Eukaryotic transcriptional dynamics: from single molecules to cell populations

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts

(2013) José Viñuelas et al.   BMC BIOLOGY

Intra-nuclear mobility and target search mechanisms of transcription factors: A single-molecule perspective on gene expression

(2012) Davide Normanno et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Transcription Stochasticity of Complex Gene Regulation Models

(2012) Anne Schwabe et al.   BIOPHYSICAL JOURNAL

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Decision Making in Living Cells: Lessons from a Simple System

(2011) Ido Golding   Annual Review of Biophysics

Chromosomal Position Effects Are Linked to Sir2-Mediated Variation in Transcriptional Burst Size

(2011) Cory Batenchuk et al.   BIOPHYSICAL JOURNAL

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

Modeling the Cell Cycle: Why Do Certain Circuits Oscillate?

(2011) James E. Ferrell et al.   CELL

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

What do expression dynamics tell us about the mechanism of transcription?

(2011) Daniel R Larson   CURRENT OPINION IN GENETICS & DEVELOPMENT

Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation

(2011) Ute Schmidt et al.   JOURNAL OF CELL BIOLOGY

The road less traveled: New views of steroid receptor action from the path of dose–response curves

(2011) S. Stoney Simons et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Cellular reprogramming by the conjoint action of ER , FOXA1, and GATA3 to a ligand-inducible growth state

(2011) S. L. Kong et al.   Molecular Systems Biology

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

General properties of transcriptional time series in Escherichia coli

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

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

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

Dynamic Analysis of Stochastic Transcription Cycles

(2011) Claire V. Harper et al.   PLOS BIOLOGY

Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability

(2011) Alistair N. Boettiger et al.   PLoS Computational Biology

Transcriptional Bursting from the HIV-1 Promoter Is a Significant Source of Stochastic Noise in HIV-1 Gene Expression

(2010) Abhyudai Singh et al.   BIOPHYSICAL JOURNAL

Cross-Validating FRAP and FCS to Quantify the Impact of Photobleaching on In Vivo Binding Estimates

(2010) Timothy J. Stasevich et al.   BIOPHYSICAL JOURNAL

On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter

(2010) Antoine Coulon et al.   BMC Systems Biology

Nuclear proteins: finding and binding target sites in chromatin

(2010) Martin E. van Royen et al.   CHROMOSOME RESEARCH

Methylation of H3K4 Is Required for Inheritance of Active Transcriptional States

(2010) Tetsuya Muramoto et al.   CURRENT BIOLOGY

FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?

(2010) Florian Mueller et al.   CURRENT OPINION IN CELL BIOLOGY

Oscillatory control of signalling molecules

(2010) Pawel Paszek et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Digital nature of the immediate-early transcriptional response

(2010) M. Stevense et al.   DEVELOPMENT

Highly Compacted Chromatin Formed In Vitro Reflects the Dynamics of Transcription Activation In Vivo

(2010) Guohong Li et al.   MOLECULAR CELL

In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport

(2010) David Grünwald et al.   NATURE

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

Single-allele analysis of transcription kinetics in living mammalian cells

(2010) Sharon Yunger et al.   NATURE METHODS

Inducible gene expression: diverse regulatory mechanisms

(2010) Vikki M. Weake et al.   NATURE REVIEWS GENETICS

Transcription of functionally related constitutive genes is not coordinated

(2010) Saumil J Gandhi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

(2010) F. Erdel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population robustness arising from cellular heterogeneity

(2010) P. Paszek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A theoretical framework for gene induction and experimental comparisons

(2010) K. M. Ong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones

(2010) R. B. Deal et al.   SCIENCE

Live cell imaging and systems biology

(2010) Myong-Hee Sung et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency

(2010) Ron Skupsky et al.   PLoS Computational Biology

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

Imaging Transcription in Living Cells

(2009) Xavier Darzacq et al.   Annual Review of Biophysics

The basal initiation machinery: beyond the general transcription factors

(2009) Timothy W. Sikorski et al.   CURRENT OPINION IN CELL BIOLOGY

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

Kinetic Complexity of the Global Response to Glucocorticoid Receptor Action

(2009) Sam John et al.   ENDOCRINOLOGY

Incorporating nucleosomes into thermodynamic models of transcription regulation

(2009) T. Raveh-Sadka et al.   GENOME RESEARCH

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

(2009) A. Weiner et al.   GENOME RESEARCH

Combinatorial probabilistic chromatin interactions produce transcriptional heterogeneity

(2009) T. C. Voss et al.   JOURNAL OF CELL SCIENCE

Chromatin Remodelers Act Globally, Sequence Positions Nucleosomes Locally

(2009) Peretz D. Partensky et al.   JOURNAL OF MOLECULAR BIOLOGY

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

Intersubunit coordination in a homomeric ring ATPase

(2009) Jeffrey R. Moffitt et al.   NATURE

The logic of chromatin architecture and remodelling at promoters

(2009) Bradley R. Cairns   NATURE

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Rates of in situ transcription and splicing in large human genes

(2009) Jarnail Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Thermodynamics of Intragenic Nucleosome Ordering

(2009) G. Chevereau et al.   PHYSICAL REVIEW LETTERS

Elongation dynamics shape bursty transcription and translation

(2009) Maciej Dobrzyński et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single molecule view of gene expression

(2009) Daniel R. Larson et al.   TRENDS IN CELL BIOLOGY

Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures

(2009) Dirk Müller et al.   PLoS Computational Biology

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription

(2008) Hinrich Boeger et al.   CELL

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Marking time: The dynamic role of chromatin and covalent modification in transcription

(2008) George Reid et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Chromatin Remodeling Complexes Interact Dynamically with a Glucocorticoid Receptor–regulated Promoter

(2008) Thomas A. Johnson et al.   MOLECULAR BIOLOGY OF THE CELL

Modulation of RNA Polymerase Assembly Dynamics in Transcriptional Regulation

(2008) Stanislaw A. Gorski et al.   MOLECULAR CELL

Mediator-Dependent Recruitment of TFIIH Modules in Preinitiation Complex

(2008) Cyril Esnault et al.   MOLECULAR CELL

Cyclical DNA methylation of a transcriptionally active promoter

(2008) Raphaël Métivier et al.   NATURE

Chromatin decouples promoter threshold from dynamic range

(2008) Felix H. Lam et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Regulatory activity revealed by dynamic correlations in gene expression noise

(2008) Mary J Dunlop et al.   NATURE GENETICS

A quantitative model of transcription factor–activated gene expression

(2008) Harold D Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Transcriptional control of noise in gene expression

(2008) Álvaro Sánchez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of TATA-binding protein dynamics in living yeast cells

(2008) R. O. Sprouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression

(2008) J. M. Pedraza et al.   SCIENCE

Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter

(2008) T. S. Karpova et al.   SCIENCE

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology