Genetic Interactions of <i>DST1</i> in <i>Saccharomyces cerevisiae</i> Suggest a Role of TFIIS in the Initiation-Elongation Transition

Malagón, Francisco; Tong, Amy; Shafer, Brenda K.; Strathern, Jeffrey N.

doi:10.1534/genetics.166.3.1215

Cited by 54 publications

(55 citation statements)

References 162 publications

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“…Thus the MED31/SOH1 subunit of the Mediator displays genetic interactions not only with Pol II (34), but also with TFIIB (34) and several transcription elongation factors that include SII (35), the last in turn displaying close relationships with hSpt4-hSpt5/DSIF (36)(37)(38)(39). Furthermore, consistent with its role in early elongation, TFIIB has also been connected to diverse elongation and processing factors (40).…”

Section: Discussionmentioning

confidence: 98%

Identification of a regulator of transcription elongation as an accessory factor for the human Mediator coactivator

Malik

Barrero

Jones

2007

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

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The multiprotein Mediator coactivator complex is universally required for transcription of metazoan genes. It has been proposed to function by interfacing between transcriptional activators and the RNA polymerase II machinery. However, in vitro transcription systems reconstituted from homogeneous preparations of RNA polymerase II, the general transcription initiation factors, and the cofactor PC4 display relatively robust activator (HNF-4)-dependent activity, which, nonetheless, can be further stimulated by Mediator. By contrast, an unfractionated nuclear extract-based system in which Mediator has been immunodepleted displays a nearabsolute dependence on ectopic Mediator. Here, we identified and purified an activity, MSA-2, that confers extract-like Mediator responsiveness to our reconstituted system. Mass spectrometric analyses identified its two constituent polypeptides as hSpt5 and hSpt4, which also comprise the elongation factor DSIF. Mechanistically, MSA-2/DSIF acts by restricting overall transcription in the pure system, thereby imposing a strong Mediator dependence. Our data thus point to potential mechanisms for Mediator function beyond its presently believed role in promoting the initial formation of the RNA polymerase II-containing preinitiation complex.DRB sensitivity-inducing factor ͉ hepatocyte nuclear factor-4 ͉ positive cofactor 2 ͉ RNA polymerase II

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Section: Discussionmentioning

confidence: 98%

Identification of a regulator of transcription elongation as an accessory factor for the human Mediator coactivator

Malik

Barrero

Jones

2007

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

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“…Recent genome mapping experiments in Drosophila melanogaster tissue culture cells have highlighted differences in H2A.Z nucleosome compositions associated with polymerase pausing, suggesting potential roles in elongation (100). Genetic screens in budding yeast have revealed that many of the strongest genetic interactions involving htz1⌬ strains are with genes encoding transcription elongation factors, including dst1, rpb9, set2, spt4, and spt16, and with multiple genes encoding subunits of the PAF complex (11,15,49,51,53,62,98,101). At present, however, the interpretations of these data are unclear.…”

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confidence: 99%

Histone Variant H2A.Z and RNA Polymerase II Transcription Elongation

Santisteban

Hang

Smith

2011

Molecular and Cellular Biology

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Nucleosomes containing histone variant H2A.Z (Htz1) serve to poise quiescent genes for activation and transcriptional initiation. However, little is known about their role in transcription elongation. Here we show that dominant mutations in the elongation genes SPT5 and SPT16 suppress the hypersensitivity of htz1⌬ strains to drugs that inhibit elongation, indicating that Htz1 functions at the level of transcription elongation. Direct kinetic measurements of RNA polymerase II (Pol II) movement across the 9.5-kb GAL10p-VPS13 gene revealed that the elongation rate of polymerase is 24% slower in the absence of Htz1. We provide evidence for two nonexclusive mechanisms. First, we observed that both the phospho-Ser2 levels in the elongating isoform of Pol II and the loading of Spt5 and Elongator over the GAL1 open reading frame (ORF) depend on Htz1. Second, in the absence of Htz1, the density of nucleosome occupancy is increased over the GAL10p-VPS13 ORF and the chromatin is refractory to remodeling during active transcription. These results establish a mechanistic role for Htz1 in transcription elongation and suggest that Htz1-containing nucleosomes facilitate Pol II passage by affecting the correct assembly and modification status of Pol II elongation complexes and by favoring efficient nucleosome remodeling over the gene.Transcription by RNA polymerase II (Pol II) takes place on a compositionally and topologically complex chromatin template at multiple steps, including promoter activation, transcription initiation, elongation, and termination. A number of mechanisms facilitate the initiation of gene transcription on chromatin templates. Two of the most prominent of these are the remodeling of nucleosomes by DNA-dependent ATPase complexes and the covalent posttranslational modification of histone proteins (20,90). At a minimum, these pathways are thought to act by establishing a permissive chromatin structure at gene promoters, allowing access of site-specific transcription factors and the subsequent recruitment of polymerase and the general factors (25,69).

