Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide DOI Creative Commons
Magda Kopczyńska, Upasana Saha,

Anastasiia Romanenko

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 24, 2024

Abstract Defining the beginning of a eukaryotic protein-coding gene is relatively simple. It corresponds to first ribonucleotide incorporated by RNA polymerase II (Pol II) into nascent molecule. This nucleotide protected capping and maintained in mature messenger (mRNA). However, higher eukaryotes, end mRNA separated from sites transcription termination hundreds thousands base pairs. Currently used genomic annotations only take account transcript – where pre-mRNA cleavage occurs, while regions which terminates are unannotated. Here, we describe evidence for marker termination, could be widely applicable studies. Pol can determined genome-wide detecting phosphorylated on threonine 4 its C-terminal domain CTD-T4ph). this state pauses before leaving DNA template. Up date potent mark has been underused because place role scattered across multiple publications. We summarize observations regarding CTD-T4ph present bioinformatic analyses that further support as global animals.

Language: Английский

Activation and inhibition mechanisms of a plant helper NLR DOI

Yinyan Xiao,

Xiaoxian Wu,

Zaiqing Wang

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 12, 2025

Language: Английский

Citations

3
DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts DOI Creative Commons
Krzysztof Kuś, L. Carrique,

Tea Kecman

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 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

Language: Английский

Citations

2
PP1 PNUTS binds the restrictor and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination DOI
Benjamin Erickson, Roman O Fedoryshchak,

Nova Fong

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 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

Language: Английский

Citations

7
Mechanisms of RNA Polymerase II Termination at the 3′-End of Genes DOI Creative Commons
David López Martínez, Jesper Q. Svejstrup

Journal of Molecular Biology, Journal Year: 2024, Volume and Issue: unknown, P. 168735 - 168735

Published: Aug. 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.

Language: Английский

Citations

5
PP1/PNUTS Phosphatase Binds the Restrictor Complex and Stimulates RNA pol II Transcription Termination DOI
Benjamin Erickson, Roman O Fedoryshchak,

Nova Fong

et al.

Published: Jan. 1, 2025

The restrictor, ZC3H4/WDR82, terminates antisense transcription from bidirectional promoters, but its mechanism is poorly understood. We report that ZC3H4/WDR82 immunoprecipitate with PP1 phosphatase and nuclear targeting subunit, PNUTS, which binds to WDR82. AlphaFold predicts a complex of PP1/PNUTS restrictor where both PNUTS ZC3H4 contact A substrate trap, PP1H66K-PNUTS, comprising inactive fused the C-terminus antagonizes mediated termination whereas PP1WT-PNUTS has less effect suggesting activity required for termination. One implicated in by pol II CTD Ser5-P. PP1H66K-PNUTS induces Ser5-P hyperphosphorylation at 5' ends presumably inhibiting dephosphorylation. NET-seq analysis suggests Ser5 dephosphorylation would promote increasing pausing. Both inhibition require WDR82 binding domain mediates binding. In summary, associated via promotes efficient

Language: Английский

Citations

0
Convergent and conserved roads lead to Rome: now archaea fill the gap of transcription termination DOI
Ning Song, Meng Li

Science China Life Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

Language: Английский

Citations

0
Mechanistic insights into DXO1 and XRN3: Regulatory roles of RNA stability, transcription, and liquid-liquid phase separation in Arabidopsis thaliana DOI
Mostafakamal Shams,

Ali Khadivi

Plant Science, Journal Year: 2025, Volume and Issue: 353, P. 112413 - 112413

Published: Feb. 3, 2025

Language: Английский

Citations

0
DNA Sequence Changes Resulting from Codon Optimization Affect Gene Expression in Pichia pastoris by Altering Chromatin Accessibility DOI Creative Commons

Chaoyu Lu,

Linna Guo, Belle Fang

et al.

Journal of Fungi, Journal Year: 2025, Volume and Issue: 11(4), P. 282 - 282

Published: April 3, 2025

Codon optimization is a widely employed strategy to enhance protein expression. However, it occasionally leads unexpected transcriptional repression despite preserving amino acid sequences. This study investigates the mechanistic basis of such attenuation by analyzing two gene candidates (0432 and Fluc) in common expression chassis P. pastoris. Both genes experienced severe mRNA reduction following codon optimization. Evidenced histone H3 chromatin immunoprecipitation (ChIP) DNase I hypersensitivity assay, sequences with displayed elevated nucleosome occupancy reduced accessibility. The above change was caused an ORF sequence independent promoter, since compromised accessibility were still observed after replacing strong promoter PGAP Ppor1 or Prps8b. Our findings challenge conventional view as solely translation-centric, revealing its capacity preemptively modulate transcription through work underscores necessity integrating chromatin-level considerations into synthetic design avoid unintended silencing optimize outcomes.

Language: Английский

Citations

0
Molecular basis for the interaction between Saccharomyces cerevisiae Rtt103 and the Rat1-Rai1 complex DOI Creative Commons

Hsu-Feng Chu,

Liang Tong

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 5, 2025

The Rat1 5'-3' exoribonuclease together with its partner Rai1 have important roles in Saccharomyces cerevisiae RNA polymerase II transcription termination. Rtt103 copurifies Rat1-Rai1 S. cerevisiae, but mechanism of interaction them is not known. We report here the cryo-EM structure Rat1-Rai1-Rtt103 ternary complex at 2.9 Å resolution. found that a short segment close contact Rai1, while rest Rtt103, including C-terminal domain domain, shows no interactions or Rat1. This contrast to observations on Komagataella phaffii complex, where only has contacts Rai1. Our reveals Pro261 and Tyr263 we show P261G/Y263A mutation blocks Rat1-Rai1. suggests that, yeast, this which named segment, likely helps recruitment for

Language: Английский

Citations

0
PP1/PNUTS phosphatase binds the restrictor complex and stimulates RNA Pol II transcription termination DOI Creative Commons
Benjamin Erickson, Roman O Fedoryshchak,

Nova Fong

et al.

Cell Reports, Journal Year: 2025, Volume and Issue: 44(5), P. 115564 - 115564

Published: April 16, 2025

Language: Английский

Citations

0