A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting

Probing Mechanisms of Transcription Elongation Through Cell-to-Cell Variability of RNA Polymerase

(2020) Md Zulfikar Ali et al.   BIOPHYSICAL JOURNAL

Nucleosomal proofreading of activator–promoter interactions

(2020) Robert Shelansky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription in Living Cells: Molecular Mechanisms of Bursting

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

Gene Regulation in and out of Equilibrium

(2020) Felix Wong et al.   Annual Review of Biophysics

A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute

(2020) Jonathan Desponds et al.   eLife

Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression

(2019) Rob Phillips et al.   Annual Review of Biophysics

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

(2019) Benjamin T Donovan et al.   EMBO JOURNAL

Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity

(2019) Jeehae Park et al.   eLife

Dynamics of Notch-Dependent Transcriptional Bursting in Its Native Context

(2019) ChangHwan Lee et al.   DEVELOPMENTAL CELL

Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling

(2019) Julia Falo-Sanjuan et al.   DEVELOPMENTAL CELL

Multimodal transcriptional control of pattern formation in embryonic development

(2019) Nicholas C. Lammers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene transcription in bursting: a unified mode for realizing accuracy and stochasticity

(2018) Yaolai Wang et al.   BIOLOGICAL REVIEWS

Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting

(2018) Benjamin Zoller et al.   CELL

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

(2018) Joseph Rodriguez et al.   CELL

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

(2018) Jeremy Dufourt et al.   Nature Communications

Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern

(2018) Huy Tran et al.   PLoS Computational Biology

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

(2018) Mustafa Mir et al.   eLife

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

What shapes eukaryotic transcriptional bursting?

(2017) Damien Nicolas et al.   Molecular BioSystems

Addressing the Need for a Model Selection Framework in Systems Biology Using Information Theory

(2017) Frank DeVilbiss et al.   PROCEEDINGS OF THE IEEE

Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle

(2017) Clarissa Scholes et al.   Cell Systems

Transcription Dynamics in Living Cells

(2016) Tineke L. Lenstra et al.   Annual Review of Biophysics

Information Integration and Energy Expenditure in Gene Regulation

(2016) Javier Estrada et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos

(2016) Jonathan Desponds et al.   PLoS Computational Biology

A continuum model of transcriptional bursting

(2016) Adam M Corrigan et al.   eLife

Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics

(2015) Brian Munsky et al.   METHODS

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

From Structural Variation of Gene Molecules to Chromatin Dynamics and Transcriptional Bursting

(2015) Hinrich Boeger et al.   Genes

Mechanism of Transcriptional Bursting in Bacteria

(2014) Shasha Chong et al.   CELL

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

(2014) J. P. Bothma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model Selection in Systems Biology Depends on Experimental Design

(2014) Daniel Silk et al.   PLoS Computational Biology

Statistical Mechanics of Monod–Wyman–Changeux (MWC) Models

(2013) Sarah Marzen et al.   JOURNAL OF MOLECULAR BIOLOGY

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

Genetic Determinants and Cellular Constraints in Noisy Gene Expression

(2013) A. Sanchez et al.   SCIENCE

Origins and consequences of transcriptional discontinuity

(2011) David M Suter et al.   CURRENT OPINION IN CELL BIOLOGY

A transgenic mouse for in vivo detection of endogenous labeled mRNA

(2011) Timothée Lionnet et al.   NATURE METHODS

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

Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression

(2011) Alvaro Sanchez et al.   PLoS Computational Biology

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Single-Molecule Approaches to Stochastic Gene Expression

(2009) Arjun Raj et al.   Annual Review of Biophysics

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS