The Spt4p Subunit of Yeast DSIF Stimulates Association of the Paf1 Complex with Elongating RNA Polymerase II

Qiu, Hongfang; Hu, Cuihua; Wong, Chi Ming; Hinnebusch, Alan G.

doi:10.1128/mcb.26.8.3135-3148.2006

Cited by 66 publications

(115 citation statements)

References 54 publications

(97 reference statements)

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“…Therefore, reduced recruitment of the PAF complex could account for reduced RNAPII elongation efficiency, H2B ubiquitination, and H3K4 and H3K36 trimethylation when the Spt5 CTR is deleted. An Spt5 requirement for recruitment of the PAF complex is consistent with previous observations that SPT5 and the PAF complex interact genetically and physically (46) and that the Spt4 subunit of yeast DSIF is also required for the recruitment of the PAF complex (47).…”

Section: Resultssupporting

confidence: 78%

Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

Zhou

Kuo²,

Fillingham³

et al. 2009

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

131

184

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Elongation by RNA polymerase II (RNAPII) is a finely regulated process in which many elongation factors contribute to gene regulation. Among these factors are the polymerase-associated factor (PAF) complex, which associates with RNAPII, and several cyclin-dependent kinases, including positive transcription elongation factor b (P-TEFb) in humans and BUR kinase (Bur1-Bur2) and C-terminal domain (CTD) kinase 1 (CTDK1) in Saccharomyces cerevisiae. An important target of P-TEFb and CTDK1, but not BUR kinase, is the CTD of the Rpb1 subunit of RNAPII. Although the essential BUR kinase phosphorylates Rad6, which is required for histone H2B ubiquitination on K123, Rad6 is not essential, leaving a critical substrate(s) of BUR kinase unidentified. Here we show that BUR kinase is important for the phosphorylation in vivo of Spt5, a subunit of the essential yeast RNAPII elongation factor Spt4/Spt5, whose human orthologue is DRB sensitivity-inducing factor. BUR kinase can also phosphorylate the C-terminal region (CTR) of Spt5 in vitro. Like BUR kinase, the Spt5 CTR is important for promoting elongation by RNAPII and recruiting the PAF complex to transcribed regions. Also like BUR kinase and the PAF complex, the Spt5 CTR is important for histone H2B K123 monoubiquitination and histone H3 K4 and K36 trimethylation during transcription elongation. Our results suggest that the Spt5 CTR, which contains 15 repeats of a hexapeptide whose consensus sequence is S[T/A]WGG[A/Q], is a substrate of BUR kinase and a platform for the association of proteins that promote both transcription elongation and histone modification in transcribed regions.longation by RNA polymerase II (RNAPII) involves a number of factors that interact directly or indirectly with the enzyme (1). Among these RNAPII-interacting proteins in the budding yeast Saccharomyces cerevisiae are the RNA chain cleavage factor TFIIS, the chromatin assembly factor Spt16/Pob3 (known as FACT in higher eukaryotes), the polymerase-associated factor (PAF) complex, and Spt4/Spt5, which is orthologous to DRB sensitivityinducing factor (DSIF) in humans. These factors can associate with the transcription complex from the promoter-proximal region to the cleavage and polyadenylation signal or the transcription termination site. In higher eukaryotes, DSIF and the negative elongation factor (NELF), which appears not to exist in S. cerevisiae, restrain elongation by RNAPII soon after initiation (2). As a consequence, many inactive genes in higher eukaryotes have ''paused'' or ''poised'' RNAPII molecules downstream of their promoters (3).An important event during elongation by RNAPII is phosphorylation of the heptapeptide repeats (consensus sequence YSPTSPS) in the C-terminal domain (CTD) of Rpb1, the largest subunit of RNAPII (4). Phosphorylation on S5 of the CTD repeats is catalyzed by the Kin28 subunit (CDK7 in humans) of the general initiation factor TFIIH. S5 phosphorylation tends to decline across yeast transcription units (5, 6) and is reversed by the Ssu72 subunit (7) of the cleavage an...

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Section: Resultssupporting

confidence: 78%

Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

Zhou

Kuo²,

Fillingham³

et al. 2009

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

131

184

View full text Add to dashboard Cite

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“…Together, these results indicated that while H3K36 me2/3 was required for Rpd3C(S) binding to nucleosomes, some other factor was responsible for its recruitment to chromatin. Because various factors involved in elongation or mRNA processing, including Set2, were shown to be recruited to chromatin through elongating Pol II, 4,5,[20][21][22][23] we sought to determine whether Rpd3C(S) physically interacted with Pol II, phosphorylated at the C-terminal Domain (CTD). Co-IP experiments revealed that Rco1 co-immunoprecipitated with Ser5 phosphorylated (Ser5P) likely transferred by RSC or SWI/SNF to histone chaperones such as Asf1 or FACT which can then aid in reassembly.…”

mentioning

confidence: 99%

A role for phosphorylated Pol II CTD in modulating transcription coupled histone dynamics

Spain

Govind

2011

Transcription

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Histone acetylation modulates histone occupancy both at promoters and in coding sequences. Based on our recent observation that HDACs in the budding yeast, Saccharomyces cerevisiae, are co-transcriptionally recruited to coding regions by elongating polymerases, we propose a model in which Pol II facilitates recruitment of chromatin remodeling complexes as well as other factors required for productive elongation.

