Coordination of Transcription, RNA Processing, and Surveillance by P-TEFb Kinase on Heat Shock Genes

Ni, Zhuoyu; Schwartz, Brian E.; Werner, Janis; Suarez, Jose-Ramon; Lis, John T.

doi:10.1016/s1097-2765(03)00526-4

Cited by 218 publications

(239 citation statements)

References 53 publications

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“…As expected, inhibition of Cdk9 with DRB increased pol II occupancy at the transcription start site and decreased the CTD phospho-S2 signal at the 3′ end of GAPDH (data not shown) but it did not entirely eliminate pol II from positions near the 3′ end of the gene (Fig. 4A) consistent with previous results 38 . Importantly, both capping factors accumulated with DRB-arrested pol II at the transcription start site, suggesting that pol II complexes which are not actively transcribing, are still associated with capping factors (Figs.…”

Section: ′ and 3′ Pol II Pausing With Capping Factors On Multiple Genessupporting

confidence: 91%

“…Inhibitors of Cdk9 cause elongational arrest and can disrupt cleavage/polyadenylation 38,39 , but it is not clear how they affect recruitment of 3′ end processing factors. We investigated how DRB affects pol II, CstF and CPSF localization.…”

Section: Co-localization Of 3′ Processing Factors and Pol II At 5′ Anmentioning

confidence: 99%

“…CTD S2 phosphorylation is usually regarded as a signature of elongating pol II within a gene 5, 7 however our results suggest a role for this modification well downstream of the gene where 3′ processing factors are recruited. How DRB inhibits cleavage/polyadenylation 38,39 is not completely resolved, but it correlates with both reduced recruitment of CstF and CPSF in 3′ flanking regions and inhibition of 3′ pausing (Figs. 6B, C, Supplementary Table 2).…”

Section: Pausing Termination and Recruitment Of 3′ End Processing Fmentioning

confidence: 99%

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RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

Glover-Cutter

Kim

Espinosa

et al. 2007

Nat Struct Mol Biol

302

336

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We investigated co-transcriptional recruitment of pre-mRNA processing factors to human genes. Capping factors associate with paused RNA pol II at the 5′ ends of quiescent genes. They also track throughout actively transcribed genes, and accumulate with paused polymerase in the 3′ flanking region. 3′ processing factors CstF and CPSF are maximally recruited 0.5-1.5 kb downstream of poly (A) sites where they coincide with capping factors, Spt5, and Ser2 hyperphosphorylated, paused pol II. 3′ end processing factors also localize at transcription start sites, and this early recruitment is enhanced after polymerase arrest with DRB. These results suggest that promoters may help specify recruitment of 3′ end processing factors. We propose a dual pausing model where elongation arrests near the transcription start site and in the 3′ flank to allow co-transcriptional processing by factors recruited to the pol II ternary complex.

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Section: ′ and 3′ Pol II Pausing With Capping Factors On Multiple Genessupporting

confidence: 91%

Section: Co-localization Of 3′ Processing Factors and Pol II At 5′ Anmentioning

confidence: 99%

Section: Pausing Termination and Recruitment Of 3′ End Processing Fmentioning

confidence: 99%

See 1 more Smart Citation

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

Glover-Cutter

Kim

Espinosa

et al. 2007

Nat Struct Mol Biol

302

336

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“…Positive transcription elongation factor-b (P-TEFb) is responsible for CTD Ser 2 phosphorylation in vivo 3,[11][12][13] , making it a candidate Pgc target. Drosophila P-TEFb consists of a kinase subunit, Cdk9, and a regulatory subunit, Cyclin T (CycT) [13][14][15] .…”

