Quantifying transcription factor kinetics: At work or at play?

The Cell Biology of Genomes: Bringing the Double Helix to Life

(2013) Tom Misteli   CELL

Revisiting Point FRAP to Quantitatively Characterize Anomalous Diffusion in Live Cells

(2013) Matthew K. Daddysman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Convergence of chromatin binding estimates in live cells

(2013) Davide Mazza et al.   NATURE METHODS

Extracting intracellular diffusive states and transition rates from single-molecule tracking data

(2013) Fredrik Persson et al.   NATURE METHODS

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

(2013) Marshall J Levesque et al.   NATURE METHODS

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

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

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Probing transcription factor diffusion dynamics in the living mammalian embryo with photoactivatable fluorescence correlation spectroscopy

(2013) Gurpreet Kaur et al.   Nature Communications

Live-Cell Super-Resolution Imaging with Synthetic Fluorophores

(2012) Sebastian van de Linde et al.   Annual Review of Physical Chemistry

DNA-dependent Oct4–Sox2 interaction and diffusion properties characteristic of the pluripotent cell state revealed by fluorescence spectroscopy

(2012) Chen Sok Lam et al.   BIOCHEMICAL JOURNAL

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

Minimizing the Impact of Photoswitching of Fluorescent Proteins on FRAP Analysis

(2012) Florian Mueller et al.   BIOPHYSICAL JOURNAL

Cellular Response to Heat Shock Studied by Multiconfocal Fluorescence Correlation Spectroscopy

(2012) Meike Kloster-Landsberg et al.   BIOPHYSICAL JOURNAL

Stress-specific response of the p53-Mdm2 feedback loop

(2012) Alexander Hunziker et al.   BMC Systems Biology

Inducing local DNA damage by visible light to study chromatin repair

(2012) Kamil J. Solarczyk et al.   DNA REPAIR

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Light-mediated control of DNA transcription in yeast

(2012) Robert M. Hughes et al.   METHODS

Gene expression: Running to stand still

(2012) Tommy Kaplan et al.   NATURE

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

(2012) Colin R. Lickwar et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Spatiotemporal control of gene expression by a light-switchable transgene system

(2012) Xue Wang et al.   NATURE METHODS

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

Fast multicolor 3D imaging using aberration-corrected multifocus microscopy

(2012) Sara Abrahamsson et al.   NATURE METHODS

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

Dynamic three-dimensional tracking of single fluorescent nanoparticles deep inside living tissue

(2012) Jan-Hendrik Spille et al.   OPTICS EXPRESS

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

Targeting DNA With Fingers and TALENs

(2012) Daniel F Carlson et al.   Molecular Therapy-Nucleic Acids

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

(2011) Jasmin Speil et al.   BIOPHYSICAL JOURNAL

STED Nanoscopy Reveals Molecular Details of Cholesterol- and Cytoskeleton-Modulated Lipid Interactions in Living Cells

(2011) V. Mueller et al.   BIOPHYSICAL JOURNAL

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

(2011) Ty C. Voss et al.   CELL

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

(2011) Ho Sung Rhee et al.   CELL

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

(2011) Timothy J. Stasevich et al.   CHROMOSOMA

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Live-cell fluorescence correlation spectroscopy dissects the role of coregulator exchange and chromatin binding in retinoic acid receptor mobility

(2011) P. Brazda et al.   JOURNAL OF CELL SCIENCE

Central dogma at the single-molecule level in living cells

(2011) Gene-Wei Li et al.   NATURE

Oct4 kinetics predict cell lineage patterning in the early mammalian embryo

(2011) Nicolas Plachta et al.   NATURE CELL BIOLOGY

Validating transcripts with probes and imaging technology

(2011) Shalev Itzkovitz et al.   NATURE METHODS

Live-cell 3D super-resolution imaging in thick biological samples

(2011) Francesca Cella Zanacchi et al.   NATURE METHODS

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

(2011) D. R. Larson et al.   SCIENCE

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

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

Dissecting chromatin interactions in living cells from protein mobility maps

(2010) Fabian Erdel et al.   CHROMOSOME RESEARCH

Dynamic as well as stable protein interactions contribute to genome function and maintenance

