Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene

An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

(2021) David A. Garcia et al.   MOLECULAR CELL

Single molecule tracking and analysis framework including theory-predicted parameter settings

(2021) Timo Kuhn et al.   Scientific Reports

Inferring quantity and qualities of superimposed reaction rates from single molecule survival time distributions

(2020) Matthias Reisser et al.   Scientific Reports

Transcription in Living Cells: Molecular Mechanisms of Bursting

(2020) Joseph Rodriguez et al.   Annual Review of Biochemistry

Structure and mechanism of the RNA polymerase II transcription machinery

(2020) Allison C. Schier et al.   GENES & DEVELOPMENT

Exactly solvable models of stochastic gene expression

(2020) Lucy Ham et al.   JOURNAL OF CHEMICAL PHYSICS

Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics

(2020) Gennady Gorin et al.   PLoS One

Signaling Mechanism of Transcriptional Bursting: A Technical Resolution-Independent Study

(2020) Yaolai Wang et al.   Biology-Basel

Single-molecule imaging of the transcription factor SRF reveals prolonged chromatin-binding kinetics upon cell stimulation

(2019) Lisa Hipp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation

(2019) Andrea Callegari et al.   PLoS Genetics

Mitotic chromosome binding predicts transcription factor properties in interphase

(2019) Mahé Raccaud et al.   Nature Communications

Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting

(2019) Benjamin T Donovan et al.   EMBO JOURNAL

Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole

(2019) Aisha Yesbolatova et al.   METHODS

Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA

(2019) John W Biddle et al.   eLife

Functional instability allows access to DNA in longer transcription Activator-Like effector (TALE) arrays

(2019) Kathryn Geiger-Schuller et al.   eLife

Determining cellular CTCF and cohesin abundances to constrain 3D genome models

(2019) Claudia Cattoglio et al.   eLife

Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility

(2019) Diana A. Stavreva et al.   MOLECULAR CELL

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality

(2019) Mengyu Wang et al.   Nature Microbiology

Guided nuclear exploration increases CTCF target search efficiency

(2019) Anders S. Hansen et al.   Nature Chemical Biology

Transcription factor target site search and gene regulation in a background of unspecific binding sites

(2018) J. Hettich et al.   JOURNAL OF THEORETICAL BIOLOGY

An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation

(2018) Marc Rullan et al.   MOLECULAR CELL

Estrogen‐dependent control and cell‐to‐cell variability of transcriptional bursting

(2018) Christoph Fritzsch et al.   Molecular Systems Biology

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Modulation of transcriptional burst frequency by histone acetylation

(2018) Damien Nicolas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes

(2018) Sheila S Teves et al.   eLife

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity

(2018) Joseph Rodriguez et al.   CELL

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation

(2018) Caroline R. Bartman et al.   MOLECULAR CELL

Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast

(2018) Gunjan D. Mehta et al.   MOLECULAR CELL

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development

(2018) Matthias Reisser et al.   Nature Communications

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs

(2018) Jeremy Dufourt et al.   Nature Communications

Quantifying transcription factor binding dynamics at the single-molecule level in live cells

(2017) Diego M. Presman et al.   METHODS

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes

(2017) Aafke A. van den Berg et al.   NUCLEIC ACIDS RESEARCH

DNA residence time is a regulatory factor of transcription repression

(2017) Karen Clauß et al.   NUCLEIC ACIDS RESEARCH

Live-cell p53 single-molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity

(2017) Alessia Loffreda et al.   Nature Communications

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors

(2016) Toyoaki Natsume et al.   Cell Reports

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

Single-cell analysis of transcription kinetics across the cell cycle

(2016) Samuel O Skinner et al.   eLife

A continuum model of transcriptional bursting

(2016) Adam M Corrigan et al.   eLife

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

Structure of silent transcription intervals and noise characteristics of mammalian genes

