Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions DOI Creative Commons
Xiaoming Fu, Heta Patel, Stefano Coppola

и другие.

eLife, Год журнала: 2022, Номер 11

Опубликована: Окт. 17, 2022

Transcriptional rates are often estimated by fitting the distribution of mature mRNA numbers measured using smFISH (single molecule fluorescence in situ hybridization) with predicted telegraph model gene expression, which defines two promoter states activity and inactivity. However, fluctuations strongly affected processes downstream transcription. In addition, assumes one copy but experiments, cells may have copies as replicate their genome during cell cycle. While it is presumed that post-transcriptional noise number variation affect transcriptional parameter estimation, size error introduced remains unclear. To address this issue, here we measure both nascent distributions GAL10 yeast classify each according to its cycle phase. We infer parameters from distributions, without accounting for phase compare results live-cell transcription measurements same gene. find that: (i) correcting dynamics decreases switching initiation rate, increases fraction time spent active state, well burst size; (ii) additional correction leads further a large reduction errors estimation. Furthermore, outline how correctly adjust measurement due uncertainty site localisation when introns cannot be labelled. Simulations data, corrected phases noise, autocorrelation functions agree those obtained imaging.

Язык: Английский

Time will tell: comparing timescales to gain insight into transcriptional bursting DOI Creative Commons
Joseph V.W. Meeussen, Tineke L. Lenstra

Trends in Genetics, Год журнала: 2024, Номер 40(2), С. 160 - 174

Опубликована: Янв. 12, 2024

Recent imaging studies have captured the dynamics of regulatory events transcription inside living cells. These include factor (TF) DNA binding, chromatin remodeling and modification, enhancer-promoter (E-P) proximity, cluster formation, preinitiation complex (PIC) assembly. Together, these molecular culminate in stochastic bursts RNA synthesis, but their kinetic relationship remains largely unclear. In this review, we compare timescales upstream steps (input) with kinetics transcriptional bursting (output) to generate mechanistic models single We highlight open questions potential technical advances guide future endeavors toward a quantitative understanding regulation.

Язык: Английский

Процитировано

25
Transcription factor clusters as information transfer agents DOI Creative Commons
Rahul Munshi, Ling Jia, Sergey Ryabichko

и другие.

Science Advances, Год журнала: 2025, Номер 11(1)

Опубликована: Янв. 1, 2025

Deciphering how genes interpret information from transcription factor (TF) concentrations within the cell nucleus remains a fundamental question in gene regulation. Recent advancements have revealed heterogeneous distribution of TF molecules, posing challenges to precisely decoding concentration signals. Using high-resolution single-cell imaging fluorescently tagged Bicoid living Drosophila embryos, we show that accumulation submicrometer clusters preserves spatial maternal gradient. These provide precise cues through intensity, size, and frequency. We further discover target colocalize with these an enhancer-binding affinity-dependent manner. Our modeling suggests clustering offers faster sensing mechanism for global nuclear than freely diffusing molecules detected by simple enhancers.

Язык: Английский

Процитировано

4
Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility DOI Creative Commons
Diana A. Stavreva, David A. Garcia, Grégory Fettweis

и другие.

Molecular Cell, Год журнала: 2019, Номер 75(6), С. 1161 - 1177.e11

Опубликована: Авг. 14, 2019

Язык: Английский

Процитировано

117
Spatiotemporal coordination of transcription preinitiation complex assembly in live cells DOI Creative Commons
Vu Q. Nguyen, Anand Ranjan, Sheng Liu

и другие.

Molecular Cell, Год журнала: 2021, Номер 81(17), С. 3560 - 3575.e6

Опубликована: Авг. 9, 2021

Язык: Английский

Процитировано

101
Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model DOI Creative Commons
David A. Garcia, Grégory Fettweis, Diego M. Presman

и другие.

