Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Июль 23, 2021

Abstract Promoter-proximal pausing of RNA polymerase II is a key process regulating gene expression. In latent HIV-1 cells, it prevents viral transcription and essential for latency maintenance, while in acutely infected cells the factor Tat releases paused to induce Pausing fundamental HIV-1, but how contributes bursting stochastic reactivation unclear. Here, we performed single molecule imaging transcription. We developed quantitative analysis method that manages multiple time scales from seconds days rapidly fits many models promoter dynamics. found polymerases enter long-lived pause at promoters (>20 minutes), thereby effectively limiting Surprisingly contrast current models, appears not obligatory, with only small fraction undergoing absence Tat. One consequence occurs bursts facilitating exit providing rationale stochasticity rebounds.

Язык: Английский

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Transcription Factor Dynamics

Cold Spring Harbor Perspectives in Biology, Год журнала: 2021, Номер 13(11), С. a040949 - a040949

Опубликована: Май 17, 2021

Feiyue Lu and Timothée Lionnet Institute for Systems Genetics Cell Biology Department, NYU School of Medicine, New York, York 10016, USA Correspondence: Timothee.lionnet{at}nyulangone.org

Язык: Английский

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Analytical Time-Dependent Distributions for Gene Expression Models With Complex Promoter Switching Mechanisms

SIAM Journal on Applied Mathematics, Год журнала: 2023, Номер 83(4), С. 1572 - 1602

Опубликована: Авг. 3, 2023

.Classical gene expression models assume exponential switching time distributions between the active and inactive promoter states. However, recent experiments have shown that many genes in mammalian cells may produce nonexponential distributions, implying existence of multiple states molecular memory dynamics. Here we analytically solve a model with random bursting complex switching, derive time-dependent mRNA protein copy numbers, generalizing steady-state solution obtained [T. Zhou J. Zhang, SIAM Appl. Math., 72 (2012), pp. 789–818] [U. Herbach, 79 (2019), 1007–1029]. Using multiscale simplification techniques, find has no influence on distribution when is very fast or slow, while it significantly affects neither too nor slow. By analyzing dynamical phase diagram system, also state weakens transient stationary bimodality number distribution, enhances such bimodality.Keywordstransient distributionburstingmolecular memorymultiscale simplificationMSC codes60J2760J2892C4078A7092B05

Язык: Английский

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Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation

Cell Systems, Год журнала: 2017, Номер 4(6), С. 622 - 635.e9

Опубликована: Июнь 1, 2017

Single-cell quantification of transcription kinetics and variability promotes a mechanistic understanding gene regulation. Here, using single-molecule RNA fluorescence in situ hybridization mathematical modeling, we dissect cellular dynamics for Arabidopsis FLOWERING LOCUS C (FLC). FLC expression quantitatively determines flowering time is regulated by antisense (COOLAIR) transcription. In cells without observable COOLAIR expression, quantify initiation, elongation, intron processing, lariat degradation, as well mRNA release from the locus degradation. these heterogeneously sized cells, number increases linearly with cell size, resulting large cell-to-cell transcript level. This variation accounted cell-size-dependent, Poissonian production, but not transcriptional bursts. COOLAIR-expressing however, size contributes to decreasing size. Our analysis therefore reveals an unexpected role modulating scaling

Язык: Английский

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Rapid and efficient genetic engineering of both wild type and axenic strains of Dictyostelium discoideum

PLoS ONE, Год журнала: 2018, Номер 13(5), С. e0196809 - e0196809

Опубликована: Май 30, 2018

Dictyostelium has a mature technology for molecular-genetic manipulation based around transfection using several different selectable markers, marker re-cycling, homologous recombination and insertional mutagenesis, all supported by well-annotated genome. However this is optimized mutant, axenic cells that, unlike non-axenic wild type, can grow in liquid medium. There pressing need methods to manipulate type ones with defects macropinocytosis, neither of which media. Here we present panel molecular genetic techniques on the selection transfectants growth bacteria rather than As well as extending range strains that be manipulated, these are faster conventional methods, often giving usable numbers transfected within few days. The plasmids described here allow efficient extrachromosomal vectors, chromosomal integration at ‘safe haven’ relatively uniform cell-to-cell expression, gene knock-in knock-out an inducible expression system. We have thus created complete new system no longer requires cell feeding

Язык: Английский

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