(2015) B. Zoller et al.   Molecular Systems Biology

Combining protein and mRNA quantification to decipher transcriptional regulation

(2015) Heng Xu et al.   NATURE METHODS

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

(2015) Davide Normanno et al.   Nature Communications

Single-Molecule Imaging Reveals Dynamics of CREB Transcription Factor Bound to Its Target Sequence

(2015) Noriyuki Sugo et al.   Scientific Reports

Cellular Levels of Signaling Factors Are Sensed by β-actin Alleles to Modulate Transcriptional Pulse Intensity

(2015) Alon Kalo et al.   Cell Reports

The Influence of SV40 polyA on Gene Expression of Baculovirus Expression Vector Systems

(2015) Tamer Z. Salem et al.   PLoS One

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Mechanism of Transcriptional Bursting in Bacteria

(2014) Shasha Chong et al.   CELL

Fold Change of Nuclear NF-κB Determines TNF-Induced Transcription in Single Cells

(2014) Robin E.C. Lee et al.   MOLECULAR CELL

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

(2014) Petter Hammar et al.   NATURE GENETICS

Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity

(2014) John P Guilinger et al.   NATURE METHODS

Single-molecule analysis of transcription factor binding at transcription sites in live cells

(2014) Tatsuya Morisaki et al.   Nature Communications

Transcription Factors Modulate c-Fos Transcriptional Bursts

(2014) Adrien Senecal et al.   Cell Reports

The Mediator complex and transcription regulation

(2013) Zachary C. Poss et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins

(2013) Gražvydas Lukinavičius et al.   Nature Chemistry

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

(2013) J Christof M Gebhardt et al.   NATURE METHODS

FISH-quant: automatic counting of transcripts in 3D FISH images

(2013) Florian Mueller et al.   NATURE METHODS

Quantitative analysis of TALE–DNA interactions suggests polarity effects

(2013) Joshua F. Meckler et al.   NUCLEIC ACIDS RESEARCH

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

Direct observation of frequency modulated transcription in single cells using light activation

(2013) Daniel R Larson et al.   eLife

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers

(2013) Leila Taher et al.   GENOME BIOLOGY

Fluorescence Fluctuation Spectroscopy Enables Quantitative Imaging of Single mRNAs in Living Cells

(2012) Bin Wu et al.   BIOPHYSICAL JOURNAL

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

Transcriptional burst frequency and burst size are equally modulated across the human genome

(2012) R. D. Dar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

(2012) A. N.-S. Mak et al.   SCIENCE

Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

(2012) D. Deng et al.   SCIENCE

Activated STAT1 Transcription Factors Conduct Distinct Saltatory Movements in the Cell Nucleus

(2011) Jasmin Speil et al.   BIOPHYSICAL JOURNAL

Fast transcription rates of RNA polymerase II in human cells

(2011) Paolo Maiuri et al.   EMBO REPORTS

General properties of transcriptional time series in Escherichia coli

(2011) Lok-hang So et al.   NATURE GENETICS

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

(2011) Tomas Cermak et al.   NUCLEIC ACIDS RESEARCH

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

(2011) D. R. Larson et al.   SCIENCE

XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function

(2010) Jens Boch et al.   Annual Review of Phytopathology

Improved Tet-responsive promoters with minimized background expression

(2010) Rainer Loew et al.   BMC BIOTECHNOLOGY

Single-allele analysis of transcription kinetics in living mammalian cells

(2010) Sharon Yunger et al.   NATURE METHODS

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis

(2008) Georgyi V. Los et al.   ACS Chemical Biology

Computational analysis of the human HSPH/HSPA/DNAJ family and cloning of a human HSPH/HSPA/DNAJ expression library

(2008) Jurre Hageman et al.   CELL STRESS & CHAPERONES

Histone Modifications and Nuclear Architecture: A Review

(2008) Eva Bártová et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

On the Use of the Hill Functions in Mathematical Models of Gene Regulatory Networks

(2008) M. Santillán   Mathematical Modelling of Natural Phenomena