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“…The Vps factors consistently displayed higher occupancies of the CDS vs. UAS or promoter regions of the examined genes, consistent with a widespread role in transcription elongation. The CDS occupancies of the Vps proteins were lower than we observed previously for canonical elongation factors, including Spt4, Spt5, Bur2, and the Paf1C complex (Qiu et al 2006(Qiu et al , 2009), but they were comparable to the occupancies of subunits of SAGA (Govind et al 2007), NuA4 (Ginsburg et al 2009), and histone deacetylase complexes (Govind et al 2010), and they were significantly higher than the twofold or less enrichment of two different protein synthesis factors we analyzed at Gcn4 and Gal4 target genes. Importantly, as observed for conventional elongation factors, the association of Vps proteins with ARG1 or GAL1 CDS was strongly dependent on target gene transcription, occurring at high levels only under conditions where the relevant transcriptional activators are induced (Gcn4) or functional (Gal4).…”

Section: Discussionmentioning

confidence: 53%

“…WT vs. TATAΔ). We showed previously that this arg1-TATAD mutation does not reduce the UAS occupancy of Gcn4 itself (Qiu et al 2006).…”

Section: Vps15 and Vps34 Are Cotranscriptionally Cross-linked To The mentioning

confidence: 99%

Vps Factors Are Required for Efficient Transcription Elongation in Budding Yeast

et al. 2013

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There is increasing evidence that certain Vacuolar protein sorting (Vps) proteins, factors that mediate vesicular protein trafficking, have additional roles in regulating transcription factors at the endosome. We found that yeast mutants lacking the phosphatidylinositol 3-phosphate [PI(3)P] kinase Vps34 or its associated protein kinase Vps15 display multiple phenotypes indicating impaired transcription elongation. These phenotypes include reduced mRNA production from long or G+C-rich coding sequences (CDS) without affecting the associated GAL1 promoter activity, and a reduced rate of RNA polymerase II (Pol II) progression through lacZ CDS in vivo. Consistent with reported genetic interactions with mutations affecting the histone acetyltransferase complex NuA4, vps15D and vps34D mutations reduce NuA4 occupancy in certain transcribed CDS. vps15D and vps34D mutants also exhibit impaired localization of the induced GAL1 gene to the nuclear periphery. We found unexpectedly that, similar to known transcription elongation factors, these and several other Vps factors can be cross-linked to the CDS of genes induced by Gcn4 or Gal4 in a manner dependent on transcriptional induction and stimulated by Cdk7/Kin28-dependent phosphorylation of the Pol II C-terminal domain (CTD). We also observed colocalization of a fraction of Vps15-GFP and Vps34-GFP with nuclear pores at nucleus-vacuole (NV) junctions in live cells. These findings suggest that Vps factors enhance the efficiency of transcription elongation in a manner involving their physical proximity to nuclear pores and transcribed chromatin. N EWLY synthesized proteins that are transported from the Golgi to the lysosome/vacuole traverse the endosome, as do ubiquitinated proteins that are removed from the plasma membrane by endocytosis en route to the vacuole for degradation. Ubiquitinated cargo proteins progress through early and late endosomes, are concentrated at the outer membranes of multivesicular bodies (MVB), and are then sequestered in intralumenal vesicles (ILVs) It is thought that ESCRT-0 is recruited from the cytoplasm to the endosomal outer membrane by interaction with the phosphoinositide PI(3)P, where it acts to recruit and concentrate ubiquitinated cargo proteins and transfer them to the ESCRT-I complex. ESCRT-I activates the ESCRT-II heterotrimer that, in turn, recruits the ESCRT-III components, which are believed to assemble filaments instrumental in invagination of the MVB membrane. The AAA-ATPase Vps4, recruited by ESCRT-III subunits, functions to pinch off the membrane invaginations to produce ILVs containing cargo proteins and to recycle the ESCRT factors back to the cytoplasm (Raiborg and Stenmark 2009).

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The Spt4p Subunit of Yeast DSIF Stimulates Association of the Paf1 Complex with Elongating RNA Polymerase II

Cited by 66 publications

References 54 publications

Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

A role for phosphorylated Pol II CTD in modulating transcription coupled histone dynamics

Vps Factors Are Required for Efficient Transcription Elongation in Budding Yeast

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