Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals

Shah, Nilay; Maqbool, Muhammad Ahmad; Yahia, Yousra; Aabidine, Amal Zine El; Esnault, Cyril; Forné, Ignasi; Decker, Tim-Michael; Martin, David; Schüller, Roland; Krebs, Stefan; Blum, Helmut; Imhof, Axel; Eick, Dirk; Andrau, Jean-Christophe

doi:10.1016/j.molcel.2017.12.009

Cited by 76 publications

(82 citation statements)

References 64 publications

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“…We focused on a set of Integrator-dependent genes and found that Integrator catalyzes premature transcription termination of these genes (Figs. 6, 7), which is consistent with prior studies that suggested roles for Integrator in termination (Skaar et al 2015;Shah et al 2018;Gómez-Orte et al 2019). Some of these genes (CG8620, Pepck1, and Sirup) have promoterproximal RNAPII that rapidly turns over (Shao and Zeitlinger 2017), which may indicate that Integrator can aid in clearing paused or stalled RNAPII.…”

Section: Discussionsupporting

confidence: 87%

The Integrator complex cleaves nascent mRNAs to attenuate transcription

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Elrod

Liang

et al. 2019

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words)Cellular homeostasis requires transcriptional outputs to be coordinated, and many events post transcription initiation can dictate the levels and functions of mature transcripts. To systematically identify regulators of inducible gene expression, we performed high-throughputRNAi screening of the Drosophila Metallothionein A (MtnA) promoter. This revealed that the Integrator complex, which has a well-established role in 3' end processing of small nuclear RNAs (snRNAs), attenuates MtnA transcription during copper stress. Integrator complex subunit 11 (IntS11) endonucleolytically cleaves MtnA transcripts, resulting in premature transcription termination and degradation of the nascent RNAs by the RNA exosome, a complex also identified in the screen. Using RNA-seq, we then identified >400 additional Drosophila proteincoding genes whose expression increases upon Integrator depletion. We focused on a subset of these genes and confirmed that Integrator is bound to their 5' ends and negatively regulates their transcription via IntS11 endonuclease activity. Many non-catalytic Integrator subunits, which are largely dispensable for snRNA processing, also have regulatory roles at these protein-coding genes, possibly by controlling Integrator recruitment or RNA polymerase II dynamics.Altogether, our results suggest that attenuation via Integrator cleavage limits production of many full-length mRNAs, allowing precise control of transcription outputs.

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Section: Discussionsupporting

confidence: 87%

The Integrator complex cleaves nascent mRNAs to attenuate transcription

Tatomer

Elrod

Liang

et al. 2019

Preprint

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“…The role of PNUTS is thought to reflect the essential nature of PNUTS/PP1 since differential phosphorylation of the CTD of Pol II has been proposed to regulate the directionality of transcription at bi-directional promoters. Specifically, Tyr1 and Ser1 hyperphosphorylation of Pol II have been shown to be associated with antisense divergent transcription at mammalian promoters [112][113][114]. Spt5 regulation of Pol II elongation is involved in control of divergent antisense transcription as well as readthrough transcription at 3' end of genes in yeast [2,115], representing an additional target of PNUTS/PP1 regulation of transcription at both ends of genes.…”