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“…First, the deletion of the DST1 gene, encoding TFIIS in yeast, is colethal with the deletion of the gene encoding the Med31 subunit of the Mediator complex (9). Second, TFIIS is recruited to the promoter of GAL1, and the deletion of DST1 reduces the recruitment of the transcription machinery on the promoter of GAL1 (10).…”

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confidence: 99%

TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo

Guglielmi

Soutourina

Esnault

et al. 2007

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

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The transcription initiation and elongation steps of protein-coding genes usually rely on unrelated protein complexes. However, the TFIIS elongation factor is implicated in both processes. We found that, in the absence of the Med31 Mediator subunit, yeast cells required the TFIIS polymerase II (Pol II)-binding domain but not its RNA cleavage stimulatory activity that is associated with its elongation function. We also found that the TFIIS Pol II-interacting domain was needed for the full recruitment of Pol II to several promoters in the absence of Med31. This work demonstrated that, in addition to its thoroughly characterized role in transcription elongation, TFIIS is implicated through its Pol II-binding domain in the formation or stabilization of the transcription initiation complex in vivo.RNA polymerase II ͉ Saccharomyces cerevisiae ͉ transcription regulation ͉ Med31 ͉ Mediator subunit T he transcription of protein-coding eukaryotic genes by RNA polymerase II (Pol II) requires three successive steps: initiation, elongation, and termination. Transcription initiation of class II genes involves the binding of activators to regulatory sequences; the recruitment of RNA Pol II to the core promoter via interactions with activators, coactivators, and general transcription factors; and the initiation reaction per se with DNA strand opening and abortive initiation (1). A major coactivator target of transcriptional activators is the Mediator (2, 3). One of its activities is the recruitment and/or stabilization of Pol II at core promoters (4). After transcription initiation, Pol II enters elongation, during which it can be arrested because of the presence of specific DNA sequences that promote pausing, or because of obstacles such as DNA damage or bound proteins. To avoid or escape arrest, Pol II requires different elongation factors, including TFIIS (5). Evidence suggests that TFIIS could be implicated in both initiation and elongation.In vitro, TFIIS can reactivate arrested elongation complexes by stimulating endonucleolytic cleavage by Pol II of the nascent RNA (5). TFIIS is composed of three domains that fold independently, as demonstrated by NMR analysis of its structure (6, 7). Cleavage-stimulating activity minimally requires the Cterminal two-thirds of the protein, that is, its domain II and III separated by a 15-aa linker (7,8). Domain II forms a three-helix bundle followed by three short helices, with a basic patch on the third helix (␣-3) that is essential for TFIIS binding to Pol II (7). Crystallographic analysis of a TFIIS-Pol II complex confirmed that this basic patch lies at the TFIIS-Pol II interface (7,8). TFIIS binding to Pol II is required for domain III to reach the Pol II active site. Domain III forms a zinc ribbon that contains a conserved RSADE motif, responsible for the stimulation of RNA cleavage (7,8).TFIIS is also implicated in transcription initiation. First, the deletion of the DST1 gene, encoding TFIIS in yeast, is colethal with the deletion of the gene encoding the Med31 subunit of the Medi...

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Genetic Interactions of DST1 in Saccharomyces cerevisiae Suggest a Role of TFIIS in the Initiation-Elongation Transition

Cited by 54 publications

References 162 publications

Identification of a regulator of transcription elongation as an accessory factor for the human Mediator coactivator

Identification of a regulator of transcription elongation as an accessory factor for the human Mediator coactivator

Histone Variant H2A.Z and RNA Polymerase II Transcription Elongation

TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo

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