DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 2, 2025

Abstract Precursor messenger RNA (pre-mRNA) is processed into its functional form during polymerase II (Pol II) transcription. Although coupling between transcription and pre-mRNA processing established, the underlying mechanisms are not fully understood. We show that key termination factor, exonuclease Xrn2 engages with Pol forming a stable complex. activity stimulated by Spt5 to ensure efficient degradation of nascent leading dislodgement from DNA. Our results support model where first forms complex elongating achieve full in degrading revising current ‘torpedo’ termination, which posits precedes engagement II. also factor attenuates expression non-coding transcripts, coordinates splicing 3’-end processing. findings indicate transcribing an essential regulatory step modulating enzymes such as Xrn2, thus advancing our understanding how maturation controlled

Язык: Английский

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An extrinsic motor directs chromatin loop formation by cohesin

The EMBO Journal, Год журнала: 2024, Номер 43(19), С. 4173 - 4196

Опубликована: Авг. 19, 2024

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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Mechanisms of RNA Polymerase II Termination at the 3′-End of Genes

Journal of Molecular Biology, Год журнала: 2024, Номер unknown, С. 168735 - 168735

Опубликована: Авг. 1, 2024

RNA polymerase II (RNAPII) is responsible for the synthesis of a diverse set molecules, including protein-coding messenger RNAs (mRNAs) and many short non-coding (ncRNAs). For this purpose, RNAPII relies on multitude factors that regulate transcription cycle, from initiation promoter-proximal pausing, through elongation finally termination. termination at end genes ensures release DNA template its efficient recycling further rounds transcription. Termination tightly coupled to 3′-end mRNA processing, which constitutes an important trigger subsequent event. In review, we discuss current understanding mechanisms, focusing 'canonical' genes. We also integrate allosteric 'torpedo' models into unified model termination, describe different have been identified date, paying special attention human their mechanism action molecular level. Indeed, in recent years development novel approaches structural biology, biochemistry cell biology together led more detailed comprehension mechanisms better importance regulating gene expression, especially under cellular stress pathological situations.

Язык: Английский

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Multiple Forms and Functions of Premature Termination by RNA Polymerase II

Journal of Molecular Biology, Год журнала: 2024, Номер unknown, С. 168743 - 168743

Опубликована: Авг. 1, 2024

Язык: Английский

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Transcription termination promotes splicing efficiency and fidelity in a compact genome

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

Опубликована: Март 12, 2025

Splicing of terminal introns is coupled to 3'-end processing by cleavage and polyadenylation (CPA) mRNAs in mammalian genes. Whether this functional coupling universally conserved across eukaryotes unknown. Here we show using long read RNA sequencing S . cerevisiae that splicing inactivation does not result widespread CPA impairment lead global defects. However, 5'-extensions due termination defects from upstream genes inhibition a length-dependent manner. Additionally, for some extended RNAs resulting failed termination, observed decreased fidelity novel intergenic long-range intragenic events. These results argue against broad but efficient CPA-mediated transcription critical efficiency compact genome.

Язык: Английский

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Termination sequence between an inducible promoter and ubiquitous chromatin opening element (UCOE) reduces gene expression leakage and silencing

Journal of Biological Engineering, Год журнала: 2025, Номер 19(1)

Опубликована: Апрель 9, 2025

Язык: Английский

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Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex

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

Опубликована: Март 29, 2024

Abstract The 5’-3’ exoribonuclease Rat1 (or Xrn2) plays a pivotal role in termination of mRNA transcription by eukaryotic RNA polymerase II (RNAPII). forms complex with its partner proteins, Rai1 and Rtt103, acts as “torpedo” to bind transcribing RNAPII dissociate DNA/RNA from it. Here we report the cryo-electron microscopy structures Rat1-Rai1-Rtt103 three Rat1-Rai1-associated complexes (type-1, type-1b, type-2) yeast Komagataella phaffii . structure revealed that form heterotetramer, single Rtt103 bound between two molecules. In type-1 complex, Rat1-Rai1 heterodimer directly binds exit site extract into nuclease active site. This interaction changes path favor (the “pre-termination” state). type-1b type-2 have no DNA/RNA, likely representing “post-termination” states. These shed light on mechanism termination.

Язык: Английский

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ZC3H4/Restrictor Exerts a Stranglehold on Pervasive Transcription

Journal of Molecular Biology, Год журнала: 2024, Номер 437(1), С. 168707 - 168707

Опубликована: Июль 14, 2024

The regulation of transcription by RNA polymerase II (RNAPII) underpins all cellular processes and is perturbed in thousands diseases. In humans, RNAPII transcribes ∼20000 protein-coding genes engages apparently futile non-coding at other sites. Despite being so ubiquitous, this usually attenuated soon after initiation the resulting products are immediately degraded nuclear exosome. We others have recently described a new complex, "Restrictor", which appears to control such unproductive transcription. Underpinned binding protein, ZC3H4, Restrictor curtails unproductive/pervasive genome-wide. Here, we discuss these recent discoveries speculate on some many unknowns regarding function mechanism.

Язык: Английский

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Nuclear sorting of short RNA polymerase II transcripts

Molecular Cell, Год журнала: 2024, Номер 84(19), С. 3644 - 3655

Опубликована: Окт. 1, 2024

Язык: Английский

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