A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes

Eaton, Joshua D.; Francis, Laura; Davidson, Lee; West, Steven

doi:10.1101/gad.332833.119

Cited by 101 publications

(119 citation statements)

References 48 publications

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“…These results supported the idea that Spt5-CTR phosphorylation by Cdk9 is an accelerator of elongation 21,22 , whereas reversal of that phosphorylation by PP1 is a brake. Two recent reports extended this model to human cells, by showing that PP1 promotes Pol II slowing and termination through Spt5 dephosphorylation 30,31 . Another implicated PP4 in regulation of Spt5 phosphorylation and function during early stages of transcription in Caenorhabditis elegans 51 .…”

Section: Discussionmentioning

confidence: 99%

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Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

Parua

Kalan

Benjamin

et al. 2020

Preprint

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Reversible phosphorylation of Pol II and accessory factors helps order the 12 transcription cycle. Here we define two kinase-phosphatase switches that operate 13 at different points in human transcription. Cdk9/cyclin T1 (P-TEFb) catalyzes 14 inhibitory phosphorylation of PP1 and PP4 complexes that localize to 3' and 5' 15 ends of genes, respectively, and have overlapping but distinct specificities for 16Cdk9-dependent phosphorylations of Spt5, a factor instrumental in promoter-17 proximal pausing and elongation-rate control. PP1 dephosphorylates an Spt5 18 carboxy-terminal repeat (CTR), but not Spt5-Ser666, a site between KOW motifs 4 19 and 5, whereas PP4 can target both sites. In vivo, Spt5-CTR phosphorylation 20 decreases as transcription complexes pass the cleavage and polyadenylation 21 signal (CPS) and increases upon PP1 depletion, consistent with a PP1 function in 22In fission yeast, chemical-genetic inhibition of Cdk9 led to rapid, nearly complete 130 dephosphorylation of the Spt5 CTD (T1/2 ~20 sec); the rate of decay decreased ~4-fold in 131 dis2 mutant strains, suggesting that the fast kinetics in dis2 + cells were partly due to the 132 concomitant activation of Dis2 (PP1) when Cdk9 is inactivated 27 . In HCT116 cells, both 133 pThr806 and a phosphorylation outside the CTRs, pSer666, were lost rapidly upon 134 treatment with 250 nM NVP-2 (T1/2 ~10 min), consistent with a similar, reinforcing effect 135 of kinase inhibition and phosphatase activation (Fig. 1d). 136 137

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Section: Discussionmentioning

confidence: 99%

“…The effect of Cdk9 inhibition was recapitulated by an spt5 mutation that prevented Spt5-CTD phosphorylation 29 . Recently, human PP1 and its regulatory subunit PNUTS were implicated in Spt5-CTR dephosphorylation and Pol II deceleration downstream of the CPS 30,31 , suggesting conservation of this mechanism.…”

mentioning

confidence: 99%

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

Parua

Kalan

Benjamin

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The termination-promoting effect of Cdk9 inhibition was recapitulated by an spt5 mutation that prevented Spt5-CTD phosphorylation 29 . Recently, human PP1 and its regulatory subunit PNUTS were implicated in Spt5-CTR dephosphorylation and Pol II deceleration downstream of the CPS 30,31 , suggesting conservation of this mechanism.…”

mentioning

confidence: 99%

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

et al. 2020

View full text Add to dashboard Cite

Reversible phosphorylation of Pol II and accessory factors helps order the transcription cycle. Here, we define two kinase-phosphatase switches that operate at different points in human transcription. Cdk9/cyclin T1 (P-TEFb) catalyzes inhibitory phosphorylation of PP1 and PP4 complexes that localize to 3′ and 5′ ends of genes, respectively, and have overlapping but distinct specificities for Cdk9-dependent phosphorylations of Spt5, a factor instrumental in promoter-proximal pausing and elongation-rate control. PP1 dephosphorylates an Spt5 carboxy-terminal repeat (CTR), but not Spt5-Ser666, a site between Kyrpides-Ouzounis-Woese (KOW) motifs 4 and 5, whereas PP4 can target both sites. In vivo, Spt5-CTR phosphorylation decreases as transcription complexes pass the cleavage and polyadenylation signal (CPS) and increases upon PP1 depletion, consistent with a PP1 function in termination first uncovered in yeast. Depletion of PP4-complex subunits increases phosphorylation of both Ser666 and the CTR, and promotes redistribution of promoter-proximally paused Pol II into gene bodies. These results suggest that switches comprising Cdk9 and either PP4 or PP1 govern pause release and the elongation-termination transition, respectively.

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“…However, it turns out one must be a bit more cautious with this assumption. Several recent publications demonstrate that ASOs that target the 5’ end of an RNA can do this even on nascent RNA that is in the process of being transcribed ( Eaton et al, 2020 ; Lai et al, 2020 ; Lee and Mendell, 2020 ). This premature cleavage of RNA leads to the recruitment of XRN2 and employs the torpedo mechanism to evict the POL II transcription machinery prematurely.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, lncRNAs show signs of co-transcriptional cleavage and premature termination with Thr4p PolII enriched over the entire lncRNA body ( Schlackow et al, 2017 ). At some point the transcriptional machinery will run into a termination signal, a DNA sequence element consisting of AATAAA and downstream GU (or U)-rich motifs ( Eaton et al, 2020 ). These elements are ubiquitously present in the genome.…”

Section: Lncrna Genes In the Genomementioning

confidence: 99%

Beyond the RNA-dependent function of LncRNA genes

Ali

Grote

2020

eLife

175

116

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While long non-coding RNA (lncRNA) genes have attracted a lot of attention in the last decade, the focus regarding their mechanisms of action has been primarily on the RNA product of these genes. Recent work on several lncRNAs genes demonstrates that not only is the produced RNA species important, but also that transcription of the lncRNA locus alone can have regulatory functions. Like the functions of lncRNA transcripts, the mechanisms that underlie these genome-based functions are varied. Here we highlight some of these examples and provide an outlook on how the functional mechanisms of a lncRNA gene can be determined.

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A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes

Cited by 101 publications

References 48 publications

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

Beyond the RNA-dependent function of LncRNA genes

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