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Single-molecule imaging reveals the interplay between transcription factors, nucleosomes, and transcriptional bursting

https://doi.org/10.1101/404681
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Distance measurement by circular scanning of the excitation beam in the two‐photon microscope
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Analysis of diffusion and binding in cells using the RICS approach
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New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae
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Markovian Modeling of Gene-Product Synthesis
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Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Single-Molecule Tracking
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[18] Fluorescence resonance energy transfer and nucleic acids
inferredcites →https://doi.org/10.1016/bs.mie.2016.08.014openalex-snapshot
Methods for Investigating DNA Accessibility with Single Nucleosomes
inferredcites →https://doi.org/10.1016/j.bpj.2009.04.027openalex-snapshot
Direct Measurement of Association and Dissociation Rates of DNA Binding in Live Cells by Fluorescence Correlation Spectroscopy
inferredcites →https://doi.org/10.1016/j.bpj.2009.09.031openalex-snapshot
Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data
inferredcites →https://doi.org/10.1016/j.cell.2005.09.031openalex-snapshot
Real-Time Kinetics of Gene Activity in Individual Bacteria
inferredcites →https://doi.org/10.1016/j.cell.2010.03.048openalex-snapshot
A RSC/Nucleosome Complex Determines Chromatin Architecture and Facilitates Activator Binding
inferredcites →https://doi.org/10.1016/j.cell.2014.01.062openalex-snapshot
Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2016.05.025openalex-snapshot
Enhancer Control of Transcriptional Bursting
inferredcites →https://doi.org/10.1016/j.cell.2017.02.007openalex-snapshot
A Phase Separation Model for Transcriptional Control
inferredcites →https://doi.org/10.1016/j.celrep.2014.05.053openalex-snapshot
Transcription Factors Modulate c-Fos Transcriptional Bursts
inferredcites →https://doi.org/10.1016/j.cub.2006.03.092openalex-snapshot
Transcriptional Pulsing of a Developmental Gene
inferredcites →https://doi.org/10.1016/j.gde.2015.12.003openalex-snapshot
Pioneer transcription factors, chromatin dynamics, and cell fate control
inferredcites →https://doi.org/10.1016/j.molcel.2015.01.027openalex-snapshot
Bursty Gene Expression in the Intact Mammalian Liver
inferredcites →https://doi.org/10.1016/j.molcel.2015.09.028openalex-snapshot
Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription
inferredcites →https://doi.org/10.1016/j.molcel.2015.10.002openalex-snapshot
Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast
inferredcites →https://doi.org/10.1016/j.molcel.2016.03.007openalex-snapshot
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping
inferredcites →https://doi.org/10.1016/j.molcel.2018.04.012openalex-snapshot
An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation
inferredcites →https://doi.org/10.1016/j.ymeth.2017.03.014openalex-snapshot
Quantifying transcription factor binding dynamics at the single-molecule level in live cells
inferredcites →https://doi.org/10.1016/s0006-3495(99)77065-7openalex-snapshot
Molecular Dynamics in Living Cells Observed by Fluorescence Correlation Spectroscopy with One- and Two-Photon Excitation
inferredcites →https://doi.org/10.1016/s0076-6879(99)04003-3openalex-snapshot
Preparation of nucleosome core particle from recombinant histones
inferredcites →https://doi.org/10.1016/s1937-6448(08)01003-4openalex-snapshot
Chapter 3 Galactose Metabolism in Yeast—Structure and Regulation of the Leloir Pathway Enzymes and the Genes Encoding Them
inferredcites →https://doi.org/10.1021/nn403447sopenalex-snapshot
Robustly Passivated, Gold Nanoaperture Arrays for Single-Molecule Fluorescence Microscopy
inferredcites →https://doi.org/10.1038/nature03524openalex-snapshot
Enhancement of cellular memory by reducing stochastic transitions
inferredcites →https://doi.org/10.1038/nature08406openalex-snapshot
Gal4 turnover and transcription activation
inferredcites →https://doi.org/10.1038/ncomms8357openalex-snapshot
Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher
inferredcites →https://doi.org/10.1038/nmeth.1208openalex-snapshot
A practical guide to single-molecule FRET
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3256openalex-snapshot
A general method to improve fluorophores for live-cell and single-molecule microscopy
inferredcites →https://doi.org/10.1038/nmeth1171openalex-snapshot
