Dynamic regulation of transcriptional states by chromatin and transcription factors

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Chromatin: Receiver and Quarterback for Cellular Signals

(2013) David G. Johnson et al.   CELL

Genome-wide measurement of protein-DNA binding dynamics using competition ChIP

(2013) Colin R Lickwar et al.   Nature Protocols

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

Complex dynamics of transcription regulation

(2012) Diana A. Stavreva et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

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

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

Long-term model predictive control of gene expression at the population and single-cell levels

(2012) J. Uhlendorf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

p53 Dynamics Control Cell Fate

(2012) J. E. Purvis et al.   SCIENCE

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Targeting chromatin remodelers: Signals and search mechanisms

(2011) Fabian Erdel et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

(2011) Angeliki Magklara et al.   CELL

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

(2011) Ty C. Voss et al.   CELL

Revisiting the Central Dogma One Molecule at a Time

(2011) Carlos Bustamante et al.   CELL

Impulse Control: Temporal Dynamics in Gene Transcription

(2011) Nir Yosef et al.   CELL

ATP-dependent chromatin remodeling: genetics, genomics and mechanisms

(2011) Diana C Hargreaves et al.   CELL RESEARCH

Assembly of the transcription machinery: ordered and stable, random and dynamic, or both?

(2011) Timothy J. Stasevich et al.   CHROMOSOMA

Origins and consequences of transcriptional discontinuity

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

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

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

Recognizing and remodeling the nucleosome

(2011) Sebastian Glatt et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

(2011) Rasmus Siersbaek et al.   EMBO JOURNAL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

(2011) W. Wu et al.   GENOME RESEARCH

Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload

(2011) Marjorie A. Kuipers et al.   JOURNAL OF CELL BIOLOGY

Extranucleosomal DNA Binding Directs Nucleosome Sliding by Chd1

(2011) J. N. McKnight et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

General properties of transcriptional time series in Escherichia coli

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

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis

(2011) Prabuddha Sengupta et al.   NATURE METHODS

Signal-dependent dynamics of transcription factor translocation controls gene expression

(2011) Nan Hao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Separating intrinsic from extrinsic fluctuations in dynamic biological systems

(2011) A. Hilfinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Pioneer factors: directing transcriptional regulators within the chromatin environment

(2011) Luca Magnani et al.   TRENDS IN GENETICS

Nuclear Receptor DHR4 Controls the Timing of Steroid Hormone Pulses During Drosophila Development

(2011) Qiuxiang Ou et al.   PLOS BIOLOGY

Dynamic Analysis of Stochastic Transcription Cycles

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

A Lattice Model for Transcription Factor Access to Nucleosomal DNA

(2010) Vladimir B. Teif et al.   BIOPHYSICAL JOURNAL

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

Nucleosome dynamics and epigenetic stability

(2010) Philipp Korber et al.   Essays in Biochemistry

Genome-Wide Analysis of Estrogen Receptor   DNA Binding and Tethering Mechanisms Identifies Runx1 as a Novel Tethering Factor in Receptor-Mediated Transcriptional Activation

(2010) J. D. Stender et al.   MOLECULAR AND CELLULAR BIOLOGY

Optimized localization analysis for single-molecule tracking and super-resolution microscopy

(2010) Kim I Mortensen et al.   NATURE METHODS

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

The Biology of Chromatin Remodeling Complexes

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

Early chromatin unfolding by RUNX1: a molecular explanation for differential requirements during specification versus maintenance of the hematopoietic gene expression program

(2009) M. Hoogenkamp et al.   BLOOD

Finding distal regulatory elements in the human genome

(2009) Nathaniel D Heintzman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Kinetic Complexity of the Global Response to Glucocorticoid Receptor Action

(2009) Sam John et al.   ENDOCRINOLOGY

Combinatorial probabilistic chromatin interactions produce transcriptional heterogeneity

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

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Ultradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription

(2009) Diana A. Stavreva et al.   NATURE CELL BIOLOGY

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

Stochastic modelling for quantitative description of heterogeneous biological systems

(2009) Darren J. Wilkinson   NATURE REVIEWS GENETICS

Sustained Oscillations of NF-κB Produce Distinct Genome Scanning and Gene Expression Profiles

(2009) Myong-Hee Sung et al.   PLoS One

Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression

(2009) Christopher Vollmers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of Shifting Patterns of Pacific Ocean Warming on North Atlantic Tropical Cyclones

(2009) Hye-Mi Kim et al.   SCIENCE

Pulsatile Stimulation Determines Timing and Specificity of NF- B-Dependent Transcription

(2009) L. Ashall et al.   SCIENCE

Harmonics of Circadian Gene Transcription in Mammals

(2009) Michael E. Hughes et al.   PLoS Genetics

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME 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

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Motivations and Methods for Analyzing Pulsatile Hormone Secretion

(2008) Johannes D. Veldhuis et al.   ENDOCRINE REVIEWS

Raster image correlation spectroscopy (RICS) for measuring fast protein dynamics and concentrations with a commercial laser scanning confocal microscope

(2008) C. M. BROWN et al.   JOURNAL OF MICROSCOPY

Frequency-modulated nuclear localization bursts coordinate gene regulation

(2008) Long Cai et al.   NATURE

Activation of Estrogen Receptor-α by E2 or EGF Induces Temporally Distinct Patterns of Large-Scale Chromatin Modification and mRNA Transcription

(2008) Valeria Berno et al.   PLoS One

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

(2008) T. S. Karpova et al.   SCIENCE

Mapping the Number of Molecules and Brightness in the Laser Scanning Microscope

(2007) Michelle A. Digman et al.   BIOPHYSICAL JOURNAL