Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination

Kecman, Tea; Kuś, Krzysztof; Heo, Dong-Hyuk; Duckett, K; Birot, Adrien; Liberatori, Sabrina; Mohammed, Shabaz; Geis-Asteggiante, Lucía; Robinson, Carol V.; Vasiljeva, Lidia

doi:10.1016/j.celrep.2018.09.007

Cited by 71 publications

(92 citation statements)

References 91 publications

(117 reference statements)

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“…However, while we demonstrate LtPP1 is a component of the Leishmania complex, the purified module in T. brucei lacks a PP1 homologue. PP1 is the only catalytic component of the human PTW/PP1 complex and dephosporylation by PP1 is directly involved in regulating Pol II termination [2,3,60,61]. Therefore, the apparent lack of PP1 association with the PNUTS, Wdr82 and JBP3 complex involved in transcription termination in T. brucei is surprising.…”

Section: Discussionmentioning

confidence: 99%

“…Similar to the mammalian complex, we propose PNUTS is a scaffolding protein for the entire PJW/PP1 complex and regulates PP1 function via the PP1 binding RVxF motif. Only three substrates have been identified for PNUTS/PP1: the Pol II elongation factor Spt5, the CTD of Pol II and MYC [2,60,97,98]. MYC dephosphorylation by PP1 regulates chromatin binding and stability.…”

Section: Discussionmentioning

confidence: 99%

“…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. Similar to mammalian promoters where transcription is divergent and initiation is over a broad genomic region, previous studies have suggested that Pol II transcription initiation sites are intrinsically bi-directional in T. brucei [68,69].…”

Section: Discussionmentioning

confidence: 99%

“…Critical to this process is the regulation of protein phosphorylation by the major eukaryotic protein serine/threonine phosphatase, PP1. As recently demonstrated in the fission yeast Schizosaccharomyces pombe (S. pombe), the PP1 phosphatase Dis2 regulates termination by dephosphorylating both the Pol II-CTD as well as Spt5 [2]. This PP1-dependent dephosphorylation allows the efficient recruitment of the termination factor Seb1 as well as decreased Spt5 stimulation of Pol II elongation that enhances the ability of the torpedo exoribonuclease to catch up and destabilize the elongation complex.…”

Section: Introductionmentioning

confidence: 89%

“…PNUTS is present in both the T. brucei and Leishmania complexes and share a conserved RVxF motif ( Fig 1C). Moreover, a similar human PTW/PP1 complex suggests that PP1 confers the complex phosphatase activity critical for its regulation in Pol II termination [2,3,60,61]. The apparent lack of PP1 in the T. brucei complex is therefore surprising.…”

Section: Pnuts-pp1 Regulates Transcription Termination In T Bruceimentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 89%

Section: Pnuts-pp1 Regulates Transcription Termination In T Bruceimentioning

confidence: 99%

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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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Whole‐exome sequencing in syndromic craniosynostosis increases diagnostic yield and identifies candidate genes in osteogenic signaling pathways

Tønne

Due-Tønnessen

Vigeland

et al. 2022

American J of Med Genetics Pt A

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Craniosynostosis (CS) is a common congenital anomaly defined by premature fusion of one or more cranial sutures. Syndromic CS involves additional organ anomalies or neurocognitive deficits and accounts for 25%–30% of the cases. In a recent population‐based study by our group, 84% of the syndromic CS cases had a genetically verified diagnosis after targeted analyses. A number of different genetic causes were detected, confirming that syndromic CS is highly heterogeneous. In this study, we performed whole‐exome sequencing of 10 children and parents from the same cohort where previous genetic results were negative. We detected pathogenic, or likely pathogenic, variants in four additional genes (NFIA, EXTL3, POLR2A, and FOXP2) associated with rare conditions. In two of these (POLR2A and FOXP2), CS has not previously been reported. We further detected a rare predicted damaging variant in SH3BP4, which has not previously been related to human disease. All findings were clustered in genes involved in the pathways of osteogenesis and suture patency. We conclude that whole‐exome sequencing expands the list of genes associated with syndromic CS, and provides new candidate genes in osteogenic signaling pathways.

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The Phantom Mark: Enigmatic roles of phospho‐Threonine 4 modification of the C‐terminal domain of RNA polymerase II

2023

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The largest subunit of RNA polymerase II (Pol II) has an unusual carboxylterminal domain (CTD). This domain is composed of a tandemly repeating heptapeptide, Y 1 S 2 P 3 T 4 S 5 P 6 S 7 , that has multiple roles in regulating Pol II function and processing newly synthesized RNA. Transient phosphorylation of Ser2 and Ser5 of the YS 2 PTS 5 PS repeat have well-defined roles in recruiting different protein complexes and coordinating sequential steps in gene transcription. As such, these phospho-marks encipher a molecular recognition code, colloquially termed the CTD code. In contrast, the contribution of phospho-Threonine 4 (pThr4/pT4) to the CTD code remains opaque and contentious. Fuelling the debate on the relevance of this mark to gene expression are the findings that replacing Thr4 with a valine or alanine has varied impact on cellular function in different species and independent proteomic analyses disagree on the relative abundance of pThr4 marks. Yet, substitution with negatively charged residues is lethal and even benign mutations selectively disrupt synthesis and 3 0 processing of distinct sets of coding and non-coding transcripts. Suggestive of non-canonical roles, pThr4 marked Pol II regulates distinct gene classes in a species-and signal-responsive manner. Hinting at undiscovered roles of this elusive mark, multiple signal-responsive kinases phosphorylate Thr4 at target genes. Here, we focus on this under-explored residue and postulate that the pThr4 mark is superimposed on the canonical CTD code to selectively regulate expression of targeted genes without perturbing genome-wide transcriptional processes.

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Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination

Cited by 71 publications

References 91 publications

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

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

Whole‐exome sequencing in syndromic craniosynostosis increases diagnostic yield and identifies candidate genes in osteogenic signaling pathways

The Phantom Mark: Enigmatic roles of phospho‐Threonine 4 modification of the C‐terminal domain of RNA polymerase II

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