ELM—the Eukaryotic Linear Motif resource—2024 update

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D442 - D455

Опубликована: Ноя. 14, 2023

Abstract Short Linear Motifs (SLiMs) are the smallest structural and functional components of modular eukaryotic proteins. They also most abundant, especially when considering post-translational modifications. As well as being found throughout cell part regulatory processes, SLiMs extensively mimicked by intracellular pathogens. At heart Eukaryotic Motif (ELM) Resource is a representative (not comprehensive) database. The ELM entries created growing community skilled annotators provide an introduction to linear motif functionality for biomedical researchers. 2024 update includes 346 novel instances in areas ranging from innate immunity both protein RNA degradation systems. In total, 39 classes newly annotated motifs have been added, another 17 existing updated release now 356 incorporating 4283 individual manually curated 4274 scientific publications including >700 links experimentally determined 3D structures. recent development, InterPro module resource data. available at: http://elm.eu.org.

Язык: Английский

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A restrictor complex of ZC3H4, WDR82, and ARS2 integrates with PNUTS to control unproductive transcription

Molecular Cell, Год журнала: 2023, Номер 83(13), С. 2222 - 2239.e5

Опубликована: Июнь 16, 2023

The transcriptional termination of unstable non-coding RNAs (ncRNAs) is poorly understood compared to coding transcripts. We recently identified ZC3H4-WDR82 ("restrictor") as restricting human ncRNA transcription, but how it does this unknown. Here, we show that ZC3H4 additionally associates with ARS2 and the nuclear exosome targeting complex. domains contact WDR82 are required for restriction, suggesting their presence in a functional Consistently, ZC3H4, WDR82, co-transcriptionally control an overlapping population ncRNAs. proximal negative elongation factor, PNUTS, which enables restrictor function terminate transcription all major RNA polymerase II transcript classes. In contrast short ncRNAs, longer protein-coding supported by U1 snRNA, shields transcripts from PNUTS at hundreds genes. These data provide important insights into mechanism PNUTS.

Язык: Английский

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Nuclear mRNA decay: regulatory networks that control gene expression

Nature Reviews Genetics, Год журнала: 2024, Номер unknown

Опубликована: Апрель 18, 2024

Язык: Английский

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A CPF-like phosphatase module links transcription termination to chromatin silencing

Molecular Cell, Год журнала: 2024, Номер 84(12), С. 2272 - 2286.e7

Опубликована: Июнь 1, 2024

Язык: Английский

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Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

Genes & Development, Год журнала: 2023, Номер 37(21-24), С. 1017 - 1040

Опубликована: Ноя. 1, 2023

Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds thousands genomic cis -regulatory elements. The Restrictor complex, composed Pol II-interacting protein WDR82 and RNA-binding ZC3H4, suppresses processive transcription extragenic sites in mammalian genomes. Restrictor-driven does not involve nascent RNA cleavage, its interplay with other machineries is unclear. Here we show that efficient Restrictor-controlled units involves recruitment phosphatase 1 (PP1) regulatory subunit PNUTS, a negative regulator SPT5 elongation factor, Symplekin, associated cleavage complexes but also involved cleavage-independent phosphatase-dependent noncoding RNAs yeast. PNUTS Symplekin act synergistically with, independently from, to dampen transcription. Moreover, presence limiting nuclear levels imposes competition for among multiple machineries, resulting mutual interactions. Hence, by synergizing Restrictor, enable processive, long-range

Язык: Английский

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Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex

Cell Reports, Год журнала: 2024, Номер 43(1), С. 113639 - 113639

Опубликована: Янв. 1, 2024

The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes diverse "effectors" that promote either productive destructive outcomes. Combining AlphaFold predictions structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, ZC3H18 form competing binary ZC3H18, other compete for binding to ARS2. In ternary CBC-ARS2 is responsible the initial effector recruitment but inhibits their direct CBC. We in vivo both required degradation. propose PHAX can lead, appropriate cues, competitive displacement from CBC, thus promoting a rather than degradative fate.