mentioning

confidence: 99%

Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells

Hanyu-Nakamura¹,

Sonobe-Nojima²,

Tanigawa³

et al. 2008

Nature

199

224

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Germ cells are the only cells that transmit genetic information to the next generation, and they therefore must be prevented from differentiating inappropriately into somatic cells 1 . A common mechanism by which germline progenitors are protected from differentiation-inducing signals is a transient and global repression of RNA polymerase II (RNAPII)-dependent transcription 1 . In both Drosophila and Caenorhabditis elegans embryos, the repression of messenger RNA transcription during germ cell specification correlates with an absence of phosphorylation of Ser 2 residues in the carboxy-terminal domain of RNAPII (hereafter called CTD) 2 , a critical modification for transcriptional elongation 3 . Here we show that, in Drosophila embryos, a small protein encoded by polar granule component (pgc) is essential for repressing CTD Ser 2 phosphorylation in newly formed pole cells, the germline progenitors. Ectopic Pgc expression in somatic cells is sufficient to repress CTD Ser 2 phosphorylation. Furthermore, Pgc interacts, physically and genetically, with positive transcription elongation factor b (P-TEFb), the CTD Ser 2 kinase complex, and prevents its recruitment to transcription sites. These results indicate that Pgc is a cell-type-specific P-TEFb inhibitor that has a fundamental role in Drosophila germ cell specification. In C. elegans embryos, PIE-1 protein segregates to germline blastomeres, and is thought to repress mRNA transcription through interaction with P-TEFb 4-7 . Thus, inhibition of P-TEFb is probably a common mechanism during germ cell specification in the disparate organisms C. elegans and Drosophila. pgc RNA, a component of the Drosophila germ plasm 8 , has been implicated in the repression of CTD Ser 2 phosphorylation in early pole cells 9,10 . However, the mechanism underlying pgc-mediated transcriptional repression has been unknown. Initial characterization of its nucleotide sequence suggested that pgc RNA acts as a non-coding RNA 8 . Nevertheless, we have noticed that an AUG triplet, beginning at nucleotide 117 of the 0.7-kilobase (kb) transcript, is in a favourable context to serve as a translation initiation site 8 . Completion of the Drosophila genomic sequence revealed an error in our original manual sequencing in a region where a strong stem structure can form (an additional C exists between nucleotides 178 and 179). In the revised pgc sequence, the open reading frame (ORF) beginning at nucleotide 117 is capable of encoding a 71-amino-acid polypeptide (Fig. 1a). We found that this polypeptide

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“…2a). In order to explore how phosphorylation impacts the structure of the CTD, we used D. melanogaster positive transcription elongation factor b (Dm P-TEFb) to hyper-phosphorylate CTD2 0 in vitro 11 . Analysis of hyper-phosphorylated CTD2 0 by mass spectrometry (MS) revealed successful incorporation of up to 12 phosphates per polypeptide (Fig.…”

Section: Transgenic Flies Reveal a Ctd Region Needed For Developmentmentioning

confidence: 99%

Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain

Showalter

Gibbs

2017

Biophysical Journal

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The carboxy-terminal domain (CTD) of the RNA polymerase II (Pol II) large subunit cycles through phosphorylation states that correlate with progression through the transcription cycle and regulate nascent mRNA processing. Structural analyses of yeast and mammalian CTD are hampered by their repetitive sequences. Here we identify a region of the Drosophila melanogaster CTD that is essential for Pol II function in vivo and capitalize on natural sequence variations within it to facilitate structural analysis. Mass spectrometry and NMR spectroscopy reveal that hyper-Ser5 phosphorylation transforms the local structure of this region via proline isomerization. The sequence context of this switch tunes the activity of the phosphatase Ssu72, leading to the preferential de-phosphorylation of specific heptads. Together, context-dependent conformational switches and biased dephosphorylation suggest a mechanism for the selective recruitment of cis-proline-specific regulatory factors and region-specific modulation of the CTD code that may augment gene regulation in developmentally complex organisms.

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Coordination of Transcription, RNA Processing, and Surveillance by P-TEFb Kinase on Heat Shock Genes

Cited by 218 publications

References 53 publications

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells

Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain

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