Highly inclined thin illumination enables clear single-molecule imaging in cells
inferredcites →https://doi.org/10.1038/nsmb.1514openalex-snapshot
Single-RNA counting reveals alternative modes of gene expression in yeast
inferredcites →https://doi.org/10.1038/s41467-017-00398-7openalex-snapshot
Live-cell p53 single-molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity
inferredcites →https://doi.org/10.1038/s41586-018-0174-3openalex-snapshot
Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II
inferredcites →https://doi.org/10.1073/pnas.1017672108openalex-snapshot
Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity
inferredcites →https://doi.org/10.1073/pnas.1211902109openalex-snapshot
Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response
inferredcites →https://doi.org/10.1073/pnas.1213530109openalex-snapshot
Transcriptional burst frequency and burst size are equally modulated across the human genome
inferredcites →https://doi.org/10.1073/pnas.1312310110openalex-snapshot
Stimulus-induced modulation of transcriptional bursting in a single mammalian gene
inferredcites →https://doi.org/10.1083/jcb.201710038openalex-snapshot
Visualizing transcription factor dynamics in living cells
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/nar/gkt1319openalex-snapshot
Nucleosomes accelerate transcription factor dissociation
inferredcites →https://doi.org/10.1093/nar/gkw744openalex-snapshot
Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin
inferredcites →https://doi.org/10.1101/gad.5.7.1285openalex-snapshot
Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains.
inferredcites →https://doi.org/10.1101/gr.149096.112openalex-snapshot
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise
inferredcites →https://doi.org/10.1126/science.1098641openalex-snapshot
Control of Stochasticity in Eukaryotic Gene Expression
inferredcites →https://doi.org/10.1126/science.1141967openalex-snapshot
Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell
inferredcites →https://doi.org/10.1126/science.1202142openalex-snapshot
Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene
inferredcites →https://doi.org/10.1126/science.1239053openalex-snapshot
Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells
inferredcites →https://doi.org/10.1128/mcb.16.7.3773openalex-snapshot
DNA Sequence Preferences of GAL4 and PPR1: How a Subset of Zn 2 Cys 6 Binuclear Cluster Proteins Recognizes DNA
inferredcites →https://doi.org/10.1186/gb-2006-7-10-r100openalex-snapshot
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
inferredcites →https://doi.org/10.1371/journal.pbio.0040309openalex-snapshot
Stochastic mRNA Synthesis in Mammalian Cells
inferredcites →https://doi.org/10.1371/journal.pbio.1001621openalex-snapshot
Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression
inferredcites →https://doi.org/10.15252/embj.201695621openalex-snapshot
Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters
inferredcites →https://doi.org/10.1529/biophysj.104.044230openalex-snapshot
3-D Particle Tracking in a Two-Photon Microscope: Application to the Study of Molecular Dynamics in Cells
inferredcites →https://doi.org/10.1529/biophysj.105.066670openalex-snapshot
Chromatin Dynamics in Interphase Cells Revealed by Tracking in a Two-Photon Excitation Microscope
inferredcites →https://doi.org/10.7554/elife.00750openalex-snapshot
Direct observation of frequency modulated transcription in single cells using light activation
inferredcites →https://doi.org/10.7554/elife.03939openalex-snapshot
Kinetic competition during the transcription cycle results in stochastic RNA processing

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41467-019-14208-9openalex-snapshot
Alternative transcription cycle for bacterial RNA polymerase
inferred← citeshttps://doi.org/10.1038/s41467-022-33977-4openalex-snapshot
On-microscope staging of live cells reveals changes in the dynamics of transcriptional bursting during differentiation
inferred← citeshttps://doi.org/10.1038/s41594-023-00981-1openalex-snapshot
Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting
inferred← citeshttps://doi.org/10.2139/ssrn.3985163openalex-snapshot
Transcriptional Kinetic Synergy: A Complex Landscape Revealed by Integrating Modelling and Synthetic Biology
inferred← citeshttps://doi.org/10.3389/fgene.2024.1451461openalex-snapshot
Transcriptional bursting dynamics in gene expression
inferred← citeshttps://doi.org/10.3410/f.737264305.793574582openalex-snapshot
Faculty Opinions recommendation of Alternative transcription cycle for bacterial RNA polymerase.
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