(2010) Peter Hemmerich et al.   CHROMOSOME RESEARCH

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

Drugs for ‘protein clouds’: targeting intrinsically disordered transcription factors

(2010) A Keith Dunker et al.   CURRENT OPINION IN PHARMACOLOGY

Chromatin interaction of TATA-binding protein is dynamically regulated in human cells

(2010) P. de Graaf et al.   JOURNAL OF CELL SCIENCE

The Current State of Chromatin Immunoprecipitation

(2010) Philippe Collas   MOLECULAR BIOTECHNOLOGY

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

(2010) Kim I Mortensen et al.   NATURE METHODS

The transcriptional co-activator LEDGF/p75 displays a dynamic scan-and-lock mechanism for chromatin tethering

(2010) Jelle Hendrix et al.   NUCLEIC ACIDS RESEARCH

Single Cell Analysis of Transcriptional Activation Dynamics

(2010) Ilona U. Rafalska-Metcalf et al.   PLoS One

MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites

(2010) Christoph D. Schmid et al.   PLoS One

Light Sheet Microscopy for Single Molecule Tracking in Living Tissue

(2010) Jörg Gerhard Ritter et al.   PLoS One

Transcriptional Regulation by P53

(2010) R. Beckerman et al.   Cold Spring Harbor Perspectives in Biology

Multiscale Analysis of Dynamics and Interactions of Heterochromatin Protein 1 by Fluorescence Fluctuation Microscopy

(2009) Katharina P. Müller et al.   BIOPHYSICAL JOURNAL

Direct Measurement of Association and Dissociation Rates of DNA Binding in Live Cells by Fluorescence Correlation Spectroscopy

(2009) Ariel Michelman-Ribeiro et al.   BIOPHYSICAL JOURNAL

A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays

(2009) Danette D Hartzell et al.   BMC GENOMICS

Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy

(2009) Gerrit Heuvelman et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA

(2009) T. Sekiya et al.   GENES & DEVELOPMENT

Beyond Photobleaching, Laser Illumination Unbinds Fluorescent Proteins

(2009) Katrin G. Heinze et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

(2009) Leonid Mirny et al.   Journal of Physics A-Mathematical and Theoretical

Transcription Dynamics

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

Gal4 turnover and transcription activation

(2009) Galen A. Collins et al.   NATURE

Effects of macromolecular crowding and DNA looping on gene regulation kinetics

(2009) Gene-Wei Li et al.   Nature Physics

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome

(2009) Folkert J van Werven et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A single molecule view of gene expression

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

Differentiation Driven Changes in the Dynamic Organization of Basal Transcription Initiation

(2009) Giuseppina Giglia-Mari et al.   PLOS BIOLOGY

Crowding Effects on Diffusion in Solutions and Cells

(2008) James A. Dix et al.   Annual Review of Biophysics

Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability

(2008) Anahita Tafvizi et al.   BIOPHYSICAL JOURNAL

Evidence for a Common Mode of Transcription Factor Interaction with Chromatin as Revealed by Improved Quantitative Fluorescence Recovery after Photobleaching

(2008) Florian Mueller et al.   BIOPHYSICAL JOURNAL

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

Analysis of diffusion and binding in cells using the RICS approach

(2008) Michelle A. Digman et al.   MICROSCOPY RESEARCH AND TECHNIQUE

Modulation of RNA Polymerase Assembly Dynamics in Transcriptional Regulation

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

How the sum of its parts gets greater than the whole

(2008) Mario Brameshuber et al.   NATURE METHODS

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

(2008) Makio Tokunaga et al.   NATURE METHODS

High-density mapping of single-molecule trajectories with photoactivated localization microscopy

(2008) Suliana Manley et al.   NATURE METHODS

C-terminal diversity within the p53 family accounts for differences in DNA binding and transcriptional activity

(2008) M. Sauer et al.   NUCLEIC ACIDS RESEARCH

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

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

(2008) T. S. Karpova et al.   SCIENCE

Probing Intranuclear Environments at the Single-Molecule Level

(2007) David Grünwald et al.   BIOPHYSICAL JOURNAL