction of general elongation factors with PolII complexes in vivo. In yeast, mutation or disruption of the gene encoding SII, DST1 (gene names in this study are those designated in the Saccharomyces Genome Database; DST1 is also known as PPR2), renders cells sensitive to the base analog 6-azauracil (6AU) (19,23,24). 6AU depletes cellular levels of the RNA precursors UTP and GTP (12). Supplementing the drug-containing medium with uracil or guanine reverses this phenotype, suggesting that the drug inhibits growth because of the reduction in nucleoside triphosphate levels and thereby impairs transcription elongation (3, 12). The sensitivity of yeast to 6AU after disruption of DST1 may indicate an increased requirement by RNA polymerase for elongat...

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Complete sequence of a eukaryotic regulatory gene.

Cited by 63 publications

References 13 publications

Elongation by RNA polymerase II: the short and long of it

Elongation by RNA polymerase II: the short and long of it

The Rpb9 Subunit of RNA Polymerase II Binds Transcription Factor TFIIE and Interferes with the SAGA and Elongator Histone Acetyltransferases

Mutations in RNA Polymerase II and Elongation Factor SII Severely Reduce mRNA Levels in Saccharomyces cerevisiae

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