Section: Discussionmentioning

confidence: 99%

Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes

et al. 2020

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Base J, β-D-glucosyl-hydroxymethyluracil, is a modification of thymine DNA base involved in RNA Polymerase (Pol) II transcription termination in kinetoplastid protozoa. Little is understood regarding how specific thymine residues are targeted for J-modification or the mechanism of J regulated transcription termination. To identify proteins involved in J-synthesis, we expressed a tagged version of the J-glucosyltransferase (JGT) in Leishmania tarentolae, and identified four co-purified proteins by mass spectrometry: protein phosphatase (PP1), a homolog of Wdr82, a potential PP1 regulatory protein (PNUTS) and a protein containing a J-DNA binding domain (named JBP3). Gel shift studies indicate JBP3 is a J-DNA binding protein. Reciprocal tagging, co-IP and sucrose gradient analyses indicate PP1, JGT, JBP3, Wdr82 and PNUTS form a multimeric complex in kinetoplastids, similar to the mammalian PTW/PP1 complex involved in transcription termination via PP1 mediated dephosphorylation of Pol II. Using RNAi and analysis of Pol II termination by RNA-seq and RT-PCR, we demonstrate that ablation of PNUTS, JBP3 and Wdr82 lead to defects in Pol II termination at the 3'-end of polycistronic gene arrays in Trypanosoma brucei. Mutants also contain increased antisense RNA levels upstream of transcription start sites, suggesting an additional role of the complex in regulating termination of bi-directional transcription. In addition, PNUTS loss causes derepression of silent Variant Surface Glycoprotein genes involved in host immune evasion. Our results suggest a novel mechanistic link between base J and Pol II polycistronic transcription termination in kinetoplastids. Author summaryTrypanosoma brucei is a parasitic protozoan that causes African sleeping sickness in humans. The genome of T. brucei is organized into polycistronic gene clusters that contain multiple genes that are co-transcribed from a single promoter. We have recently described the presence of a modified DNA base J and variant of histone H3 (H3.V) at transcription termination sites within gene clusters where the loss of base J and H3.V leads to read-through transcription and the expression of downstream genes. We now PLOS Genetics | https://doi.identify a novel stable multimeric complex containing a J binding protein (JBP3), base J glucosyltransferase (JGT), PP1 phosphatase, PP1 interactive-regulatory protein (PNUTS) and Wdr82, which we refer to as PJW/PP1. A similar complex (PTW/PP1) has been shown to be involved in Pol II termination in humans and yeast. We demonstrate that PNUTS, JBP3 and Wdr82 mutants lead to read-through transcription in T. brucei. Our data suggest the PJW/PP1 complex regulates termination by recruitment to termination sites via JBP3-base J interactions and dephosphorylation of specific proteins (including Pol II and termination factors) by PP1. These findings significantly expand our understanding of mechanisms underlying transcription termination in eukaryotes, including organisms that utilize polycistronic transcription and novel epigenetic marks...

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“…However, the puzzling requirement for multiple repeats in the CTD has yet to be explained. Extensive evidence supports for a requirement of tyrosine or serine phosphorylation and dephosphorylation of the CTD during transcription cycle (5)(6)(7)(8)(9)(10)(11)(12). In addition, genetic studies in budding yeast demonstrate that pairs of heptad CTD repeats constitute the essential functional unit (13,14).…”

Section: Introductionmentioning

confidence: 98%

Oncoprotein CoAA repeats interact with RNA polymerase II CTD repeats

Xiong

Yang

et al. 2019

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The heptad repeating sequence of the Cterminal domain (CTD) of the largest subunit of RNA polymerase II is highly conserved in eukaryotes. In yeast, a CTD code consisting of pairs of heptad repeats is essential for viability. However, the strict requirement of diheptad repeats for the CTD function in transcription and splicing is unexplained. Here we show that CoAA (gene symbol RBM14), an oncoprotein and mammalian transcriptional coactivator, possesses diheptad repeats and directly interacts with the CTD. CoAA comprises 27 copies of tyrosine-rich repeats and regulates pre-mRNA synthesis and alternative splicing. Tyrosine substitutions in either the CoAA repeats or the CTD repeats diminish their interactions. Ser2or Ser5-phosphorylated CTD peptides exhibit higher binding affinity to CoAA than the corresponding non-phosphorylated CTD peptide. CoAA dynamically interacts with both the CTD and hnRNP M, which is an alternative splicing regulator also comprising diheptad repeats. Arginine methylation of CoAA switches its interaction from the hnRNP M repeats to the CTD repeats. This study provides a mechanism for CoAA at the interface of transcription and alternative splicing, and explains the functional requirement of diheptad repeats in the CTD. In the human genome, tyrosine-rich repeats similar to the CoAA repeats were only found in six oncoproteins including EWS and SYT. We suggest that the diheptad sequence is one of the signature features for the CTD interaction among oncoproteins involved in transcription and alternative splicing. We anticipate that direct RNA Pol II interaction is a mechanism in oncogenesis.

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Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals

Cited by 76 publications

References 64 publications

The Integrator complex cleaves nascent mRNAs to attenuate transcription

The Integrator complex cleaves nascent mRNAs to attenuate transcription

Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes

Oncoprotein CoAA repeats interact with RNA polymerase II CTD repeats

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