Nucleic Acids Research, Год журнала: 2021, Номер 49(12), С. 6605 - 6620

Опубликована: Фев. 11, 2021

Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in nucleus, giving important information regarding diffusion and binding behavior these proteins nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed two discrete populations TFs—one non-specifically bound chromatin another specifically target sites, as implied decades biochemical studies. However, emerging studies suggest alternate models dwell-time distributions, indicating existence more than (multi-exponential distribution), or even absence states altogether (power-law distribution). Here, we present an analytical pipeline evaluate which model best explains data. We find that a broad spectrum (including glucocorticoid receptor, oestrogen FOXA1, CTCF) power-law distribution dwell-times, blurring temporal line between non-specific specific binding, suggesting productive may involve longer events previously believed. From observations, propose continuum affinities explain TF dynamics, is consistent with complex interactions multiple domains well searching on template.

Язык: Английский

Процитировано

97
Epigenome Regulation by Dynamic Nucleosome Unwrapping DOI
Sandipan Brahma, Steven Henikoff

Trends in Biochemical Sciences, Год журнала: 2019, Номер 45(1), С. 13 - 26

Опубликована: Окт. 17, 2019

Язык: Английский

Процитировано

88
A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting DOI Creative Commons
Nicholas C Lammers, Yang Joon Kim, Jiaxi Zhao

и другие.

Current Opinion in Cell Biology, Год журнала: 2020, Номер 67, С. 147 - 157

Опубликована: Ноя. 24, 2020

Язык: Английский

Процитировано

77
Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene DOI Creative Commons

Achim P. Popp,

Johannes Hettich,

J. Christof M. Gebhardt

и другие.

Nucleic Acids Research, Год журнала: 2021, Номер 49(11), С. 6249 - 6266

Опубликована: Май 6, 2021

Abstract Transcription is a vital process activated by transcription factor (TF) binding. The active gene releases burst of transcripts before turning inactive again. While the basic course well understood, it unclear how binding TF affects frequency, duration and size transcriptional burst. We systematically varied residence time concentration synthetic characterized reporter combining single molecule imaging, RNA-FISH, live transcript visualisation analysis with novel algorithm, Burst Inference from mRNA Distributions (BIRD). For this well-defined system, we found that solely affected frequency variations in had stronger influence than concentration. This enabled us to device model transcription, which triggers multiple successive steps transits state actual synthesis decoupled presence. quantified all transition times gene, including search delay between onset transcription. Our quantitative measurements revealed detailed kinetic insight, may serve as basis for bottom-up understanding regulation.

Язык: Английский

Процитировано

72
Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin DOI Creative Commons
Jee Min Kim, Pat Visanpattanasin, Vivian Jou

и другие.

eLife, Год журнала: 2021, Номер 10

Опубликована: Июль 27, 2021

Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide architectures of regulatory DNA during cellular lifespan, but the temporal interactions between targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, INO80 remodeling complexes in budding yeast detected hyperkinetic behaviors chromatin-bound molecules that frequently transition to free state all complexes. Chromatin-bound display notably higher diffusion than nucleosomal histones, strikingly fast dissociation kinetics with 4–7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by catalytic ATPase, uncovering an additional function its established role nucleosome remodeling. Kinetic simulations show multiple can repeatedly occupy same promoter region on a timescale minutes, implicating unending ‘tug-of-war’ controls temporally shifting window accessibility transcription initiation machinery.

Язык: Английский

Процитировано

65
Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics DOI Creative Commons
Virginia L Pimmett, Matthieu Dejean, Carola Fernandez

и другие.

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

Опубликована: Июль 23, 2021

Abstract Genes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states. A major challenge transcription is understanding how composition dictates bursting, particularly multicellular organisms. We investigate two key Drosophila developmental motifs, the TATA box (TATA) Initiator (INR). Using live imaging embryos new computational methods, we demonstrate that bursting occurs on multiple timescales ranging from seconds minutes. TATA-containing promoters INR-containing exhibit distinct dynamics, with one or separate rate-limiting steps respectively. associated long states, high rates of polymerase initiation, short-lived, infrequent In contrast, INR motif leads which relates promoter-proximal pausing. Surprisingly, model suggests pausing not obligatory, but stochastically for a subset polymerases. Overall, our results provide rationale switching during zygotic genome activation.

Язык: Английский

Процитировано

64