Язык: Английский

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PP1 PNUTS binds the restrictor and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 13, 2024

Abstract The restrictor, ZC3H4/WDR82, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism poorly understood. We report that ZC3H4/WDR82 co-purifies with PP1 phosphatase and nuclear targeting subunit, PNUTS, which binds directly to WDR82 subunit of restrictor. AlphaFold predicts a quaternary complex, PPWZ, in P P1-associated NUTS Z C3H4 both contact W DR82. To investigate role protein dephosphorylation PPWZ activity, we expressed substrate trap comprising inactive H66K linked PNUTS C-terminus. -PNUTS pol II large exosome components. -PNUTS, not WT functions as dominant-negative inhibitor CTD Ser5 dephosphorylation. Both these activities require binding domain interacts show hyperphosphorylation associated higher processivity reduced pausing would counteract termination, propose by coupled termination. In summary, identify activity complex essential terminator function this heterotetramer physiologically relevant form

Язык: Английский

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Restrictor slows early transcription elongation to render RNA polymerase II susceptible to termination at non-coding RNA loci

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 10, 2025

The eukaryotic genome is broadly transcribed by RNA polymerase II (RNAPII) to produce protein-coding messenger RNAs (mRNAs) and a repertoire of non-coding (ncRNAs). Whereas RNAPII very processive during mRNA transcription, it terminates rapidly synthesis many ncRNAs, particularly those that arise opportunistically from accessible chromatin at gene promoters or enhancers. divergent fates versus ncRNA species raise questions about how associated machineries discriminate functional spurious transcription. Restrictor complex, comprised the binding protein ZC3H4 RNAPII-interacting WDR82, has been implicated in restraining expression ncRNAs. However, determinants targeting mechanism transcription suppression remain unclear. Here, we investigate using unbiased sequence screens, rapid degradation followed nascent sequencing. We find promiscuously suppresses early elongation RNAPII, but this activity blocked most mRNAs presence 5' splice site. Consequently, critical determinant directionality prevents transcriptional interference. Finally, our data indicate rather than directly terminating acts reducing rate elongation, rendering susceptible termination other machineries.

Язык: Английский

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Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination

Nucleic Acids Research, Год журнала: 2025, Номер 53(5)

Опубликована: Фев. 27, 2025

Abstract The histone chaperone and transcription elongation factor SPT6 is integral to RNA polymerase II (RNAPII) activity. also plays a crucial role in regulating termination, although the mechanisms involved are largely unknown. In an attempt identify pathways employed by this regulation, we found that, while its partner IWS1 interact co-localize with RNAPII, their functions diverge significantly at gene termination sites. Depletion of SPT6, but not IWS1, results extensive readthrough transcription, indicating that independently regulates termination. Further analysis identified cleavage polyadenylation PCF11 phosphatase regulatory protein PNUTS collaborate process. These findings suggest may facilitate recruiting RNAPII. Additionally, jointly restrict promoter upstream transcripts (PROMPTs), whereas presence essential for accumulation absence hundreds genes. Thus, PCF11, have both distinct overlapping Our data highlight pivotal ensuring proper 5′ 3′-ends

Язык: Английский

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The MYCN oncoprotein is an RNA-binding accessory factor of the nuclear exosome targeting complex

Molecular Cell, Год журнала: 2024, Номер 84(11), С. 2070 - 2086.e20

Опубликована: Май 3, 2024

The MYCN oncoprotein binds active promoters in a heterodimer with its partner protein MAX. also interacts the nuclear exosome, 3′-5′ exoribonuclease complex, suggesting function RNA metabolism. Here, we show that forms stable high-molecular-weight complexes exosome and multiple RNA-binding proteins. vitro cells via conserved sequence termed MYCBoxI. In cells, associates thousands of intronic transcripts together ZCCHC8 subunit targeting complex enhances their processing. Perturbing results global re-localization from to RNAs. On chromatin, is then replaced by MNT(MXD6) repressor protein, inhibiting MYCN-dependent transcription. RNA-binding-deficient alleles limits MYCN's ability activate cell growth-related genes but required for promote progression through S phase enhance stress resilience neuroblastoma cells.

Язык: Английский

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